Eisen JA

References (148)

Title : Phylogenetically driven sequencing of extremely halophilic archaea reveals strategies for static and dynamic osmo-response - Becker_2014_PLoS.Genet_10_e1004784
Author(s) : Becker EA , Seitzer PM , Tritt A , Larsen D , Krusor M , Yao AI , Wu D , Madern D , Eisen JA , Darling AE , Facciotti MT
Ref : PLoS Genet , 10 :e1004784 , 2014
Abstract : Organisms across the tree of life use a variety of mechanisms to respond to stress-inducing fluctuations in osmotic conditions. Cellular response mechanisms and phenotypes associated with osmoadaptation also play important roles in bacterial virulence, human health, agricultural production and many other biological systems. To improve understanding of osmoadaptive strategies, we have generated 59 high-quality draft genomes for the haloarchaea (a euryarchaeal clade whose members thrive in hypersaline environments and routinely experience drastic changes in environmental salinity) and analyzed these new genomes in combination with those from 21 previously sequenced haloarchaeal isolates. We propose a generalized model for haloarchaeal management of cytoplasmic osmolarity in response to osmotic shifts, where potassium accumulation and sodium expulsion during osmotic upshock are accomplished via secondary transport using the proton gradient as an energy source, and potassium loss during downshock is via a combination of secondary transport and non-specific ion loss through mechanosensitive channels. We also propose new mechanisms for magnesium and chloride accumulation. We describe the expansion and differentiation of haloarchaeal general transcription factor families, including two novel expansions of the TATA-binding protein family, and discuss their potential for enabling rapid adaptation to environmental fluxes. We challenge a recent high-profile proposal regarding the evolutionary origins of the haloarchaea by showing that inclusion of additional genomes significantly reduces support for a proposed large-scale horizontal gene transfer into the ancestral haloarchaeon from the bacterial domain. The combination of broad (17 genera) and deep (>/=5 species in four genera) sampling of a phenotypically unified clade has enabled us to uncover both highly conserved and specialized features of osmoadaptation. Finally, we demonstrate the broad utility of such datasets, for metagenomics, improvements to automated gene annotation and investigations of evolutionary processes.
ESTHER : Becker_2014_PLoS.Genet_10_e1004784
PubMedSearch : Becker_2014_PLoS.Genet_10_e1004784
PubMedID: 25393412
Gene_locus related to this paper: 9eury-m0a9w6 , 9eury-m0c9s2 , 9eury-m0cx66 , 9eury-m0fpi4 , halpt-m0fxy0 , 9eury-m0jb87 , halvd-metxa

Title : Draft Genome Sequences of Extended-Spectrum beta-Lactamase-Producing Escherichia coli Strains Isolated from Patients in Lebanon - Tokajian_2014_Genome.Announc_2_e00123
Author(s) : Tokajian S , Eisen JA , Jospin G , Farra A , Coil DA
Ref : Genome Announc , 2 : , 2014
Abstract : We present the draft genome sequences of nine extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli strains isolated from stool samples collected from patients admitted for gastrointestinal and urological procedures/surgeries. An average of 3,889,300 paired-end reads per sample were generated, which assembled in 77 to 157 contigs.
ESTHER : Tokajian_2014_Genome.Announc_2_e00123
PubMedSearch : Tokajian_2014_Genome.Announc_2_e00123
PubMedID: 24558252
Gene_locus related to this paper: ecoli-IROD , ecoli-IROE , ecoli-yaim , ecoli-ybff , ecoli-ycfp , ecoli-yqia , ecoli-YfhR , ecolx-f4suw9 , ecolx-g0dan0

Title : Draft Genome Sequence of Microbacterium sp. Strain UCD-TDU (Phylum Actinobacteria) - Bendiks_2013_Genome.Announc_1_e0012013
Author(s) : Bendiks ZA , Lang JM , Darling AE , Eisen JA , Coil DA
Ref : Genome Announc , 1 :e0012013 , 2013
Abstract : Here, we present the draft genome sequence of Microbacterium sp. strain UCD-TDU, a member of the phylum Actinobacteria. The assembly contains 3,746,321 bp (in 8 scaffolds). This strain was isolated from a residential toilet as part of an undergraduate student research project to sequence reference genomes of microbes from the built environment.
ESTHER : Bendiks_2013_Genome.Announc_1_e0012013
PubMedSearch : Bendiks_2013_Genome.Announc_1_e0012013
PubMedID: 23516225
Gene_locus related to this paper: 9mico-a0a022l4z9 , 9mico-a0a022l9k5 , 9mico-a0a022la20

Title : Draft Genome Sequence of Dietzia sp. Strain UCD-THP (Phylum Actinobacteria) - Diep_2013_Genome.Announc_1_E00197
Author(s) : Diep AL , Lang JM , Darling AE , Eisen JA , Coil DA
Ref : Genome Announc , 1 : , 2013
Abstract : Here, we present the draft genome sequence of an actinobacterium, Dietzia sp. strain UCD-THP, isolated from a residential toilet handle. The assembly contains 3,915,613 bp. The genome sequences of only two other Dietzia species have been published, those of Dietzia alimentaria and Dietzia cinnamea.
ESTHER : Diep_2013_Genome.Announc_1_E00197
PubMedSearch : Diep_2013_Genome.Announc_1_E00197
PubMedID: 23661480
Gene_locus related to this paper: 9acto-a0a022lsb1 , 9acto-a0a022llm7 , 9actn-a0a022lc77 , 9actn-a0a022leh7 , 9actn-a0a022lh57

Title : Draft Genome Sequence of Curtobacterium flaccumfaciens Strain UCD-AKU (Phylum Actinobacteria) - Flanagan_2013_Genome.Announc_1_E00244
Author(s) : Flanagan JC , Lang JM , Darling AE , Eisen JA , Coil DA
Ref : Genome Announc , 1 : , 2013
Abstract : Here we present the draft genome of an actinobacterium, Curtobacterium flaccumfaciens strain UCD-AKU, isolated from a residential carpet. The genome assembly contains 3,692,614 bp in 130 contigs. This is the first member of the Curtobacterium genus to be sequenced.
ESTHER : Flanagan_2013_Genome.Announc_1_E00244
PubMedSearch : Flanagan_2013_Genome.Announc_1_E00244
PubMedID: 23682147
Gene_locus related to this paper: 9mico-a0a022lxu2 , 9mico-a0a022lg01 , 9mico-a0a022lrt6 , 9mico-a0a022l1k4 , 9mico-a0a022lew0 , 9mico-a0a022lt92

Title : Draft Genome Sequence of Leucobacter sp. Strain UCD-THU (Phylum Actinobacteria) - Holland-Moritz_2013_Genome.Announc_1_S69
Author(s) : Holland-Moritz HE , Bevans DR , Lang JM , Darling AE , Eisen JA , Coil DA
Ref : Genome Announc , 1 : , 2013
Abstract : Here we present the draft genome of Leucobacter sp. strain UCD-THU. The genome contains 3,317,267 bp in 11 scaffolds. This strain was isolated from a residential toilet as part of an undergraduate project to sequence reference genomes of microbes from the built environment.
ESTHER : Holland-Moritz_2013_Genome.Announc_1_S69
PubMedSearch : Holland-Moritz_2013_Genome.Announc_1_S69
PubMedID: 23792744
Gene_locus related to this paper: 9mico-a0a061lzf2 , 9mico-a0a061m0a9

Title : Complete genome sequence of Coriobacterium glomerans type strain (PW2(T)) from the midgut of Pyrrhocoris apterus L. (red soldier bug) - Stackebrandt_2013_Stand.Genomic.Sci_8_15
Author(s) : Stackebrandt E , Zeytun A , Lapidus A , Nolan M , Lucas S , Hammon N , Deshpande S , Cheng JF , Tapia R , Goodwin LA , Pitluck S , Liolios K , Pagani I , Ivanova N , Mavromatis K , Mikhailova N , Huntemann M , Pati A , Chen A , Palaniappan K , Chang YJ , Land M , Hauser L , Rohde M , Pukall R , Goker M , Detter JC , Woyke T , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP
Ref : Stand Genomic Sci , 8 :15 , 2013
Abstract : Coriobacterium glomerans Haas and Konig 1988, is the only species of the genus Coriobacterium, family Coriobacteriaceae, order Coriobacteriales, phylum Actinobacteria. The bacterium thrives as an endosymbiont of pyrrhocorid bugs, i.e. the red fire bug Pyrrhocoris apterus L. The rationale for sequencing the genome of strain PW2(T) is its endosymbiotic life style which is rare among members of Actinobacteria. Here we describe the features of this symbiont, together with the complete genome sequence and its annotation. This is the first complete genome sequence of a member of the genus Coriobacterium and the sixth member of the order Coriobacteriales for which complete genome sequences are now available. The 2,115,681 bp long single replicon genome with its 1,804 protein-coding and 54 RNA genes is part of the G enomic E ncyclopedia of Bacteria and Archaea project.
ESTHER : Stackebrandt_2013_Stand.Genomic.Sci_8_15
PubMedSearch : Stackebrandt_2013_Stand.Genomic.Sci_8_15
PubMedID: 23961308
Gene_locus related to this paper: corgp-f2n8w7

Title : Complete genome sequence of the halophilic bacterium Spirochaeta africana type strain (Z-7692(T)) from the alkaline Lake Magadi in the East African Rift - Liolos_2013_Stand.Genomic.Sci_8_165
Author(s) : Liolos K , Abt B , Scheuner C , Teshima H , Held B , Lapidus A , Nolan M , Lucas S , Deshpande S , Cheng JF , Tapia R , Goodwin LA , Pitluck S , Pagani I , Ivanova N , Mavromatis K , Mikhailova N , Huntemann M , Pati A , Chen A , Palaniappan K , Land M , Rohde M , Tindall BJ , Detter JC , Goker M , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Woyke T , Klenk HP , Kyrpides NC
Ref : Stand Genomic Sci , 8 :165 , 2013
Abstract : Spirochaeta africana Zhilina et al. 1996 is an anaerobic, aerotolerant, spiral-shaped bacterium that is motile via periplasmic flagella. The type strain of the species, Z-7692(T), was isolated in 1993 or earlier from a bacterial bloom in the brine under the trona layer in a shallow lagoon of the alkaline equatorial Lake Magadi in Kenya. Here we describe the features of this organism, together with the complete genome sequence, and annotation. Considering the pending reclassification of S. caldaria to the genus Treponema, S. africana is only the second 'true' member of the genus Spirochaeta with a genome-sequenced type strain to be published. The 3,285,855 bp long genome of strain Z-7692(T) with its 2,817 protein-coding and 57 RNA genes is a part of the G enomic E ncyclopedia of B acteria and A rchaea project.
ESTHER : Liolos_2013_Stand.Genomic.Sci_8_165
PubMedSearch : Liolos_2013_Stand.Genomic.Sci_8_165
PubMedID: 23991249
Gene_locus related to this paper: spiaz-h9uj53

Title : Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing - Shih_2013_Proc.Natl.Acad.Sci.U.S.A_110_1053
Author(s) : Shih PM , Wu D , Latifi A , Axen SD , Fewer DP , Talla E , Calteau A , Cai F , Tandeau de Marsac N , Rippka R , Herdman M , Sivonen K , Coursin T , Laurent T , Goodwin L , Nolan M , Davenport KW , Han CS , Rubin EM , Eisen JA , Woyke T , Gugger M , Kerfeld CA
Ref : Proc Natl Acad Sci U S A , 110 :1053 , 2013
Abstract : The cyanobacterial phylum encompasses oxygenic photosynthetic prokaryotes of a great breadth of morphologies and ecologies; they play key roles in global carbon and nitrogen cycles. The chloroplasts of all photosynthetic eukaryotes can trace their ancestry to cyanobacteria. Cyanobacteria also attract considerable interest as platforms for "green" biotechnology and biofuels. To explore the molecular basis of their different phenotypes and biochemical capabilities, we sequenced the genomes of 54 phylogenetically and phenotypically diverse cyanobacterial strains. Comparison of cyanobacterial genomes reveals the molecular basis for many aspects of cyanobacterial ecophysiological diversity, as well as the convergence of complex morphologies without the acquisition of novel proteins. This phylum-wide study highlights the benefits of diversity-driven genome sequencing, identifying more than 21,000 cyanobacterial proteins with no detectable similarity to known proteins, and foregrounds the diversity of light-harvesting proteins and gene clusters for secondary metabolite biosynthesis. Additionally, our results provide insight into the distribution of genes of cyanobacterial origin in eukaryotic nuclear genomes. Moreover, this study doubles both the amount and the phylogenetic diversity of cyanobacterial genome sequence data. Given the exponentially growing number of sequenced genomes, this diversity-driven study demonstrates the perspective gained by comparing disparate yet related genomes in a phylum-wide context and the insights that are gained from it.
ESTHER : Shih_2013_Proc.Natl.Acad.Sci.U.S.A_110_1053
PubMedSearch : Shih_2013_Proc.Natl.Acad.Sci.U.S.A_110_1053
PubMedID: 23277585
Gene_locus related to this paper: 9cyan-k9et81 , cyagp-k9p8h6 , noss7-k9r280 , cyaap-k9z9m7 , synp3-k9ryw0 , anacc-k9zr49 , 9chro-l8lle9 , 9cyan-l8m3q8 , 9cyan-l8mv15 , stac7-k9xpe1 , 9cyan-k9f0z6 , synp3-k9rq00 , noss7-k9qm01 , stac7-k9xsv0

Title : Genome sequence of the thermophilic fresh-water bacterium Spirochaeta caldaria type strain (H1(T)), reclassification of Spirochaeta caldaria, Spirochaeta stenostrepta, and Spirochaeta zuelzerae in the genus Treponema as Treponema caldaria comb. nov., Treponema stenostrepta comb. nov., and Treponema zuelzerae comb. nov., and emendation of the genus Treponema - Abt_2013_Stand.Genomic.Sci_8_88
Author(s) : Abt B , Goker M , Scheuner C , Han C , Lu M , Misra M , Lapidus A , Nolan M , Lucas S , Hammon N , Deshpande S , Cheng JF , Tapia R , Goodwin LA , Pitluck S , Liolios K , Pagani I , Ivanova N , Mavromatis K , Mikhailova N , Huntemann M , Pati A , Chen A , Palaniappan K , Land M , Hauser L , Jeffries CD , Rohde M , Spring S , Gronow S , Detter JC , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Woyke T , Klenk HP
Ref : Stand Genomic Sci , 8 :88 , 2013
Abstract : Spirochaeta caldaria Pohlschroeder et al. 1995 is an obligately anaerobic, spiral-shaped bacterium that is motile via periplasmic flagella. The type strain, H1(T), was isolated in 1990 from cyanobacterial mat samples collected at a freshwater hot spring in Oregon, USA, and is of interest because it enhances the degradation of cellulose when grown in co-culture with Clostridium thermocellum. Here we provide a taxonomic re-evaluation for S. caldaria based on phylogenetic analyses of 16S rRNA sequences and whole genomes, and propose the reclassification of S. caldaria and two other Spirochaeta species as members of the emended genus Treponema. Whereas genera such as Borrelia and Sphaerochaeta possess well-distinguished genomic features related to their divergent lifestyles, the physiological and functional genomic characteristics of Spirochaeta and Treponema appear to be intermixed and are of little taxonomic value. The 3,239,340 bp long genome of strain H1(T) with its 2,869 protein-coding and 59 RNA genes is a part of the G enomic E ncyclopedia of Bacteria and Archaea project.
ESTHER : Abt_2013_Stand.Genomic.Sci_8_88
PubMedSearch : Abt_2013_Stand.Genomic.Sci_8_88
PubMedID: 23961314
Gene_locus related to this paper: trech-f8f1l1

Title : Draft genome sequence of an Actinobacterium, Brachybacterium muris strain UCD-AY4 - Lo_2013_Genome.Announc_1_e0008613
Author(s) : Lo JR , Lang JM , Darling AE , Eisen JA , Coil DA
Ref : Genome Announc , 1 :e0008613 , 2013
Abstract : Here we present the draft genome of an actinobacterium, Brachybacterium muris UCD-AY4. The assembly contains 3,257,338 bp and has a GC content of 70%. This strain was isolated from a residential bath towel and has a 16S rRNA gene 99.7% identical to that of the original B. muris strain, C3H-21.
ESTHER : Lo_2013_Genome.Announc_1_e0008613
PubMedSearch : Lo_2013_Genome.Announc_1_e0008613
PubMedID: 23516213
Gene_locus related to this paper: 9mico-a0a022ks77

Title : Genome sequence of the orange-pigmented seawater bacterium Owenweeksia hongkongensis type strain (UST20020801(T)) - Riedel_2012_Stand.Genomic.Sci_7_120
Author(s) : Riedel T , Held B , Nolan M , Lucas S , Lapidus A , Tice H , Del Rio TG , Cheng JF , Han C , Tapia R , Goodwin LA , Pitluck S , Liolios K , Mavromatis K , Pagani I , Ivanova N , Mikhailova N , Pati A , Chen A , Palaniappan K , Rohde M , Tindall BJ , Detter JC , Goker M , Woyke T , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Klenk HP , Kyrpides NC
Ref : Stand Genomic Sci , 7 :120 , 2012
Abstract : Owenweeksia hongkongensis Lau et al. 2005 is the sole member of the monospecific genus Owenweeksia in the family Cryomorphaceae, a poorly characterized family at the genome level thus far. This family comprises seven genera within the class Flavobacteria. Family members are known to be psychrotolerant, rod-shaped and orange pigmented (beta-carotene), typical for Flavobacteria. For growth, seawater and complex organic nutrients are necessary. The genome of O. hongkongensis UST20020801(T) is only the second genome of a member of the family Cryomorphaceae whose sequence has been deciphered. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,000,057 bp long chromosome with its 3,518 protein-coding and 45 RNA genes is a part of the GenomicEncyclopedia ofBacteriaandArchaea project.
ESTHER : Riedel_2012_Stand.Genomic.Sci_7_120
PubMedSearch : Riedel_2012_Stand.Genomic.Sci_7_120
PubMedID: 23450211
Gene_locus related to this paper: owehd-g8r0w8

Title : Genome sequence of the flexirubin-pigmented soil bacterium Niabella soli type strain (JS13-8(T)) - Anderson_2012_Stand.Genomic.Sci_7_210
Author(s) : Anderson I , Munk C , Lapidus A , Nolan M , Lucas S , Tice H , Del Rio TG , Cheng JF , Han C , Tapia R , Goodwin L , Pitluck S , Liolios K , Mavromatis K , Pagani I , Mikhailova N , Pati A , Chen A , Palaniappan K , Land M , Rohde M , Tindall BJ , Goker M , Detter JC , Woyke T , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP , Ivanova N
Ref : Stand Genomic Sci , 7 :210 , 2012
Abstract : Niabella soli Weon et al. 2008 is a member of the Chitinophagaceae, a family within the class Sphingobacteriia that is poorly characterized at the genome level, thus far. N. soli strain JS13-8(T) is of interest for its ability to produce a variety of glycosyl hydrolases. The genome of N. soli strain JS13-8(T) is only the second genome sequence of a type strain from the family Chitinophagaceae to be published, and the first one from the genus Niabella. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,697,343 bp long chromosome with its 3,931 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia ofBacteria andArchaea project.
ESTHER : Anderson_2012_Stand.Genomic.Sci_7_210
PubMedSearch : Anderson_2012_Stand.Genomic.Sci_7_210
PubMedID: 23408178

Title : Complete genome sequence of the sulfur compounds oxidizing chemolithoautotroph Sulfuricurvum kujiense type strain (YK-1(T)) - Han_2012_Stand.Genomic.Sci_6_94
Author(s) : Han C , Kotsyurbenko O , Chertkov O , Held B , Lapidus A , Nolan M , Lucas S , Hammon N , Deshpande S , Cheng JF , Tapia R , Goodwin LA , Pitluck S , Liolios K , Pagani I , Ivanova N , Mavromatis K , Mikhailova N , Pati A , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Brambilla EM , Rohde M , Spring S , Sikorski J , Goker M , Woyke T , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP , Detter JC
Ref : Stand Genomic Sci , 6 :94 , 2012
Abstract : Sulfuricurvum kujiense Kodama and Watanabe 2004 is the type species of the monotypic genus Sulfuricurvum, which belongs to the family Helicobacteraceae in the class Epsilonproteobacteria. The species is of interest because it is frequently found in crude oil and oil sands where it utilizes various reduced sulfur compounds such as elemental sulfur, sulfide and thiosulfate as electron donors. Members of the species do not utilize sugars, organic acids or hydrocarbons as carbon and energy sources. This genome sequence represents the type strain of the only species in the genus Sulfuricurvum. The genome, which consists of a circular chromosome of 2,574,824 bp length and four plasmids of 118,585 bp, 71,513 bp, 51,014 bp, and 3,421 bp length, respectively, harboring a total of 2,879 protein-coding and 61 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Han_2012_Stand.Genomic.Sci_6_94
PubMedSearch : Han_2012_Stand.Genomic.Sci_6_94
PubMedID: 22675602
Gene_locus related to this paper: sulky-e4u307

Title : Permanent draft genome sequence of the gliding predator Saprospira grandis strain Sa g1 (= HR1) - Mavromatis_2012_Stand.Genomic.Sci_6_210
Author(s) : Mavromatis K , Chertkov O , Lapidus A , Nolan M , Lucas S , Tice H , Del Rio TG , Cheng JF , Han C , Tapia R , Bruce D , Goodwin LA , Pitluck S , Huntemann M , Liolios K , Pagani I , Ivanova N , Mikhailova N , Pati A , Chen A , Palaniappan K , Land M , Brambilla EM , Rohde M , Spring S , Goker M , Detter JC , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP , Woyke T
Ref : Stand Genomic Sci , 6 :210 , 2012
Abstract : Saprospira grandis Gross 1911 is a member of the Saprospiraceae, a family in the class 'Sphingobacteria' that remains poorly characterized at the genomic level. The species is known for preying on other marine bacteria via 'ixotrophy'. S. grandis strain Sa g1 was isolated from decaying crab carapace in France and was selected for genome sequencing because of its isolated location in the tree of life. Only one type strain genome has been published so far from the Saprospiraceae, while the sequence of strain Sa g1 represents the second genome to be published from a non-type strain of S. grandis. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,495,250 bp long Improved-High-Quality draft of the genome with its 3,536 protein-coding and 62 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Mavromatis_2012_Stand.Genomic.Sci_6_210
PubMedSearch : Mavromatis_2012_Stand.Genomic.Sci_6_210
PubMedID: 22768364
Gene_locus related to this paper: sapgl-h6kz52 , 9bact-j0p3n9

Title : Genome sequence of the homoacetogenic bacterium Holophaga foetida type strain (TMBS4(T)) - Anderson_2012_Stand.Genomic.Sci_6_174
Author(s) : Anderson I , Held B , Lapidus A , Nolan M , Lucas S , Tice H , Del Rio TG , Cheng JF , Han C , Tapia R , Goodwin LA , Pitluck S , Liolios K , Mavromatis K , Pagani I , Ivanova N , Mikhailova N , Pati A , Chen A , Palaniappan K , Land M , Brambilla EM , Rohde M , Spring S , Goker M , Detter JC , Woyke T , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Klenk HP , Kyrpides NC
Ref : Stand Genomic Sci , 6 :174 , 2012
Abstract : Holophaga foetida Liesack et al. 1995 is a member of the phylum Acidobacteria and is of interest for its ability to anaerobically degrade aromatic compounds and for its production of volatile sulfur compounds through a unique pathway. The genome of H. foetida strain TMBS4(T) is the first to be sequenced for a representative of the class Holophagae. Here we describe the features of this organism, together with the complete genome sequence (improved high quality draft), and annotation. The 4,127,237 bp long chromosome with its 3,615 protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Anderson_2012_Stand.Genomic.Sci_6_174
PubMedSearch : Anderson_2012_Stand.Genomic.Sci_6_174
PubMedID: 22768361
Gene_locus related to this paper: 9bact-h1nzy5

Title : Genome sequence of the Antarctic rhodopsins-containing flavobacterium Gillisia limnaea type strain (R-8282(T)) - Riedel_2012_Stand.Genomic.Sci_7_107
Author(s) : Riedel T , Held B , Nolan M , Lucas S , Lapidus A , Tice H , Del Rio TG , Cheng JF , Han C , Tapia R , Goodwin LA , Pitluck S , Liolios K , Mavromatis K , Pagani I , Ivanova N , Mikhailova N , Pati A , Chen A , Palaniappan K , Land M , Rohde M , Tindall BJ , Detter JC , Goker M , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP , Woyke T
Ref : Stand Genomic Sci , 7 :107 , 2012
Abstract : Gillisia limnaea Van Trappen et al. 2004 is the type species of the genus Gillisia, which is a member of the well characterized family Flavobacteriaceae. The genome of G. limnea R-8282(T) is the first sequenced genome (permanent draft) from a type strain of the genus Gillisia. Here we describe the features of this organism, together with the permanent-draft genome sequence and annotation. The 3,966,857 bp long chromosome (two scaffolds) with its 3,569 protein-coding and 51 RNA genes is a part of the GenomicEncyclopedia of Bacteria and Archaea project.
ESTHER : Riedel_2012_Stand.Genomic.Sci_7_107
PubMedSearch : Riedel_2012_Stand.Genomic.Sci_7_107
PubMedID: 23450183
Gene_locus related to this paper: 9flao-h2bu38

Title : Complete genome sequence of the aerobic, heterotroph Marinithermus hydrothermalis type strain (T1(T)) from a deep-sea hydrothermal vent chimney - Copeland_2012_Stand.Genomic.Sci_6_21
Author(s) : Copeland A , Gu W , Yasawong M , Lapidus A , Lucas S , Deshpande S , Pagani I , Tapia R , Cheng JF , Goodwin LA , Pitluck S , Liolios K , Ivanova N , Mavromatis K , Mikhailova N , Pati A , Chen A , Palaniappan K , Land M , Pan C , Brambilla EM , Rohde M , Tindall BJ , Sikorski J , Goker M , Detter JC , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP , Woyke T
Ref : Stand Genomic Sci , 6 :21 , 2012
Abstract : Marinithermus hydrothermalis Sako et al. 2003 is the type species of the monotypic genus Marinithermus. M. hydrothermalis T1(T) was the first isolate within the phylum "Thermus-Deinococcus" to exhibit optimal growth under a salinity equivalent to that of sea water and to have an absolute requirement for NaCl for growth. M. hydrothermalis T1(T) is of interest because it may provide a new insight into the ecological significance of the aerobic, thermophilic decomposers in the circulation of organic compounds in deep-sea hydrothermal vent ecosystems. This is the first completed genome sequence of a member of the genus Marinithermus and the seventh sequence from the family Thermaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,269,167 bp long genome with its 2,251 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Copeland_2012_Stand.Genomic.Sci_6_21
PubMedSearch : Copeland_2012_Stand.Genomic.Sci_6_21
PubMedID: 22675595
Gene_locus related to this paper: marht-f2nq80

Title : Complete genome sequence of Haliscomenobacter hydrossis type strain (O) - Daligault_2011_Stand.Genomic.Sci_4_352
Author(s) : Daligault H , Lapidus A , Zeytun A , Nolan M , Lucas S , Del Rio TG , Tice H , Cheng JF , Tapia R , Han C , Goodwin L , Pitluck S , Liolios K , Pagani I , Ivanova N , Huntemann M , Mavromatis K , Mikhailova N , Pati A , Chen A , Palaniappan K , Land M , Hauser L , Brambilla EM , Rohde M , Verbarg S , Goker M , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP , Woyke T
Ref : Stand Genomic Sci , 4 :352 , 2011
Abstract : Haliscomenobacter hydrossis van Veen et al. 1973 is the type species of the genus Haliscomenobacter, which belongs to order "Sphingobacteriales". The species is of interest because of its isolated phylogenetic location in the tree of life, especially the so far genomically uncharted part of it, and because the organism grows in a thin, hardly visible hyaline sheath. Members of the species were isolated from fresh water of lakes and from ditch water. The genome of H. hydrossis is the first completed genome sequence reported from a member of the family "Saprospiraceae". The 8,771,651 bp long genome with its three plasmids of 92 kbp, 144 kbp and 164 kbp length contains 6,848 protein-coding and 60 RNA genes, and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Daligault_2011_Stand.Genomic.Sci_4_352
PubMedSearch : Daligault_2011_Stand.Genomic.Sci_4_352
PubMedID: 21886862
Gene_locus related to this paper: halh1-f4kq83 , halh1-f4kt82 , halh1-f4l3j3 , halh1-f4krm2 , halh1-f4kqu5 , halh1-f4l2w7

Title : Complete genome sequence of Bacteroides helcogenes type strain (P 36-108) - Pati_2011_Stand.Genomic.Sci_4_45
Author(s) : Pati A , Gronow S , Zeytun A , Lapidus A , Nolan M , Hammon N , Deshpande S , Cheng JF , Tapia R , Han C , Goodwin L , Pitluck S , Liolios K , Pagani I , Ivanova N , Mavromatis K , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Detter JC , Brambilla E , Rohde M , Goker M , Woyke T , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP , Lucas S
Ref : Stand Genomic Sci , 4 :45 , 2011
Abstract : Bacteroides helcogenes Benno et al. 1983 is of interest because of its isolated phylogenetic location and, although it has been found in pig feces and is known to be pathogenic for pigs, occurrence of this bacterium is rare and it does not cause significant damage in intensive animal husbandry. The genome of B. helcogenes P 36-108(T) is already the fifth completed and published type strain genome from the genus Bacteroides in the family Bacteroidaceae. The 3,998,906 bp long genome with its 3,353 protein-coding and 83 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Pati_2011_Stand.Genomic.Sci_4_45
PubMedSearch : Pati_2011_Stand.Genomic.Sci_4_45
PubMedID: 21475586
Gene_locus related to this paper: bact6-e6sny5 , bact6-e6sqv4 , bact6-e6str2 , bact6-e6suh8 , bact6-e6suk4 , bact6-e6sn75

Title : Complete genome sequence of Desulfobulbus propionicus type strain (1pr3) - Pagani_2011_Stand.Genomic.Sci_4_100
Author(s) : Pagani I , Lapidus A , Nolan M , Lucas S , Hammon N , Deshpande S , Cheng JF , Chertkov O , Davenport K , Tapia R , Han C , Goodwin L , Pitluck S , Liolios K , Mavromatis K , Ivanova N , Mikhailova N , Pati A , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Detter JC , Brambilla E , Kannan KP , Djao OD , Rohde M , Pukall R , Spring S , Goker M , Sikorski J , Woyke T , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP
Ref : Stand Genomic Sci , 4 :100 , 2011
Abstract : Desulfobulbus propionicus Widdel 1981 is the type species of the genus Desulfobulbus, which belongs to the family Desulfobulbaceae. The species is of interest because of its great implication in the sulfur cycle in aquatic sediments, its large substrate spectrum and a broad versatility in using various fermentation pathways. The species was the first example of a pure culture known to disproportionate elemental sulfur to sulfate and sulfide. This is the first completed genome sequence of a member of the genus Desulfobulbus and the third published genome sequence from a member of the family Desulfobulbaceae. The 3,851,869 bp long genome with its 3,351 protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Pagani_2011_Stand.Genomic.Sci_4_100
PubMedSearch : Pagani_2011_Stand.Genomic.Sci_4_100
PubMedID: 21475592
Gene_locus related to this paper: despd-e8rdj0 , despd-e8rjl1

Title : Complete genome sequence of Cellulophaga algicola type strain (IC166) - Abt_2011_Stand.Genomic.Sci_4_72
Author(s) : Abt B , Lu M , Misra M , Han C , Nolan M , Lucas S , Hammon N , Deshpande S , Cheng JF , Tapia R , Goodwin L , Pitluck S , Liolios K , Pagani I , Ivanova N , Mavromatis K , Ovchinikova G , Pati A , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Detter JC , Brambilla E , Rohde M , Tindall BJ , Goker M , Woyke T , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP , Lapidus A
Ref : Stand Genomic Sci , 4 :72 , 2011
Abstract : Cellulophaga algicola Bowman 2000 belongs to the family Flavobacteriaceae within the phylum 'Bacteroidetes' and was isolated from Melosira collected from the Eastern Antarctic coastal zone. The species is of interest because its members produce a wide range of extracellular enzymes capable of degrading proteins and polysaccharides with temperature optima of 20-30 degrees C. This is the first completed genome sequence of a member of the genus Cellulophaga. The 4,888,353 bp long genome with its 4,285 protein-coding and 62 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Abt_2011_Stand.Genomic.Sci_4_72
PubMedSearch : Abt_2011_Stand.Genomic.Sci_4_72
PubMedID: 21475589
Gene_locus related to this paper: celad-e6x4e5 , celad-e6x420 , celad-e6x777 , celad-e6xbe7

Title : Complete genome sequence of Cellulophaga lytica type strain (LIM-21) - Pati_2011_Stand.Genomic.Sci_4_221
Author(s) : Pati A , Abt B , Teshima H , Nolan M , Lapidus A , Lucas S , Hammon N , Deshpande S , Cheng JF , Tapia R , Han C , Goodwin L , Pitluck S , Liolios K , Pagani I , Mavromatis K , Ovchinikova G , Chen A , Palaniappan K , Land M , Hauser L , Jeffries CD , Detter JC , Brambilla EM , Kannan KP , Rohde M , Spring S , Goker M , Woyke T , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP , Ivanova N
Ref : Stand Genomic Sci , 4 :221 , 2011
Abstract : Cellulophaga lytica (Lewin 1969) Johansen et al. 1999 is the type species of the genus Cellulophaga, which belongs to the family Flavobacteriaceae within the phylum 'Bacteroidetes' and was isolated from marine beach mud in Limon, Costa Rica. The species is of biotechnological interest because its members produce a wide range of extracellular enzymes capable of degrading proteins and polysaccharides. After the genome sequence of Cellulophaga algicola this is the second completed genome sequence of a member of the genus Cellulophaga. The 3,765,936 bp long genome with its 3,303 protein-coding and 55 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Pati_2011_Stand.Genomic.Sci_4_221
PubMedSearch : Pati_2011_Stand.Genomic.Sci_4_221
PubMedID: 21677859
Gene_locus related to this paper: cellc-f0re62 , cellc-f0rek7 , cellc-f0rf75 , cellc-f0rgt2

Title : Complete genome sequence of Thermomonospora curvata type strain (B9) - Chertkov_2011_Stand.Genomic.Sci_4_13
Author(s) : Chertkov O , Sikorski J , Nolan M , Lapidus A , Lucas S , Del Rio TG , Tice H , Cheng JF , Goodwin L , Pitluck S , Liolios K , Ivanova N , Mavromatis K , Mikhailova N , Ovchinnikova G , Pati A , Chen A , Palaniappan K , Djao OD , Land M , Hauser L , Chang YJ , Jeffries CD , Brettin T , Han C , Detter JC , Rohde M , Goker M , Woyke T , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Klenk HP , Kyrpides NC
Ref : Stand Genomic Sci , 4 :13 , 2011
Abstract : Thermomonospora curvata Henssen 1957 is the type species of the genus Thermomonospora. This genus is of interest because members of this clade are sources of new antibiotics, enzymes, and products with pharmacological activity. In addition, members of this genus participate in the active degradation of cellulose. This is the first complete genome sequence of a member of the family Thermomonosporaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 5,639,016 bp long genome with its 4,985 protein-coding and 76 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Chertkov_2011_Stand.Genomic.Sci_4_13
PubMedSearch : Chertkov_2011_Stand.Genomic.Sci_4_13
PubMedID: 21475583
Gene_locus related to this paper: thecd-d1a9g5 , thecd-d1a2h1 , thecd-d1a1k1 , thecd-d1a1x8 , thecd-d1a2g9 , thecd-d1a3k3 , thecd-d1a4i6 , thecd-d1a7b6 , thecd-d1a8l9 , thecd-d1a9a3 , thecd-d1a9i2 , thecd-d1a9k7 , thecd-d1a765 , thecd-d1a838 , thecd-d1a847 , thecd-d1aah2 , thecd-d1abb9 , thecd-d1abi3 , thecd-d1abk7 , thecd-d1abn5 , thecd-d1acm8 , thecd-d1acs0 , thecd-d1adv4 , thecd-d1adw6 , thecd-d1aef0 , thecd-d1aat0 , thecd-d1aat5 , thecd-d1aat1 , thecd-d1a9g2 , thecd-d1aep2 , thecd-d1a6x9 , thecd-d1ab99

Title : Complete genome sequence of Calditerrivibrio nitroreducens type strain (Yu37-1) - Pitluck_2011_Stand.Genomic.Sci_4_54
Author(s) : Pitluck S , Sikorski J , Zeytun A , Lapidus A , Nolan M , Lucas S , Hammon N , Deshpande S , Cheng JF , Tapia R , Han C , Goodwin L , Liolios K , Pagani I , Ivanova N , Mavromatis K , Pati A , Chen A , Palaniappan K , Hauser L , Chang YJ , Jeffries CD , Detter JC , Brambilla E , Djao OD , Rohde M , Spring S , Goker M , Woyke T , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP , Land M
Ref : Stand Genomic Sci , 4 :54 , 2011
Abstract : Calditerrivibrio nitroreducens Iino et al. 2008 is the type species of the genus Calditerrivibrio. The species is of interest because of its important role in the nitrate cycle as nitrate reducer and for its isolated phylogenetic position in the Tree of Life. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the third complete genome sequence of a member of the family Deferribacteraceae. The 2,216,552 bp long genome with its 2,128 protein-coding and 50 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Pitluck_2011_Stand.Genomic.Sci_4_54
PubMedSearch : Pitluck_2011_Stand.Genomic.Sci_4_54
PubMedID: 21475587

Title : Complete genome sequence of Paludibacter propionicigenes type strain (WB4) - Gronow_2011_Stand.Genomic.Sci_4_36
Author(s) : Gronow S , Munk C , Lapidus A , Nolan M , Lucas S , Hammon N , Deshpande S , Cheng JF , Tapia R , Han C , Goodwin L , Pitluck S , Liolios K , Ivanova N , Mavromatis K , Mikhailova N , Pati A , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Brambilla E , Rohde M , Goker M , Detter JC , Woyke T , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP
Ref : Stand Genomic Sci , 4 :36 , 2011
Abstract : Paludibacter propionicigenes Ueki et al. 2006 is the type species of the genus Paludibacter, which belongs to the family Porphyromonadaceae. The species is of interest because of the position it occupies in the tree of life where it can be found in close proximity to members of the genus Dysgonomonas. This is the first completed genome sequence of a member of the genus Paludibacter and the third sequence from the family Porphyromonadaceae. The 3,685,504 bp long genome with its 3,054 protein-coding and 64 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Gronow_2011_Stand.Genomic.Sci_4_36
PubMedSearch : Gronow_2011_Stand.Genomic.Sci_4_36
PubMedID: 21475585
Gene_locus related to this paper: palpw-e4t0i0 , palpw-e4t5j4 , palpw-e4t287 , palpw-e4t2d5 , palpw-e4t2d6 , palpw-e4t5h4

Title : Complete genome sequence of Weeksella virosa type strain (9751) - Lang_2011_Stand.Genomic.Sci_4_81
Author(s) : Lang E , Teshima H , Lucas S , Lapidus A , Hammon N , Deshpande S , Nolan M , Cheng JF , Pitluck S , Liolios K , Pagani I , Mikhailova N , Ivanova N , Mavromatis K , Pati A , Tapia R , Han C , Goodwin L , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Brambilla EM , Kopitz M , Rohde M , Goker M , Tindall BJ , Detter JC , Woyke T , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Klenk HP , Kyrpides NC
Ref : Stand Genomic Sci , 4 :81 , 2011
Abstract : Weeksella virosa Holmes et al. 1987 is the sole member and type species of the genus Weeksella which belongs to the family Flavobacteriaceae of the phylum Bacteroidetes. Twenty-nine isolates, collected from clinical specimens provided the basis for the taxon description. While the species seems to be a saprophyte of the mucous membranes of healthy man and warm-blooded animals a causal relationship with disease has been reported in a few instances. Except for the ability to produce indole and to hydrolyze Tween and proteins such as casein and gelatin, this aerobic, non-motile, non-pigmented bacterial species is metabolically inert in most traditional biochemical tests. The 2,272,954 bp long genome with its 2,105 protein-coding and 76 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Lang_2011_Stand.Genomic.Sci_4_81
PubMedSearch : Lang_2011_Stand.Genomic.Sci_4_81
PubMedID: 21475590
Gene_locus related to this paper: weevc-f0nz59 , weevc-f0p0t6 , weevc-f0p2m6 , weevc-f0p272 , weevc-f0nzv7 , weevc-f0p2m3

Title : Complete genome sequence of Truepera radiovictrix type strain (RQ-24) - Ivanova_2011_Stand.Genomic.Sci_4_91
Author(s) : Ivanova N , Rohde C , Munk C , Nolan M , Lucas S , Del Rio TG , Tice H , Deshpande S , Cheng JF , Tapia R , Han C , Goodwin L , Pitluck S , Liolios K , Mavromatis K , Mikhailova N , Pati A , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Brambilla E , Rohde M , Goker M , Tindall BJ , Woyke T , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP , Lapidus A
Ref : Stand Genomic Sci , 4 :91 , 2011
Abstract : Truepera radiovictrix Albuquerque et al. 2005 is the type species of the genus Truepera within the phylum "Deinococcus/Thermus". T. radiovictrix is of special interest not only because of its isolated phylogenetic location in the order Deinococcales, but also because of its ability to grow under multiple extreme conditions in alkaline, moderately saline, and high temperature habitats. Of particular interest is the fact that, T. radiovictrix is also remarkably resistant to ionizing radiation, a feature it shares with members of the genus Deinococcus. This is the first completed genome sequence of a member of the family Trueperaceae and the fourth type strain genome sequence from a member of the order Deinococcales. The 3,260,398 bp long genome with its 2,994 protein-coding and 52 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Ivanova_2011_Stand.Genomic.Sci_4_91
PubMedSearch : Ivanova_2011_Stand.Genomic.Sci_4_91
PubMedID: 21475591
Gene_locus related to this paper: trurr-d7cxw6

Title : Complete genome sequence of Oceanithermus profundus type strain (506) - Pati_2011_Stand.Genomic.Sci_4_210
Author(s) : Pati A , Zhang X , Lapidus A , Nolan M , Lucas S , Del Rio TG , Tice H , Cheng JF , Tapia R , Han C , Goodwin L , Pitluck S , Liolios K , Pagani I , Ivanova N , Mavromatis K , Chen A , Palaniappan K , Hauser L , Jeffries CD , Brambilla EM , Rohl A , Mwirichia R , Rohde M , Tindall BJ , Sikorski J , Wirth R , Goker M , Woyke T , Detter JC , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP , Land M
Ref : Stand Genomic Sci , 4 :210 , 2011
Abstract : Oceanithermus profundus Miroshnichenko et al. 2003 is the type species of the genus Oceanithermus, which belongs to the family Thermaceae. The genus currently comprises two species whose members are thermophilic and are able to reduce sulfur compounds and nitrite. The organism is adapted to the salinity of sea water, is able to utilize a broad range of carbohydrates, some proteinaceous substrates, organic acids and alcohols. This is the first completed genome sequence of a member of the genus Oceanithermus and the fourth sequence from the family Thermaceae. The 2,439,291 bp long genome with its 2,391 protein-coding and 54 RNA genes consists of one chromosome and a 135,351 bp long plasmid, and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Pati_2011_Stand.Genomic.Sci_4_210
PubMedSearch : Pati_2011_Stand.Genomic.Sci_4_210
PubMedID: 21677858
Gene_locus related to this paper: ocep5-e4u9z9 , ocep5-e4u767

Title : Complete genome sequence of Tsukamurella paurometabola type strain (no. 33) - Munk_2011_Stand.Genomic.Sci_4_342
Author(s) : Munk AC , Lapidus A , Lucas S , Nolan M , Tice H , Cheng JF , Del Rio TG , Goodwin L , Pitluck S , Liolios K , Huntemann M , Ivanova N , Mavromatis K , Mikhailova N , Pati A , Chen A , Palaniappan K , Tapia R , Han C , Land M , Hauser L , Chang YJ , Jeffries CD , Brettin T , Yasawong M , Brambilla EM , Rohde M , Sikorski J , Goker M , Detter JC , Woyke T , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP
Ref : Stand Genomic Sci , 4 :342 , 2011
Abstract : Tsukamurella paurometabola corrig. (Steinhaus 1941) Collins et al. 1988 is the type species of the genus Tsukamurella, which is the type genus to the family Tsukamurellaceae. The species is not only of interest because of its isolated phylogenetic location, but also because it is a human opportunistic pathogen with some strains of the species reported to cause lung infection, lethal meningitis, and necrotizing tenosynovitis. This is the first completed genome sequence of a member of the genus Tsukamurella and the first genome sequence of a member of the family Tsukamurellaceae. The 4,479,724 bp long genome contains a 99,806 bp long plasmid and a total of 4,335 protein-coding and 56 RNA genes, and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Munk_2011_Stand.Genomic.Sci_4_342
PubMedSearch : Munk_2011_Stand.Genomic.Sci_4_342
PubMedID: 21886861
Gene_locus related to this paper: tsupd-d5uxc3

Title : Complete genome sequence of Bacteroides salanitronis type strain (BL78) - Gronow_2011_Stand.Genomic.Sci_4_191
Author(s) : Gronow S , Held B , Lucas S , Lapidus A , Del Rio TG , Nolan M , Tice H , Deshpande S , Cheng JF , Pitluck S , Liolios K , Pagani I , Ivanova N , Mavromatis K , Pati A , Tapia R , Han C , Goodwin L , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Brambilla EM , Rohde M , Goker M , Detter JC , Woyke T , Bristow J , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP , Eisen JA
Ref : Stand Genomic Sci , 4 :191 , 2011
Abstract : Bacteroides salanitronis Lan et al. 2006 is a species of the genus Bacteroides, which belongs to the family Bacteroidaceae. The species is of interest because it was isolated from the gut of a chicken and the growing awareness that the anaerobic microflora of the cecum is of benefit for the host and may impact poultry farming. The 4,308,663 bp long genome consists of a 4.24 Mbp chromosome and three plasmids (6 kbp, 19 kbp, 40 kbp) containing 3,737 protein-coding and 101 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Gronow_2011_Stand.Genomic.Sci_4_191
PubMedSearch : Gronow_2011_Stand.Genomic.Sci_4_191
PubMedID: 21677856
Gene_locus related to this paper: bacsh-f0qz10 , bacsh-f0qz83 , bacsh-f0r0m7 , bacsh-f0r0s7 , bacsh-f0r5r9 , bacsh-f0r030 , bacsh-f0r440 , bacsh-f0r869 , bacsh-f0qzb0 , bacsh-f0r6i2

Title : Complete genome sequence of Isosphaera pallida type strain (IS1B) - Goker_2011_Stand.Genomic.Sci_4_63
Author(s) : Goker M , Cleland D , Saunders E , Lapidus A , Nolan M , Lucas S , Hammon N , Deshpande S , Cheng JF , Tapia R , Han C , Goodwin L , Pitluck S , Liolios K , Pagani I , Ivanova N , Mavromatis K , Pati A , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Detter JC , Beck B , Woyke T , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP
Ref : Stand Genomic Sci , 4 :63 , 2011
Abstract : Isosphaera pallida (ex Woronichin 1927) Giovannoni et al. 1995 is the type species of the genus Isosphaera. The species is of interest because it was the first heterotrophic bacterium known to be phototactic, and it occupies an isolated phylogenetic position within the Planctomycetaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first complete genome sequence of a member of the genus Isosphaera and the third of a member of the family Planctomycetaceae. The 5,472,964 bp long chromosome and the 56,340 bp long plasmid with a total of 3,763 protein-coding and 60 RNA genes are part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Goker_2011_Stand.Genomic.Sci_4_63
PubMedSearch : Goker_2011_Stand.Genomic.Sci_4_63
PubMedID: 21475588
Gene_locus related to this paper: isopi-e8qx42 , isopi-e8qz61 , isopi-e8r2k6 , isopi-e8r4h2 , isopi-e8r5e4 , isopi-e8r123 , isopi-e8qz30

Title : Non-contiguous finished genome sequence of Bacteroides coprosuis type strain (PC139) - Land_2011_Stand.Genomic.Sci_4_233
Author(s) : Land M , Held B , Gronow S , Abt B , Lucas S , Del Rio TG , Nolan M , Tice H , Cheng JF , Pitluck S , Liolios K , Pagani I , Ivanova N , Mavromatis K , Mikhailova N , Pati A , Tapia R , Han C , Goodwin L , Chen A , Palaniappan K , Hauser L , Brambilla EM , Rohde M , Goker M , Detter JC , Woyke T , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP , Lapidus A
Ref : Stand Genomic Sci , 4 :233 , 2011
Abstract : Bacteroides coprosuis Whitehead et al. 2005 belongs to the genus Bacteroides, which is a member of the family Bacteroidaceae. Members of the genus Bacteroides in general are known as beneficial protectors of animal guts against pathogenic microorganisms, and as contributors to the degradation of complex molecules such as polysaccharides. B. coprosuis itself was isolated from a manure storage pit of a swine facility, but has not yet been found in an animal host. The species is of interest solely because of its isolated phylogenetic location. The genome of B. coprosuis is already the 5(th) sequenced type strain genome from the genus Bacteroides. The 2,991,798 bp long genome with its 2,461 protein-coding and 78 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Land_2011_Stand.Genomic.Sci_4_233
PubMedSearch : Land_2011_Stand.Genomic.Sci_4_233
PubMedID: 21677860
Gene_locus related to this paper: 9bace-f3zpr3 , 9bace-f3zre7

Title : Complete genome sequence of Mahella australiensis type strain (50-1 BON) - Sikorski_2011_Stand.Genomic.Sci_4_331
Author(s) : Sikorski J , Teshima H , Nolan M , Lucas S , Hammon N , Deshpande S , Cheng JF , Pitluck S , Liolios K , Pagani I , Ivanova N , Huntemann M , Mavromatis K , Ovchinikova G , Pati A , Tapia R , Han C , Goodwin L , Chen A , Palaniappan K , Land M , Hauser L , Ngatchou-Djao OD , Rohde M , Pukall R , Spring S , Abt B , Goker M , Detter JC , Woyke T , Bristow J , Markowitz V , Hugenholtz P , Eisen JA , Kyrpides NC , Klenk HP , Lapidus A
Ref : Stand Genomic Sci , 4 :331 , 2011
Abstract : Mahella australiensis Bonilla Salinas et al. 2004 is the type species of the genus Mahella, which belongs to the family Thermoanaerobacteraceae. The species is of interest because it differs from other known anaerobic spore-forming bacteria in its G+C content, and in certain phenotypic traits, such as carbon source utilization and relationship to temperature. Moreover, it has been discussed that this species might be an indigenous member of petroleum and oil reservoirs. This is the first completed genome sequence of a member of the genus Mahella and the ninth completed type strain genome sequence from the family Thermoanaerobacteraceae. The 3,135,972 bp long genome with its 2,974 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Sikorski_2011_Stand.Genomic.Sci_4_331
PubMedSearch : Sikorski_2011_Stand.Genomic.Sci_4_331
PubMedID: 21886860
Gene_locus related to this paper: maha5-f3zvv5

Title : Complete genome sequence of Leadbetterella byssophila type strain (4M15) - Abt_2011_Stand.Genomic.Sci_4_2
Author(s) : Abt B , Teshima H , Lucas S , Lapidus A , Del Rio TG , Nolan M , Tice H , Cheng JF , Pitluck S , Liolios K , Pagani I , Ivanova N , Mavromatis K , Pati A , Tapia R , Han C , Goodwin L , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Rohde M , Goker M , Tindall BJ , Detter JC , Woyke T , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Klenk HP , Kyrpides NC
Ref : Stand Genomic Sci , 4 :2 , 2011
Abstract : Leadbetterella byssophila Weon et al. 2005 is the type species of the genus Leadbetterella of the family Cytophagaceae in the phylum Bacteroidetes. Members of the phylum Bacteroidetes are widely distributed in nature, especially in aquatic environments. They are of special interest for their ability to degrade complex biopolymers. L. byssophila occupies a rather isolated position in the tree of life and is characterized by its ability to hydrolyze starch and gelatine, but not agar, cellulose or chitin. Here we describe the features of this organism, together with the complete genome sequence, and annotation. L. byssophila is already the 16(th) member of the family Cytophagaceae whose genome has been sequenced. The 4,059,653 bp long single replicon genome with its 3,613 protein-coding and 53 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Abt_2011_Stand.Genomic.Sci_4_2
PubMedSearch : Abt_2011_Stand.Genomic.Sci_4_2
PubMedID: 21475582
Gene_locus related to this paper: leab4-e4rqy5 , leab4-e4ru27 , leab4-e4ruf5 , leab4-e4rul3 , leab4-e4rut6 , leab4-e4rwa2 , leab4-e4rwt5 , leab4-e4rwv8 , leab4-e4ry52 , leab4-e4rzw2

Title : Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21) - Chang_2011_Stand.Genomic.Sci_5_97
Author(s) : Chang YJ , Land M , Hauser L , Chertkov O , Del Rio TG , Nolan M , Copeland A , Tice H , Cheng JF , Lucas S , Han C , Goodwin L , Pitluck S , Ivanova N , Ovchinikova G , Pati A , Chen A , Palaniappan K , Mavromatis K , Liolios K , Brettin T , Fiebig A , Rohde M , Abt B , Goker M , Detter JC , Woyke T , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP , Lapidus A
Ref : Stand Genomic Sci , 5 :97 , 2011
Abstract : Ktedonobacter racemifer corrig. Cavaletti et al. 2007 is the type species of the genus Ktedonobacter, which in turn is the type genus of the family Ktedonobacteraceae, the type family of the order Ktedonobacterales within the class Ktedonobacteria in the phylum 'Chloroflexi'. Although K. racemifer shares some morphological features with the actinobacteria, it is of special interest because it was the first cultivated representative of a deep branching unclassified lineage of otherwise uncultivated environmental phylotypes tentatively located within the phylum 'Chloroflexi'. The aerobic, filamentous, non-motile, spore-forming Gram-positive heterotroph was isolated from soil in Italy. The 13,661,586 bp long non-contiguous finished genome consists of ten contigs and is the first reported genome sequence from a member of the class Ktedonobacteria. With its 11,453 protein-coding and 87 RNA genes, it is the largest prokaryotic genome reported so far. It comprises a large number of over-represented COGs, particularly genes associated with transposons, causing the genetic redundancy within the genome being considerably larger than expected by chance. This work is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Chang_2011_Stand.Genomic.Sci_5_97
PubMedSearch : Chang_2011_Stand.Genomic.Sci_5_97
PubMedID: 22180814
Gene_locus related to this paper: 9chlr-d6ttv1 , 9chlr-d6thn5 , 9chlr-d6tk73 , 9chlr-d6tzq4 , 9chlr-d6tri7 , 9chlr-d6tuz4 , 9chlr-d6tri9 , 9chlr-d6tsy5 , 9chlr-d6u5k6 , 9chlr-d6u6a8 , 9chlr-d6tye6 , 9chlr-d6tpj9

Title : Complete genome sequence of the thermophilic, hydrogen-oxidizing Bacillus tusciae type strain (T2) and reclassification in the new genus, Kyrpidia gen. nov. as Kyrpidia tusciae comb. nov. and emendation of the family Alicyclobacillaceae da Costa and Rainey, 2010 - Klenk_2011_Stand.Genomic.Sci_5_121
Author(s) : Klenk HP , Lapidus A , Chertkov O , Copeland A , Del Rio TG , Nolan M , Lucas S , Chen F , Tice H , Cheng JF , Han C , Bruce D , Goodwin L , Pitluck S , Pati A , Ivanova N , Mavromatis K , Daum C , Chen A , Palaniappan K , Chang YJ , Land M , Hauser L , Jeffries CD , Detter JC , Rohde M , Abt B , Pukall R , Goker M , Bristow J , Markowitz V , Hugenholtz P , Eisen JA
Ref : Stand Genomic Sci , 5 :121 , 2011
Abstract : Bacillus tusciae Bonjour & Aragno 1994 is a hydrogen-oxidizing, thermoacidophilic spore former that lives as a facultative chemolithoautotroph in solfataras. Although 16S rRNA gene sequencing was well established at the time of the initial description of the organism, 16S sequence data were not available and the strain was placed into the genus Bacillus based on limited chemotaxonomic information. Despite the now obvious misplacement of strain T2 as a member of the genus Bacillus in 16S rRNA-based phylogenetic trees, the misclassification remained uncorrected for many years, which was likely due to the extremely difficult, analysis-hampering cultivation conditions and poor growth rate of the strain. Here we provide a taxonomic re-evaluation of strain T2T (= DSM 2912 = NBRC 15312) and propose its reclassification as the type strain of a new species, Kyrpidia tusciae, and the type species of the new genus Kyrpidia, which is a sister-group of Alicyclobacillus. The family Alicyclobacillaceae da Costa and Rainey, 2010 is emended. The 3,384,766 bp genome with its 3,323 protein-coding and 78 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Klenk_2011_Stand.Genomic.Sci_5_121
PubMedSearch : Klenk_2011_Stand.Genomic.Sci_5_121
PubMedID: 22180816

Title : Complete genome sequence of Marivirga tractuosa type strain (H-43) - Pagani_2011_Stand.Genomic.Sci_4_154
Author(s) : Pagani I , Chertkov O , Lapidus A , Lucas S , Del Rio TG , Tice H , Copeland A , Cheng JF , Nolan M , Saunders E , Pitluck S , Held B , Goodwin L , Liolios K , Ovchinikova G , Ivanova N , Mavromatis K , Pati A , Chen A , Palaniappan K , Land M , Hauser L , Jeffries CD , Detter JC , Han C , Tapia R , Ngatchou-Djao OD , Rohde M , Goker M , Spring S , Sikorski J , Woyke T , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Klenk HP , Kyrpides NC
Ref : Stand Genomic Sci , 4 :154 , 2011
Abstract : Marivirga tractuosa (Lewin 1969) Nedashkovskaya et al. 2010 is the type species of the genus Marivirga, which belongs to the family Flammeovirgaceae. Members of this genus are of interest because of their gliding motility. The species is of interest because representative strains show resistance to several antibiotics, including gentamicin, kanamycin, neomycin, polymixin and streptomycin. This is the first complete genome sequence of a member of the family Flammeovirgaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,511,574 bp long chromosome and the 4,916 bp plasmid with their 3,808 protein-coding and 49 RNA genes are a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Pagani_2011_Stand.Genomic.Sci_4_154
PubMedSearch : Pagani_2011_Stand.Genomic.Sci_4_154
PubMedID: 21677852
Gene_locus related to this paper: marth-e4tt12

Title : Complete genome sequence of Desulfarculus baarsii type strain (2st14) - Sun_2010_Stand.Genomic.Sci_3_276
Author(s) : Sun H , Spring S , Lapidus A , Davenport K , Del Rio TG , Tice H , Nolan M , Copeland A , Cheng JF , Lucas S , Tapia R , Goodwin L , Pitluck S , Ivanova N , Pagani I , Mavromatis K , Ovchinnikova G , Pati A , Chen A , Palaniappan K , Hauser L , Chang YJ , Jeffries CD , Detter JC , Han C , Rohde M , Brambilla E , Goker M , Woyke T , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP , Land M
Ref : Stand Genomic Sci , 3 :276 , 2010
Abstract : Desulfarculus baarsii (Widdel 1981) Kuever et al. 2006 is the type and only species of the genus Desulfarculus, which represents the family Desulfarculaceae and the order Desulfarculales. This species is a mesophilic sulfate-reducing bacterium with the capability to oxidize acetate and fatty acids of up to 18 carbon atoms completely to CO(2). The acetyl-CoA/CODH (Wood-Ljungdahl) pathway is used by this species for the complete oxidation of carbon sources and autotrophic growth on formate. The type strain 2st14(T) was isolated from a ditch sediment collected near the University of Konstanz, Germany. This is the first completed genome sequence of a member of the order Desulfarculales. The 3,655,731 bp long single replicon genome with its 3,303 protein-coding and 52 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Sun_2010_Stand.Genomic.Sci_3_276
PubMedSearch : Sun_2010_Stand.Genomic.Sci_3_276
PubMedID: 21304732
Gene_locus related to this paper: desb2-e1qfv0 , desb2-e1qiq4 , desb2-e1qd85

Title : Complete genome sequence of Gordonia bronchialis type strain (3410) - Ivanova_2010_Stand.Genomic.Sci_2_19
Author(s) : Ivanova N , Sikorski J , Jando M , Lapidus A , Nolan M , Lucas S , Del Rio TG , Tice H , Copeland A , Cheng JF , Chen F , Bruce D , Goodwin L , Pitluck S , Mavromatis K , Ovchinnikova G , Pati A , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Chain P , Saunders E , Han C , Detter JC , Brettin T , Rohde M , Goker M , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Klenk HP , Kyrpides NC
Ref : Stand Genomic Sci , 2 :19 , 2010
Abstract : Gordonia bronchialis Tsukamura 1971 is the type species of the genus. G. bronchialis is a human-pathogenic organism that has been isolated from a large variety of human tissues. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the family Gordoniaceae. The 5,290,012 bp long genome with its 4,944 protein-coding and 55 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Ivanova_2010_Stand.Genomic.Sci_2_19
PubMedSearch : Ivanova_2010_Stand.Genomic.Sci_2_19
PubMedID: 21304674
Gene_locus related to this paper: gorb4-d0lfd8

Title : Complete genome sequence of Methanoplanus petrolearius type strain (SEBR 4847) - Brambilla_2010_Stand.Genomic.Sci_3_203
Author(s) : Brambilla E , Djao OD , Daligault H , Lapidus A , Lucas S , Hammon N , Nolan M , Tice H , Cheng JF , Han C , Tapia R , Goodwin L , Pitluck S , Liolios K , Ivanova N , Mavromatis K , Mikhailova N , Pati A , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Rohde M , Spring S , Sikorski J , Goker M , Woyke T , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP
Ref : Stand Genomic Sci , 3 :203 , 2010
Abstract : Methanoplanus petrolearius Ollivier et al. 1998 is the type strain of the genus Methanoplanus. The strain was originally isolated from an offshore oil field from the Gulf of Guinea. Members of the genus Methanoplanus are of interest because they play an important role in the carbon cycle and also because of their significant contribution to the global warming by methane emission in the atmosphere. Like other archaea of the family Methanomicrobiales, the members of the genus Methanoplanus are able to use CO(2) and H(2) as a source of carbon and energy; acetate is required for growth and probably also serves as carbon source. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first complete genome sequence of a member of the family Methanomicrobiaceae and the sixth complete genome sequence from the order Methanomicrobiales. The 2,843,290 bp long genome with its 2,824 protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Brambilla_2010_Stand.Genomic.Sci_3_203
PubMedSearch : Brambilla_2010_Stand.Genomic.Sci_3_203
PubMedID: 21304750
Gene_locus related to this paper: metp4-e1rj85 , metp4-e1rk92 , metp4-e1ree0

Title : Complete genome sequence of Haliangium ochraceum type strain (SMP-2) - Ivanova_2010_Stand.Genomic.Sci_2_96
Author(s) : Ivanova N , Daum C , Lang E , Abt B , Kopitz M , Saunders E , Lapidus A , Lucas S , Glavina Del Rio T , Nolan M , Tice H , Copeland A , Cheng JF , Chen F , Bruce D , Goodwin L , Pitluck S , Mavromatis K , Pati A , Mikhailova N , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Detter JC , Brettin T , Rohde M , Goker M , Bristow J , Markowitz V , Eisen JA , Hugenholtz P , Kyrpides NC , Klenk HP
Ref : Stand Genomic Sci , 2 :96 , 2010
Abstract : Haliangium ochraceum Fudou et al. 2002 is the type species of the genus Haliangium in the myxococcal family 'Haliangiaceae'. Members of the genus Haliangium are the first halophilic myxobacterial taxa described. The cells of the species follow a multicellular lifestyle in highly organized biofilms, called swarms, they decompose bacterial and yeast cells as most myxobacteria do. The fruiting bodies contain particularly small coccoid myxospores. H. ochraceum encodes the first actin homologue identified in a bacterial genome. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the myxococcal suborder Nannocystineae, and the 9,446,314 bp long single replicon genome with its 6,898 protein-coding and 53 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Ivanova_2010_Stand.Genomic.Sci_2_96
PubMedSearch : Ivanova_2010_Stand.Genomic.Sci_2_96
PubMedID: 21304682
Gene_locus related to this paper: halo1-d0lid9 , halo1-d0lm49 , halo1-d0lrn3 , halo1-d0ljm2

Title : Complete genome sequence of Coraliomargarita akajimensis type strain (04OKA010-24) - Mavromatis_2010_Stand.Genomic.Sci_2_290
Author(s) : Mavromatis K , Abt B , Brambilla E , Lapidus A , Copeland A , Deshpande S , Nolan M , Lucas S , Tice H , Cheng JF , Han C , Detter JC , Woyke T , Goodwin L , Pitluck S , Held B , Brettin T , Tapia R , Ivanova N , Mikhailova N , Pati A , Liolios K , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Rohde M , Goker M , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Klenk HP , Kyrpides NC
Ref : Stand Genomic Sci , 2 :290 , 2010
Abstract : Coraliomargarita akajimensis Yoon et al. 2007 is the type species of the genus Coraliomargarita. C. akajimensis is an obligately aerobic, Gram-negative, non-spore-forming, non-motile, spherical bacterium that was isolated from seawater surrounding the hard coral Galaxea fascicularis. C. akajimensis is of special interest because of its phylogenetic position in a genomically under-studied area of the bacterial diversity. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the family Puniceicoccaceae. The 3,750,771 bp long genome with its 3,137 protein-coding and 55 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Mavromatis_2010_Stand.Genomic.Sci_2_290
PubMedSearch : Mavromatis_2010_Stand.Genomic.Sci_2_290
PubMedID: 21304713
Gene_locus related to this paper: corad-d5ehl2 , corad-d5ene2 , corad-d5epb6 , corad-d5epc2 , corad-d5epz5

Title : Complete genome sequence of Conexibacter woesei type strain (ID131577) - Pukall_2010_Stand.Genomic.Sci_2_212
Author(s) : Pukall R , Lapidus A , Glavina Del Rio T , Copeland A , Tice H , Cheng JF , Lucas S , Chen F , Nolan M , Bruce D , Goodwin L , Pitluck S , Mavromatis K , Ivanova N , Ovchinnikova G , Pati A , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Chain P , Meincke L , Sims D , Brettin T , Detter JC , Rohde M , Goker M , Bristow J , Eisen JA , Markowitz V , Kyrpides NC , Klenk HP , Hugenholtz P
Ref : Stand Genomic Sci , 2 :212 , 2010
Abstract : The genus Conexibacter (Monciardini et al. 2003) represents the type genus of the family Conexibacteraceae (Stackebrandt 2005, emend. Zhi et al. 2009) with Conexibacter woesei as the type species of the genus. C. woesei is a representative of a deep evolutionary line of descent within the class Actinobacteria. Strain ID131577(T) was originally isolated from temperate forest soil in Gerenzano (Italy). Cells are small, short rods that are motile by peritrichous flagella. They may form aggregates after a longer period of growth and, then as a typical characteristic, an undulate structure is formed by self-aggregation of flagella with entangled bacterial cells. Here we describe the features of the organism, together with the complete sequence and annotation. The 6,359,369 bp long genome of C. woesei contains 5,950 protein-coding and 48 RNA genes and is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Pukall_2010_Stand.Genomic.Sci_2_212
PubMedSearch : Pukall_2010_Stand.Genomic.Sci_2_212
PubMedID: 21304704
Gene_locus related to this paper: conwi-d3fc89

Title : Complete genome sequence of Haloterrigena turkmenica type strain (4k) - Saunders_2010_Stand.Genomic.Sci_2_107
Author(s) : Saunders E , Tindall BJ , Fahnrich R , Lapidus A , Copeland A , Del Rio TG , Lucas S , Chen F , Tice H , Cheng JF , Han C , Detter JC , Bruce D , Goodwin L , Chain P , Pitluck S , Pati A , Ivanova N , Mavromatis K , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Brettin T , Rohde M , Goker M , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Klenk HP , Kyrpides NC
Ref : Stand Genomic Sci , 2 :107 , 2010
Abstract : Haloterrigena turkmenica (Zvyagintseva and Tarasov 1987) Ventosa et al. 1999, comb. nov. is the type species of the genus Haloterrigena in the euryarchaeal family Halobacteriaceae. It is of phylogenetic interest because of the yet unclear position of the genera Haloterrigena and Natrinema within the Halobacteriaceae, which created some taxonomic problems historically. H. turkmenica, was isolated from sulfate saline soil in Turkmenistan, is a relatively fast growing, chemoorganotrophic, carotenoid-containing, extreme halophile, requiring at least 2 M NaCl for growth. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the genus Haloterrigena, but the eighth genome sequence from a member of the family Halobacteriaceae. The 5,440,782 bp genome (including six plasmids) with its 5,287 protein-coding and 63 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Saunders_2010_Stand.Genomic.Sci_2_107
PubMedSearch : Saunders_2010_Stand.Genomic.Sci_2_107
PubMedID: 21304683
Gene_locus related to this paper: halsp-YUXL , haltv-d2rs70 , haltv-d2rtx9 , haltv-d2rwf4 , haltv-d2rwl5 , haltv-d2rxg6 , haltv-d2rxv9 , haltv-d2ry22 , haltv-d2rzg9 , haltv-d2rzl4 , haltv-d2s3c9

Title : The complete genome sequence of Haloferax volcanii DS2, a model archaeon - Hartman_2010_PLoS.One_5_e9605
Author(s) : Hartman AL , Norais C , Badger JH , Delmas S , Haldenby S , Madupu R , Robinson J , Khouri H , Ren Q , Lowe TM , Maupin-Furlow J , Pohlschroder M , Daniels C , Pfeiffer F , Allers T , Eisen JA
Ref : PLoS ONE , 5 :e9605 , 2010
Abstract : BACKGROUND: Haloferax volcanii is an easily culturable moderate halophile that grows on simple defined media, is readily transformable, and has a relatively stable genome. This, in combination with its biochemical and genetic tractability, has made Hfx. volcanii a key model organism, not only for the study of halophilicity, but also for archaeal biology in general. METHODOLOGY/PRINCIPAL FINDINGS: We report here the sequencing and analysis of the genome of Hfx. volcanii DS2, the type strain of this species. The genome contains a main 2.848 Mb chromosome, three smaller chromosomes pHV1, 3, 4 (85, 438, 636 kb, respectively) and the pHV2 plasmid (6.4 kb). CONCLUSIONS/SIGNIFICANCE: The completed genome sequence, presented here, provides an invaluable tool for further in vivo and in vitro studies of Hfx. volcanii.
ESTHER : Hartman_2010_PLoS.One_5_e9605
PubMedSearch : Hartman_2010_PLoS.One_5_e9605
PubMedID: 20333302
Gene_locus related to this paper: halvd-d4gpd7 , halvd-d4gtr7 , halvd-d4gug3 , halvd-d4gug9 , halvd-d4gz20 , halvd-metxa

Title : Complete genome sequence of Nocardiopsis dassonvillei type strain (IMRU 509) - Sun_2010_Stand.Genomic.Sci_3_325
Author(s) : Sun H , Lapidus A , Nolan M , Lucas S , Del Rio TG , Tice H , Cheng JF , Tapia R , Han C , Goodwin L , Pitluck S , Pagani I , Ivanova N , Mavromatis K , Mikhailova N , Pati A , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Djao OD , Rohde M , Sikorski J , Goker M , Woyke T , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP
Ref : Stand Genomic Sci , 3 :325 , 2010
Abstract : Nocardiopsis dassonvillei (Brocq-Rousseau 1904) Meyer 1976 is the type species of the genus Nocardiopsis, which in turn is the type genus of the family Nocardiopsaceae. This species is of interest because of its ecological versatility. Members of N. dassonvillei have been isolated from a large variety of natural habitats such as soil and marine sediments, from different plant and animal materials as well as from human patients. Moreover, representatives of the genus Nocardiopsis participate actively in biopolymer degradation. This is the first complete genome sequence in the family Nocardiopsaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 6,543,312 bp long genome consist of a 5.77 Mbp chromosome and a 0.78 Mbp plasmid and with its 5,570 protein-coding and 77 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Sun_2010_Stand.Genomic.Sci_3_325
PubMedSearch : Sun_2010_Stand.Genomic.Sci_3_325
PubMedID: 21304737
Gene_locus related to this paper: nocdd-d7auf1 , nocdd-d7avl6 , nocdd-d7b2j7 , nocdd-d7b3b3 , nocdd-d7b6l9 , nocdd-d7b210 , nocdd-d7b279 , nocdd-d7b3k0 , nocdd-d7awb2

Title : Complete genome sequence of Cellulomonas flavigena type strain (134) - Abt_2010_Stand.Genomic.Sci_3_15
Author(s) : Abt B , Foster B , Lapidus A , Clum A , Sun H , Pukall R , Lucas S , Glavina Del Rio T , Nolan M , Tice H , Cheng JF , Pitluck S , Liolios K , Ivanova N , Mavromatis K , Ovchinnikova G , Pati A , Goodwin L , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Rohde M , Goker M , Woyke T , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP
Ref : Stand Genomic Sci , 3 :15 , 2010
Abstract : Cellulomonas flavigena (Kellerman and McBeth 1912) Bergey et al. 1923 is the type species of the genus Cellulomonas of the actinobacterial family Cellulomonadaceae. Members of the genus Cellulomonas are of special interest for their ability to degrade cellulose and hemicellulose, particularly with regard to the use of biomass as an alternative energy source. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the genus Cellulomonas, and next to the human pathogen Tropheryma whipplei the second complete genome sequence within the actinobacterial family Cellulomonadaceae. The 4,123,179 bp long single replicon genome with its 3,735 protein-coding and 53 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Abt_2010_Stand.Genomic.Sci_3_15
PubMedSearch : Abt_2010_Stand.Genomic.Sci_3_15
PubMedID: 21304688
Gene_locus related to this paper: celfn-d5uif8 , celfn-d5uil9 , celfn-d5ukl6 , celfn-d5ulu1 , celfn-d5ulp3 , celfn-d5ul75 , celfn-d5ufu5 , celfn-d5ugh8

Title : Complete genome sequence of Vulcanisaeta distributa type strain (IC-017) - Mavromatis_2010_Stand.Genomic.Sci_3_117
Author(s) : Mavromatis K , Sikorski J , Pabst E , Teshima H , Lapidus A , Lucas S , Nolan M , Glavina Del Rio T , Cheng JF , Bruce D , Goodwin L , Pitluck S , Liolios K , Ivanova N , Mikhailova N , Pati A , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Rohde M , Spring S , Goker M , Wirth R , Woyke T , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Klenk HP , Kyrpides NC
Ref : Stand Genomic Sci , 3 :117 , 2010
Abstract : Vulcanisaeta distributa Itoh et al. 2002 belongs to the family Thermoproteaceae in the phylum Crenarchaeota. The genus Vulcanisaeta is characterized by a global distribution in hot and acidic springs. This is the first genome sequence from a member of the genus Vulcanisaeta and seventh genome sequence in the family Thermoproteaceae. The 2,374,137 bp long genome with its 2,544 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia of Bacteriaand Archaea project.
ESTHER : Mavromatis_2010_Stand.Genomic.Sci_3_117
PubMedSearch : Mavromatis_2010_Stand.Genomic.Sci_3_117
PubMedID: 21304741
Gene_locus related to this paper: vuldi-e1qt20 , vuldi-e1qqi6

Title : Complete genome sequence of Ferrimonas balearica type strain (PAT) - Nolan_2010_Stand.Genomic.Sci_3_174
Author(s) : Nolan M , Sikorski J , Davenport K , Lucas S , Del Rio TG , Tice H , Cheng JF , Goodwin L , Pitluck S , Liolios K , Ivanova N , Mavromatis K , Ovchinnikova G , Pati A , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Tapia R , Brettin T , Detter JC , Han C , Yasawong M , Rohde M , Tindall BJ , Goker M , Woyke T , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP , Lapidus A
Ref : Stand Genomic Sci , 3 :174 , 2010
Abstract : Ferrimonas balearica Rossello-Mora et al. 1996 is the type species of the genus Ferrimonas, which belongs to the family Ferrimonadaceae within the Gammaproteobacteria. The species is a Gram-negative, motile, facultatively anaerobic, non spore-forming bacterium, which is of special interest because it is a chemoorganotroph and has a strictly respiratory metabolism with oxygen, nitrate, Fe(III)-oxyhydroxide, Fe(III)-citrate, MnO(2), selenate, selenite and thiosulfate as electron acceptors. This is the first completed genome sequence of a member of the genus Ferrimonas and also the first sequence from a member of the family Ferrimonadaceae. The 4,279,159 bp long genome with its 3,803 protein-coding and 144 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Nolan_2010_Stand.Genomic.Sci_3_174
PubMedSearch : Nolan_2010_Stand.Genomic.Sci_3_174
PubMedID: 21304747
Gene_locus related to this paper: ferbd-e1slj2 , ferbd-e1sm86 , ferbd-e1sm96 , ferbd-e1sr13 , ferbd-e1sv19 , ferbd-e1sva3 , ferbd-e1swh8 , ferbd-e1ss88 , ferbd-e1swm0 , ferbd-e1snp4

Title : Complete genome sequence of Arcanobacterium haemolyticum type strain (11018) - Yasawong_2010_Stand.Genomic.Sci_3_126
Author(s) : Yasawong M , Teshima H , Lapidus A , Nolan M , Lucas S , Glavina Del Rio T , Tice H , Cheng JF , Bruce D , Detter C , Tapia R , Han C , Goodwin L , Pitluck S , Liolios K , Ivanova N , Mavromatis K , Mikhailova N , Pati A , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Rohde M , Sikorski J , Pukall R , Goker M , Woyke T , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP
Ref : Stand Genomic Sci , 3 :126 , 2010
Abstract : Arcanobacterium haemolyticum (ex MacLean et al. 1946) Collins et al. 1983 is the type species of the genus Arcanobacterium, which belongs to the family Actinomycetaceae. The strain is of interest because it is an obligate parasite of the pharynx of humans and farm animal; occasionally, it causes pharyngeal or skin lesions. It is a Gram-positive, nonmotile and non-sporulating bacterium. The strain described in this study was isolated from infections amongst American soldiers of certain islands of the North and West Pacific. This is the first completed sequence of a member of the genus Arcanobacterium and the ninth type strain genome from the family Actinomycetaceae. The 1,986,154 bp long genome with its 1,821 protein-coding and 64 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Yasawong_2010_Stand.Genomic.Sci_3_126
PubMedSearch : Yasawong_2010_Stand.Genomic.Sci_3_126
PubMedID: 21304742
Gene_locus related to this paper: archd-d7bl98 , archd-d7bm52 , archd-d7bne1 , archd-d7bkh7

Title : Complete genome sequence of Planctomyces limnophilus type strain (Mu 290) - Labutti_2010_Stand.Genomic.Sci_3_47
Author(s) : LaButti K , Sikorski J , Schneider S , Nolan M , Lucas S , Glavina Del Rio T , Tice H , Cheng JF , Goodwin L , Pitluck S , Liolios K , Ivanova N , Mavromatis K , Mikhailova N , Pati A , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Tindall BJ , Rohde M , Goker M , Woyke T , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP , Lapidus A
Ref : Stand Genomic Sci , 3 :47 , 2010
Abstract : Planctomyces limnophilus Hirsch and Muller 1986 belongs to the order Planctomycetales, which differs from other bacterial taxa by several distinctive features such as internal cell compartmentalization, multiplication by forming buds directly from the spherical, ovoid or pear-shaped mother cell and a cell wall which is stabilized by a proteinaceous layer rather than a peptidoglycan layer. Besides Pirellula staleyi, this is the second completed genome sequence of the family Planctomycetaceae. P. limnophilus is of interest because it differs from Pirellula by the presence of a stalk and its structure of fibril bundles, its cell shape and size, the formation of multicellular rosettes, low salt tolerance and red pigmented colonies. The 5,460,085 bp long genome with its 4,304 protein-coding and 66 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Labutti_2010_Stand.Genomic.Sci_3_47
PubMedSearch : Labutti_2010_Stand.Genomic.Sci_3_47
PubMedID: 21304691
Gene_locus related to this paper: plal2-d5spy8 , plal2-d5ssg7 , plal2-d5ssq1 , plal2-d5stl8 , plal2-d5su74 , plal2-d5swy9 , plal2-d5sxa1 , plal2-d5sxi9 , plal2-d5swp5

Title : Complete genome sequence of Acidaminococcus fermentans type strain (VR4) - Chang_2010_Stand.Genomic.Sci_3_1
Author(s) : Chang YJ , Pukall R , Saunders E , Lapidus A , Copeland A , Nolan M , Glavina Del Rio T , Lucas S , Chen F , Tice H , Cheng JF , Han C , Detter JC , Bruce D , Goodwin L , Pitluck S , Mikhailova N , Liolios K , Pati A , Ivanova N , Mavromatis K , Chen A , Palaniappan K , Land M , Hauser L , Jeffries CD , Brettin T , Rohde M , Goker M , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP
Ref : Stand Genomic Sci , 3 :1 , 2010
Abstract : Acidaminococcus fermentans (Rogosa 1969) is the type species of the genus Acidaminococcus, and is of phylogenetic interest because of its isolated placement in a genomically little characterized region of the Firmicutes. A. fermentans is known for its habitation of the gastrointestinal tract and its ability to oxidize trans-aconitate. Its anaerobic fermentation of glutamate has been intensively studied and will now be complemented by the genomic basis. The strain described in this report is a nonsporulating, nonmotile, Gram-negative coccus, originally isolated from a pig alimentary tract. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the family Acidaminococcaceae, and the 2,329,769 bp long genome with its 2,101 protein-coding and 81 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Chang_2010_Stand.Genomic.Sci_3_1
PubMedSearch : Chang_2010_Stand.Genomic.Sci_3_1
PubMedID: 21304687
Gene_locus related to this paper: acifv-d2rju3 , acifv-d2rk38 , acifv-d2rmp3

Title : Complete genome sequence of Sulfurimonas autotrophica type strain (OK10) - Sikorski_2010_Stand.Genomic.Sci_3_194
Author(s) : Sikorski J , Munk C , Lapidus A , Ngatchou Djao OD , Lucas S , Glavina Del Rio T , Nolan M , Tice H , Han C , Cheng JF , Tapia R , Goodwin L , Pitluck S , Liolios K , Ivanova N , Mavromatis K , Mikhailova N , Pati A , Sims D , Meincke L , Brettin T , Detter JC , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Rohde M , Lang E , Spring S , Goker M , Woyke T , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP
Ref : Stand Genomic Sci , 3 :194 , 2010
Abstract : Sulfurimonas autotrophica Inagaki et al. 2003 is the type species of the genus Sulfurimonas. This genus is of interest because of its significant contribution to the global sulfur cycle as it oxidizes sulfur compounds to sulfate and by its apparent habitation of deep-sea hydrothermal and marine sulfidic environments as potential ecological niche. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the second complete genome sequence of the genus Sulfurimonas and the 15(th) genome in the family Helicobacteraceae. The 2,153,198 bp long genome with its 2,165 protein-coding and 55 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Sikorski_2010_Stand.Genomic.Sci_3_194
PubMedSearch : Sikorski_2010_Stand.Genomic.Sci_3_194
PubMedID: 21304749
Gene_locus related to this paper: sulao-e0up24 , sulao-e0ute6 , sulao-metxa

Title : Complete genome sequence of Olsenella uli type strain (VPI D76D-27C) - Goker_2010_Stand.Genomic.Sci_3_76
Author(s) : Goker M , Held B , Lucas S , Nolan M , Yasawong M , Glavina Del Rio T , Tice H , Cheng JF , Bruce D , Detter JC , Tapia R , Han C , Goodwin L , Pitluck S , Liolios K , Ivanova N , Mavromatis K , Mikhailova N , Pati A , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Rohde M , Sikorski J , Pukall R , Woyke T , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP , Lapidus A
Ref : Stand Genomic Sci , 3 :76 , 2010
Abstract : Olsenella uli (Olsen et al. 1991) Dewhirst et al. 2001 is the type species of the genus Olsenella, which belongs to the actinobacterial family Coriobacteriaceae. The species is of interest because it is frequently isolated from dental plaque in periodontitis patients and can cause primary endodontic infection. The species is a Gram-positive, non-motile and non-sporulating bacterium. The strain described in this study was isolated from human gingival crevices. This is the first completed sequence of the genus Olsenella and the fifth sequence from a member of the family Coriobacteriaceae. The 2,051,896 bp long genome with its 1,795 protein-coding and 55 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Goker_2010_Stand.Genomic.Sci_3_76
PubMedSearch : Goker_2010_Stand.Genomic.Sci_3_76
PubMedID: 21304694
Gene_locus related to this paper: olsuv-e1qw86 , olsuv-e1qw87 , olsuv-e1qz20 , olsuv-e1qwd9

Title : Complete genome sequence of Intrasporangium calvum type strain (7 KIP) - Del Rio_2010_Stand.Genomic.Sci_3_294
Author(s) : Del Rio TG , Chertkov O , Yasawong M , Lucas S , Deshpande S , Cheng JF , Detter C , Tapia R , Han C , Goodwin L , Pitluck S , Liolios K , Ivanova N , Mavromatis K , Pati A , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Rohde M , Pukall R , Sikorski J , Goker M , Woyke T , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP , Lapidus A
Ref : Stand Genomic Sci , 3 :294 , 2010
Abstract : Intrasporangium calvum Kalakoutskii et al. 1967 is the type species of the genus Intrasporangium, which belongs to the actinobacterial family Intrasporangiaceae. The species is a Gram-positive bacterium that forms a branching mycelium, which tends to break into irregular fragments. The mycelium of this strain may bear intercalary vesicles but does not contain spores. The strain described in this study is an airborne organism that was isolated from a school dining room in 1967. One particularly interesting feature of I. calvum is that the type of its menaquinone is different from all other representatives of the family Intrasporangiaceae. This is the first completed genome sequence from a member of the genus Intrasporangium and also the first sequence from the family Intrasporangiaceae. The 4,024,382 bp long genome with its 3,653 protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Del Rio_2010_Stand.Genomic.Sci_3_294
PubMedSearch : Del Rio_2010_Stand.Genomic.Sci_3_294
PubMedID: 21304734
Gene_locus related to this paper: intc7-e6s7p7 , intc7-e6s9d8 , intc7-e6sds3 , intc7-e6s7a1 , intc7-e6sc55

Title : Complete genome sequence of Syntrophothermus lipocalidus type strain (TGB-C1) - Djao_2010_Stand.Genomic.Sci_3_268
Author(s) : Djao OD , Zhang X , Lucas S , Lapidus A , Del Rio TG , Nolan M , Tice H , Cheng JF , Han C , Tapia R , Goodwin L , Pitluck S , Liolios K , Ivanova N , Mavromatis K , Mikhailova N , Ovchinnikova G , Pati A , Brambilla E , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Rohde M , Sikorski J , Spring S , Goker M , Detter JC , Woyke T , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP
Ref : Stand Genomic Sci , 3 :268 , 2010
Abstract : Syntrophothermus lipocalidus Sekiguchi et al. 2000 is the type species of the genus Syntrophothermus. The species is of interest because of its strictly anaerobic lifestyle, its participation in the primary step of the degradation of organic maters, and for releasing products which serve as substrates for other microorganisms. It also contributes significantly to maintain a regular pH in its environment by removing the fatty acids through beta-oxidation. The strain is able to metabolize isobutyrate and butyrate, which are the substrate and the product of degradation of the substrate, respectively. This is the first complete genome sequence of a member of the genus Syntrophothermus and the second in the family Syntrophomonadaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,405,559 bp long genome with its 2,385 protein-coding and 55 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Djao_2010_Stand.Genomic.Sci_3_268
PubMedSearch : Djao_2010_Stand.Genomic.Sci_3_268
PubMedID: 21304731
Gene_locus related to this paper: synlt-d7cpg4

Title : Non-contiguous finished genome sequence of Aminomonas paucivorans type strain (GLU-3) - Pitluck_2010_Stand.Genomic.Sci_3_285
Author(s) : Pitluck S , Yasawong M , Held B , Lapidus A , Nolan M , Copeland A , Lucas S , Del Rio TG , Tice H , Cheng JF , Chertkov O , Goodwin L , Tapia R , Han C , Liolios K , Ivanova N , Mavromatis K , Ovchinnikova G , Pati A , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Pukall R , Spring S , Rohde M , Sikorski J , Goker M , Woyke T , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP
Ref : Stand Genomic Sci , 3 :285 , 2010
Abstract : Aminomonas paucivorans Baena et al. 1999 is the type species of the genus Aminomonas, which belongs to the family Synergistaceae. The species is of interest because it is an asaccharolytic chemoorganotrophic bacterium which ferments quite a number of amino acids. This is the first finished genome sequence (with one gap in a rDNA region) of a member of the genus Aminomonas and the third sequence from the family Synergistaceae. The 2,630,120 bp long genome with its 2,433 protein-coding and 61 RNA genes is a part of the GenomicEncyclopedia ofBacteria andArchaea project.
ESTHER : Pitluck_2010_Stand.Genomic.Sci_3_285
PubMedSearch : Pitluck_2010_Stand.Genomic.Sci_3_285
PubMedID: 21304733
Gene_locus related to this paper: 9bact-e3cyn3

Title : Complete genome sequence of Thermaerobacter marianensis type strain (7p75a) - Han_2010_Stand.Genomic.Sci_3_337
Author(s) : Han C , Gu W , Zhang X , Lapidus A , Nolan M , Copeland A , Lucas S , Del Rio TG , Tice H , Cheng JF , Tapia R , Goodwin L , Pitluck S , Pagani I , Ivanova N , Mavromatis K , Mikhailova N , Pati A , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Schneider S , Rohde M , Goker M , Pukall R , Woyke T , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP , Detter JC
Ref : Stand Genomic Sci , 3 :337 , 2010
Abstract : Thermaerobacter marianensis Takai et al. 1999 is the type species of the genus Thermaerobacter, which belongs to the Clostridiales family Incertae Sedis XVII. The species is of special interest because T. marianensis is an aerobic, thermophilic marine bacterium, originally isolated from the deepest part in the western Pacific Ocean (Mariana Trench) at the depth of 10.897m. Interestingly, the taxonomic status of the genus has not been clarified until now. The genus Thermaerobacter may represent a very deep group within the Firmicutes or potentially a novel phylum. The 2,844,696 bp long genome with its 2,375 protein-coding and 60 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Han_2010_Stand.Genomic.Sci_3_337
PubMedSearch : Han_2010_Stand.Genomic.Sci_3_337
PubMedID: 21304738
Gene_locus related to this paper: them7-e6sh68 , them7-e6shq4 , them7-e6shv1

Title : Complete genome sequence of Acetohalobium arabaticum type strain (Z-7288) - Sikorski_2010_Stand.Genomic.Sci_3_57
Author(s) : Sikorski J , Lapidus A , Chertkov O , Lucas S , Copeland A , Glavina Del Rio T , Nolan M , Tice H , Cheng JF , Han C , Brambilla E , Pitluck S , Liolios K , Ivanova N , Mavromatis K , Mikhailova N , Pati A , Bruce D , Detter C , Tapia R , Goodwin L , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Rohde M , Goker M , Spring S , Woyke T , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP
Ref : Stand Genomic Sci , 3 :57 , 2010
Abstract : Acetohalobium arabaticum Zhilina and Zavarzin 1990 is of special interest because of its physiology and its participation in the anaerobic C(1)-trophic chain in hypersaline environments. This is the first completed genome sequence of the family Halobacteroidaceae and only the second genome sequence in the order Halanaerobiales. The 2,469,596 bp long genome with its 2,353 protein-coding and 90 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Sikorski_2010_Stand.Genomic.Sci_3_57
PubMedSearch : Sikorski_2010_Stand.Genomic.Sci_3_57
PubMedID: 21304692
Gene_locus related to this paper: aceaz-d9qsg6 , aceaz-d9qqr0

Title : Complete genome sequence of Methanothermus fervidus type strain (V24S) - Anderson_2010_Stand.Genomic.Sci_3_315
Author(s) : Anderson I , Djao OD , Misra M , Chertkov O , Nolan M , Lucas S , Lapidus A , Del Rio TG , Tice H , Cheng JF , Tapia R , Han C , Goodwin L , Pitluck S , Liolios K , Ivanova N , Mavromatis K , Mikhailova N , Pati A , Brambilla E , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Sikorski J , Spring S , Rohde M , Eichinger K , Huber H , Wirth R , Goker M , Detter JC , Woyke T , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Klenk HP , Kyrpides NC
Ref : Stand Genomic Sci , 3 :315 , 2010
Abstract : Methanothermus fervidus Stetter 1982 is the type strain of the genus Methanothermus. This hyperthermophilic genus is of a thought to be endemic in Icelandic hot springs. M. fervidus was not only the first characterized organism with a maximal growth temperature (97 degrees C) close to the boiling point of water, but also the first archaeon in which a detailed functional analysis of its histone protein was reported and the first one in which the function of 2,3-cyclodiphosphoglycerate in thermoadaptation was characterized. Strain V24S(T) is of interest because of its very low substrate ranges, it grows only on H(2) + CO(2). This is the first completed genome sequence of the family Methanothermaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1,243,342 bp long genome with its 1,311 protein-coding and 50 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Anderson_2010_Stand.Genomic.Sci_3_315
PubMedSearch : Anderson_2010_Stand.Genomic.Sci_3_315
PubMedID: 21304736

Title : Complete genome sequence of Aminobacterium colombiense type strain (ALA-1) - Chertkov_2010_Stand.Genomic.Sci_2_280
Author(s) : Chertkov O , Sikorski J , Brambilla E , Lapidus A , Copeland A , Glavina Del Rio T , Nolan M , Lucas S , Tice H , Cheng JF , Han C , Detter JC , Bruce D , Tapia R , Goodwin L , Pitluck S , Liolios K , Ivanova N , Mavromatis K , Ovchinnikova G , Pati A , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Spring S , Rohde M , Goker M , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP
Ref : Stand Genomic Sci , 2 :280 , 2010
Abstract : Aminobacterium colombiense Baena et al. 1999 is the type species of the genus Aminobacterium. This genus is of large interest because of its isolated phylogenetic location in the family Synergistaceae, its strictly anaerobic lifestyle, and its ability to grow by fermentation of a limited range of amino acids but not carbohydrates. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the second completed genome sequence of a member of the family Synergistaceae and the first genome sequence of a member of the genus Aminobacterium. The 1,980,592 bp long genome with its 1,914 protein-coding and 56 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Chertkov_2010_Stand.Genomic.Sci_2_280
PubMedSearch : Chertkov_2010_Stand.Genomic.Sci_2_280
PubMedID: 21304712

Title : Complete genome sequence of Spirochaeta smaragdinae type strain (SEBR 4228) - Mavromatis_2010_Stand.Genomic.Sci_3_136
Author(s) : Mavromatis K , Yasawong M , Chertkov O , Lapidus A , Lucas S , Nolan M , Del Rio TG , Tice H , Cheng JF , Pitluck S , Liolios K , Ivanova N , Tapia R , Han C , Bruce D , Goodwin L , Pati A , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Detter JC , Rohde M , Brambilla E , Spring S , Goker M , Sikorski J , Woyke T , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Klenk HP , Kyrpides NC
Ref : Stand Genomic Sci , 3 :136 , 2010
Abstract : Spirochaeta smaragdinae Magot et al. 1998 belongs to the family Spirochaetaceae. The species is Gram-negative, motile, obligately halophilic and strictly anaerobic and is of interest because it is able to ferment numerous polysaccharides. S. smaragdinae is the only species of the family Spirochaetaceae known to reduce thiosulfate or element sulfur to sulfide. This is the first complete genome sequence in the family Spirochaetaceae. The 4,653,970 bp long genome with its 4,363 protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Mavromatis_2010_Stand.Genomic.Sci_3_136
PubMedSearch : Mavromatis_2010_Stand.Genomic.Sci_3_136
PubMedID: 21304743
Gene_locus related to this paper: spiss-e1r584 , spiss-e1rce8

Title : Complete genome sequence of Streptosporangium roseum type strain (NI 9100) - Nolan_2010_Stand.Genomic.Sci_2_29
Author(s) : Nolan M , Sikorski J , Jando M , Lucas S , Lapidus A , Glavina Del Rio T , Chen F , Tice H , Pitluck S , Cheng JF , Chertkov O , Sims D , Meincke L , Brettin T , Han C , Detter JC , Bruce D , Goodwin L , Land M , Hauser L , Chang YJ , Jeffries CD , Ivanova N , Mavromatis K , Mikhailova N , Chen A , Palaniappan K , Chain P , Rohde M , Goker M , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP
Ref : Stand Genomic Sci , 2 :29 , 2010
Abstract : Streptosporangium roseum Crauch 1955 is the type strain of the species which is the type species of the genus Streptosporangium. The 'pinkish coiled Streptomyces-like organism with a spore case' was isolated from vegetable garden soil in 1955. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the family Streptosporangiaceae, and the second largest microbial genome sequence ever deciphered. The 10,369,518 bp long genome with its 9421 protein-coding and 80 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Nolan_2010_Stand.Genomic.Sci_2_29
PubMedSearch : Nolan_2010_Stand.Genomic.Sci_2_29
PubMedID: 21304675
Gene_locus related to this paper: strrd-d2aqk6 , strrd-d2aqt5 , strrd-d2ar22 , strrd-d2ar75 , strrd-d2arp5 , strrd-d2auf6 , strrd-d2aw37 , strrd-d2awh0 , strrd-d2awp2 , strrd-d2axt7 , strrd-d2ayh4 , strrd-d2ayq3 , strrd-d2ayx8 , strrd-d2az98 , strrd-d2b0g2 , strrd-d2b0t3 , strrd-d2b0u2 , strrd-d2b0u6 , strrd-d2b0w5 , strrd-d2b2m3 , strrd-d2b2r7 , strrd-d2b3g9 , strrd-d2b3i2 , strrd-d2b3i7 , strrd-d2b4f5 , strrd-d2b4y4 , strrd-d2b4z9 , strrd-d2b5z6 , strrd-d2b6v8 , strrd-d2b6y3 , strrd-d2b7a9 , strrd-d2b7h6 , strrd-d2b9k5 , strrd-d2b9n9 , strrd-d2b152 , strrd-d2b235 , strrd-d2b519 , strrd-d2b540 , strrd-d2b638 , strrd-d2b812 , strrd-d2ba59 , strrd-d2bae6 , strrd-d2bai2 , strrd-d2bbp7 , strrd-d2bc04 , strrd-d2bc32 , strrd-d2bc93 , strrd-d2bd97 , strrd-d2bdh0 , strrd-d2bdh1 , strrd-d2bdl4 , strrd-d2bdq5 , strrd-d2bdt5 , strrd-d2bdv3 , strrd-d2be60 , strrd-d2be88 , strrd-d2bf33 , strrd-d2bf77 , strrd-d2b7c2 , strrd-d2awc2 , strrd-d2as88 , strrd-d2aw56 , strrd-d2b3r3 , strrd-d2bf75 , strrd-d2b2d4 , strrd-d2b1i6

Title : Complete genome sequence of Xylanimonas cellulosilytica type strain (XIL07) - Foster_2010_Stand.Genomic.Sci_2_1
Author(s) : Foster B , Pukall R , Abt B , Nolan M , Glavina Del Rio T , Chen F , Lucas S , Tice H , Pitluck S , Cheng JF , Chertkov O , Brettin T , Han C , Detter JC , Bruce D , Goodwin L , Ivanova N , Mavromatis K , Pati A , Mikhailova N , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Chain P , Rohde M , Goker M , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP , Lapidus A
Ref : Stand Genomic Sci , 2 :1 , 2010
Abstract : Xylanimonas cellulosilytica Rivas et al. 2003 is the type species of the genus Xylanimonas of the actinobacterial family Promicromonosporaceae. The species X. cellulosilytica is of interest because of its ability to hydrolyze cellulose and xylan. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the large family Promicromonosporaceae, and the 3,831,380 bp long genome (one chromosome plus an 88,604 bp long plasmid) with its 3485 protein-coding and 61 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Foster_2010_Stand.Genomic.Sci_2_1
PubMedSearch : Foster_2010_Stand.Genomic.Sci_2_1
PubMedID: 21304672

Title : Complete genome sequence of Meiothermus ruber type strain (21) - Tindall_2010_Stand.Genomic.Sci_3_26
Author(s) : Tindall BJ , Sikorski J , Lucas S , Goltsman E , Copeland A , Glavina Del Rio T , Nolan M , Tice H , Cheng JF , Han C , Pitluck S , Liolios K , Ivanova N , Mavromatis K , Ovchinnikova G , Pati A , Fahnrich R , Goodwin L , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Rohde M , Goker M , Woyke T , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP , Lapidus A
Ref : Stand Genomic Sci , 3 :26 , 2010
Abstract : Meiothermus ruber (Loginova et al. 1984) Nobre et al. 1996 is the type species of the genus Meiothermus. This thermophilic genus is of special interest, as its members share relatively low degrees of 16S rRNA gene sequence similarity and constitute a separate evolutionary lineage from members of the genus Thermus, from which they can generally be distinguished by their slightly lower temperature optima. The temperature related split is in accordance with the chemotaxonomic feature of the polar lipids. M. ruber is a representative of the low-temperature group. This is the first completed genome sequence of the genus Meiothermus and only the third genome sequence to be published from a member of the family Thermaceae. The 3,097,457 bp long genome with its 3,052 protein-coding and 53 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Tindall_2010_Stand.Genomic.Sci_3_26
PubMedSearch : Tindall_2010_Stand.Genomic.Sci_3_26
PubMedID: 21304689
Gene_locus related to this paper: meird-d3pkm5 , meird-d3pnp5 , meird-d3pnr1 , meird-d3pnw2 , meird-d3pq15 , meird-d3pqm5 , meird-d3ps60

Title : Complete genome sequence of Ignisphaera aggregans type strain (AQ1.S1) - Goker_2010_Stand.Genomic.Sci_3_66
Author(s) : Goker M , Held B , Lapidus A , Nolan M , Spring S , Yasawong M , Lucas S , Glavina Del Rio T , Tice H , Cheng JF , Goodwin L , Tapia R , Pitluck S , Liolios K , Ivanova N , Mavromatis K , Mikhailova N , Pati A , Chen A , Palaniappan K , Brambilla E , Land M , Hauser L , Chang YJ , Jeffries CD , Brettin T , Detter JC , Han C , Rohde M , Sikorski J , Woyke T , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP
Ref : Stand Genomic Sci , 3 :66 , 2010
Abstract : Ignisphaera aggregans Niederberger et al. 2006 is the type and sole species of genus Ignisphaera. This archaeal species is characterized by a coccoid-shape and is strictly anaerobic, moderately acidophilic, heterotrophic hyperthermophilic and fermentative. The type strain AQ1.S1(T) was isolated from a near neutral, boiling spring in Kuirau Park, Rotorua, New Zealand. This is the first completed genome sequence of the genus Ignisphaera and the fifth genome (fourth type strain) sequence in the family Desulfurococcaceae. The 1,875,953 bp long genome with its 2,009 protein-coding and 52 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Goker_2010_Stand.Genomic.Sci_3_66
PubMedSearch : Goker_2010_Stand.Genomic.Sci_3_66
PubMedID: 21304693

Title : Complete genome sequence of Meiothermus silvanus type strain (VI-R2) - Sikorski_2010_Stand.Genomic.Sci_3_37
Author(s) : Sikorski J , Tindall BJ , Lowry S , Lucas S , Nolan M , Copeland A , Glavina Del Rio T , Tice H , Cheng JF , Han C , Pitluck S , Liolios K , Ivanova N , Mavromatis K , Mikhailova N , Pati A , Goodwin L , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Rohde M , Goker M , Woyke T , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP , Lapidus A
Ref : Stand Genomic Sci , 3 :37 , 2010
Abstract : Meiothermus silvanus (Tenreiro et al. 1995) Nobre et al. 1996 belongs to a thermophilic genus whose members share relatively low degrees of 16S rRNA gene sequence similarity. Meiothermus constitutes an evolutionary lineage separate from members of the genus Thermus, from which they can generally be distinguished by their slightly lower temperature optima. M. silvanus is of special interest as it causes colored biofilms in the paper making industry and may thus be of economic importance as a biofouler. This is the second completed genome sequence of a member of the genus Meiothermus and only the third genome sequence to be published from a member of the family Thermaceae. The 3,721,669 bp long genome with its 3,667 protein-coding and 55 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Sikorski_2010_Stand.Genomic.Sci_3_37
PubMedSearch : Sikorski_2010_Stand.Genomic.Sci_3_37
PubMedID: 21304690
Gene_locus related to this paper: meisd-d7bbz4 , meisd-d7bbu2 , meisd-d7bjh0 , meisd-d7bez6 , meisd-d7bfp6

Title : Complete genome sequence of Alicyclobacillus acidocaldarius type strain (104-IA) - Mavromatis_2010_Stand.Genomic.Sci_2_9
Author(s) : Mavromatis K , Sikorski J , Lapidus A , Glavina Del Rio T , Copeland A , Tice H , Cheng JF , Lucas S , Chen F , Nolan M , Bruce D , Goodwin L , Pitluck S , Ivanova N , Ovchinnikova G , Pati A , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Chain P , Meincke L , Sims D , Chertkov O , Han C , Brettin T , Detter JC , Wahrenburg C , Rohde M , Pukall R , Goker M , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Klenk HP , Kyrpides NC
Ref : Stand Genomic Sci , 2 :9 , 2010
Abstract : Alicyclobacillus acidocaldarius (Darland and Brock 1971) is the type species of the larger of the two genera in the bacillal family 'Alicyclobacillaceae'. A. acidocaldarius is a free-living and non-pathogenic organism, but may also be associated with food and fruit spoilage. Due to its acidophilic nature, several enzymes from this species have since long been subjected to detailed molecular and biochemical studies. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the family 'Alicyclobacillaceae'. The 3,205,686 bp long genome (chromosome and three plasmids) with its 3,153 protein-coding and 82 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Mavromatis_2010_Stand.Genomic.Sci_2_9
PubMedSearch : Mavromatis_2010_Stand.Genomic.Sci_2_9
PubMedID: 21304673

Title : Complete genome sequence of Sphaerobacter thermophilus type strain (S 6022) - Pati_2010_Stand.Genomic.Sci_2_49
Author(s) : Pati A , LaButti K , Pukall R , Nolan M , Glavina Del Rio T , Tice H , Cheng JF , Lucas S , Chen F , Copeland A , Ivanova N , Mavromatis K , Mikhailova N , Pitluck S , Bruce D , Goodwin L , Land M , Hauser L , Chang YJ , Jeffries CD , Chen A , Palaniappan K , Chain P , Brettin T , Sikorski J , Rohde M , Goker M , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP , Lapidus A
Ref : Stand Genomic Sci , 2 :49 , 2010
Abstract : Sphaerobacter thermophilus Demharter et al. 1989 is the sole and type species of the genus Sphaerobacter, which is the type genus of the family Sphaerobacteraceae, the order Sphaerobacterales and the subclass Sphaerobacteridae. Phylogenetically, it belongs to the genomically little studied class of the Thermomicrobia in the bacterial phylum Chloroflexi. Here, the genome of strain S 6022(T) is described which is an obligate aerobe that was originally isolated from an aerated laboratory-scale fermentor that was pulse fed with municipal sewage sludge. We describe the features of this organism, together with the complete genome and annotation. This is the first complete genome sequence of the thermomicrobial subclass Sphaerobacteridae, and the second sequence from the chloroflexal class Thermomicrobia. The 3,993,764 bp genome with its 3,525 protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Pati_2010_Stand.Genomic.Sci_2_49
PubMedSearch : Pati_2010_Stand.Genomic.Sci_2_49
PubMedID: 21304677

Title : Complete genome sequence of 'Thermobaculum terrenum' type strain (YNP1) - Kiss_2010_Stand.Genomic.Sci_3_153
Author(s) : Kiss H , Cleland D , Lapidus A , Lucas S , Del Rio TG , Nolan M , Tice H , Han C , Goodwin L , Pitluck S , Liolios K , Ivanova N , Mavromatis K , Ovchinnikova G , Pati A , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Lu M , Brettin T , Detter JC , Goker M , Tindall BJ , Beck B , McDermott TR , Woyke T , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP , Cheng JF
Ref : Stand Genomic Sci , 3 :153 , 2010
Abstract : 'Thermobaculum terrenum' Botero et al. 2004 is the sole species within the proposed genus 'Thermobaculum'. Strain YNP1(T) is the only cultivated member of an acid tolerant, extremely thermophilic species belonging to a phylogenetically isolated environmental clone group within the phylum Chloroflexi. At present, the name 'Thermobaculum terrenum' is not yet validly published as it contravenes Rule 30 (3a) of the Bacteriological Code. The bacterium was isolated from a slightly acidic extreme thermal soil in Yellowstone National Park, Wyoming (USA). Depending on its final taxonomic allocation, this is likely to be the third completed genome sequence of a member of the class Thermomicrobia and the seventh type strain genome from the phylum Chloroflexi. The 3,101,581 bp long genome with its 2,872 protein-coding and 58 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Kiss_2010_Stand.Genomic.Sci_3_153
PubMedSearch : Kiss_2010_Stand.Genomic.Sci_3_153
PubMedID: 21304745
Gene_locus related to this paper: thet1-d1cbe2 , thet1-d1cbh1 , thet1-d1cbh5 , thet1-d1cdw7 , thet1-d1cej0 , thet1-d1cfr4 , thet1-d1chv7 , thet1-d1cih9

Title : Complete genome sequence of Ilyobacter polytropus type strain (CuHbu1) - Sikorski_2010_Stand.Genomic.Sci_3_304
Author(s) : Sikorski J , Chertkov O , Lapidus A , Nolan M , Lucas S , Del Rio TG , Tice H , Cheng JF , Tapia R , Han C , Goodwin L , Pitluck S , Liolios K , Ivanova N , Mavromatis K , Mikhailova N , Pati A , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Brambilla E , Yasawong M , Rohde M , Pukall R , Spring S , Goker M , Woyke T , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP
Ref : Stand Genomic Sci , 3 :304 , 2010
Abstract : Ilyobacter polytropus Stieb and Schink 1984 is the type species of the genus Ilyobacter, which belongs to the fusobacterial family Fusobacteriaceae. The species is of interest because its members are able to ferment quite a number of sugars and organic acids. I. polytropus has a broad versatility in using various fermentation pathways. Also, its members do not degrade poly-beta-hydroxybutyrate but only the monomeric 3-hydroxybutyrate. This is the first completed genome sequence of a member of the genus Ilyobacter and the second sequence from the family Fusobacteriaceae. The 3,132,314 bp long genome with its 2,934 protein-coding and 108 RNA genes consists of two chromosomes (2 and 1 Mbp long) and one plasmid, and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Sikorski_2010_Stand.Genomic.Sci_3_304
PubMedSearch : Sikorski_2010_Stand.Genomic.Sci_3_304
PubMedID: 21304735

Title : Complete genome sequence of Archaeoglobus profundus type strain (AV18) - von Jan_2010_Stand.Genomic.Sci_2_327
Author(s) : von Jan M , Lapidus A , Del Rio TG , Copeland A , Tice H , Cheng JF , Lucas S , Chen F , Nolan M , Goodwin L , Han C , Pitluck S , Liolios K , Ivanova N , Mavromatis K , Ovchinnikova G , Chertkov O , Pati A , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Saunders E , Brettin T , Detter JC , Chain P , Eichinger K , Huber H , Spring S , Rohde M , Goker M , Wirth R , Woyke T , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP
Ref : Stand Genomic Sci , 2 :327 , 2010
Abstract : Archaeoglobus profundus (Burggraf et al. 1990) is a hyperthermophilic archaeon in the euryarchaeal class Archaeoglobi, which is currently represented by the single family Archaeoglobaceae, containing six validly named species and two strains ascribed to the genus 'Geoglobus' which is taxonomically challenged as the corresponding type species has no validly published name. All members were isolated from marine hydrothermal habitats and are obligate anaerobes. Here we describe the features of the organism, together with the complete genome sequence and annotation. This is the second completed genome sequence of a member of the class Archaeoglobi. The 1,563,423 bp genome with its 1,858 protein-coding and 52 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : von Jan_2010_Stand.Genomic.Sci_2_327
PubMedSearch : von Jan_2010_Stand.Genomic.Sci_2_327
PubMedID: 21304717

Title : Complete genome sequence of Arcobacter nitrofigilis type strain (CI) - Pati_2010_Stand.Genomic.Sci_2_300
Author(s) : Pati A , Gronow S , Lapidus A , Copeland A , Glavina Del Rio T , Nolan M , Lucas S , Tice H , Cheng JF , Han C , Chertkov O , Bruce D , Tapia R , Goodwin L , Pitluck S , Liolios K , Ivanova N , Mavromatis K , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Detter JC , Rohde M , Goker M , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Klenk HP , Kyrpides NC
Ref : Stand Genomic Sci , 2 :300 , 2010
Abstract : Arcobacter nitrofigilis (McClung et al. 1983) Vandamme et al. 1991 is the type species of the genus Arcobacter in the family Campylobacteraceae within the Epsilonproteobacteria. The species was first described in 1983 as Campylobacter nitrofigilis [1] after its detection as a free-living, nitrogen-fixing Campylobacter species associated with Spartina alterniflora Loisel roots [2]. It is of phylogenetic interest because of its lifestyle as a symbiotic organism in a marine environment in contrast to many other Arcobacter species which are associated with warm-blooded animals and tend to be pathogenic. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a type stain of the genus Arcobacter. The 3,192,235 bp genome with its 3,154 protein-coding and 70 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Pati_2010_Stand.Genomic.Sci_2_300
PubMedSearch : Pati_2010_Stand.Genomic.Sci_2_300
PubMedID: 21304714
Gene_locus related to this paper: arcnc-d5v0e6 , arcnc-d5v643

Title : Complete genome sequence of Brachyspira murdochii type strain (56-150) - Pati_2010_Stand.Genomic.Sci_2_260
Author(s) : Pati A , Sikorski J , Gronow S , Munk C , Lapidus A , Copeland A , Glavina Del Tio T , Nolan M , Lucas S , Chen F , Tice H , Cheng JF , Han C , Detter JC , Bruce D , Tapia R , Goodwin L , Pitluck S , Liolios K , Ivanova N , Mavromatis K , Mikhailova N , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Spring S , Rohde M , Goker M , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP
Ref : Stand Genomic Sci , 2 :260 , 2010
Abstract : Brachyspira murdochii Stanton et al. 1992 is a non-pathogenic, host-associated spirochete of the family Brachyspiraceae. Initially isolated from the intestinal content of a healthy swine, the 'group B spirochaetes' were first described as Serpulina murdochii. Members of the family Brachyspiraceae are of great phylogenetic interest because of the extremely isolated location of this family within the phylum 'Spirochaetes'. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a type strain of a member of the family Brachyspiraceae and only the second genome sequence from a member of the genus Brachyspira. The 3,241,804 bp long genome with its 2,893 protein-coding and 40 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Pati_2010_Stand.Genomic.Sci_2_260
PubMedSearch : Pati_2010_Stand.Genomic.Sci_2_260
PubMedID: 21304710
Gene_locus related to this paper: bram5-d5u3y5 , bram5-d5u7a7 , bram5-d5u9f8 , bram5-d5ua75 , bram5-d5u886

Title : Permanent draft genome sequence of Dethiosulfovibrio peptidovorans type strain (SEBR 4207) - Labutti_2010_Stand.Genomic.Sci_3_85
Author(s) : LaButti K , Mayilraj S , Clum A , Lucas S , Glavina Del Rio T , Nolan M , Tice H , Cheng JF , Pitluck S , Liolios K , Ivanova N , Mavromatis K , Mikhailova N , Pati A , Goodwin L , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Rohde M , Spring S , Goker M , Woyke T , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP , Lapidus A
Ref : Stand Genomic Sci , 3 :85 , 2010
Abstract : Dethiosulfovibrio peptidovorans Magot et al. 1997 is the type species of the genus Dethiosulfovibrio of the family Synergistaceae in the recently created phylum Synergistetes. The strictly anaerobic, vibriod, thiosulfate-reducing bacterium utilizes peptides and amino acids, but neither sugars nor fatty acids. It was isolated from an offshore oil well where it was been reported to be involved in pitting corrosion of mild steel. Initially, this bacterium was described as a distant relative of the genus Thermoanaerobacter, but was not assigned to a genus, it was subsequently placed into the novel phylum Synergistetes. A large number of repeats in the genome sequence prevented an economically justifiable closure of the last gaps. This is only the third published genome from a member of the phylum Synergistetes. The 2,576,359 bp long genome consists of three contigs with 2,458 protein-coding and 59 RNA genes and is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Labutti_2010_Stand.Genomic.Sci_3_85
PubMedSearch : Labutti_2010_Stand.Genomic.Sci_3_85
PubMedID: 21304695

Title : Complete genome sequence of Desulfohalobium retbaense type strain (HR(100)) - Spring_2010_Stand.Genomic.Sci_2_38
Author(s) : Spring S , Nolan M , Lapidus A , Glavina Del Rio T , Copeland A , Tice H , Cheng JF , Lucas S , Land M , Chen F , Bruce D , Goodwin L , Pitluck S , Ivanova N , Mavromatis K , Mikhailova N , Pati A , Chen A , Palaniappan K , Hauser L , Chang YJ , Jeffries CD , Munk C , Kiss H , Chain P , Han C , Brettin T , Detter JC , Schuler E , Goker M , Rohde M , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP
Ref : Stand Genomic Sci , 2 :38 , 2010
Abstract : Desulfohalobium retbaense (Ollivier et al. 1991) is the type species of the polyphyletic genus Desulfohalobium, which comprises, at the time of writing, two species and represents the family Desulfohalobiaceae within the Deltaproteobacteria. D. retbaense is a moderately halophilic sulfate-reducing bacterium, which can utilize H(2) and a limited range of organic substrates, which are incompletely oxidized to acetate and CO(2), for growth. The type strain HR(100) (T) was isolated from sediments of the hypersaline Retba Lake in Senegal. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the family Desulfohalobiaceae. The 2,909,567 bp genome (one chromosome and a 45,263 bp plasmid) with its 2,552 protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Spring_2010_Stand.Genomic.Sci_2_38
PubMedSearch : Spring_2010_Stand.Genomic.Sci_2_38
PubMedID: 21304676
Gene_locus related to this paper: sphtd-d1c5v2

Title : Complete genome sequence of Segniliparus rotundus type strain (CDC 1076) - Sikorski_2010_Stand.Genomic.Sci_2_203
Author(s) : Sikorski J , Lapidus A , Copeland A , Misra M , Glavina Del Rio T , Nolan M , Lucas S , Chen F , Tice H , Cheng JF , Jando M , Schneider S , Bruce D , Goodwin L , Pitluck S , Liolios K , Mikhailova N , Pati A , Ivanova N , Mavromatis K , Chen A , Palaniappan K , Chertkov O , Land M , Hauser L , Chang YJ , Jeffries CD , Brettin T , Detter JC , Han C , Rohde M , Goker M , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP
Ref : Stand Genomic Sci , 2 :203 , 2010
Abstract : Segniliparus rotundus Butler 2005 is the type species of the genus Segniliparus, which is currently the only genus in the corynebacterial family Segniliparaceae. This family is of large interest because of a novel late-emerging genus-specific mycolate pattern. The type strain has been isolated from human sputum and is probably an opportunistic pathogen. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the family Segniliparaceae. The 3,157,527 bp long genome with its 3,081 protein-coding and 52 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Sikorski_2010_Stand.Genomic.Sci_2_203
PubMedSearch : Sikorski_2010_Stand.Genomic.Sci_2_203
PubMedID: 21304703
Gene_locus related to this paper: segrd-d6z8m1 , segrd-d6z8p5 , segrd-d6z9l9 , segrd-d6za06 , segrd-d6zaa6 , segrd-d6zav0 , segrd-d6zbl4 , segrd-d6zbs4 , segrd-d6zc43 , segrd-d6zca1 , segrd-d6zcn6 , segrd-d6zdf7 , segrd-d6zds6 , segrd-d6zdt4 , segrd-d6zdz3 , segrd-d6zed7 , segrd-d6zej1 , segrd-d6zfg4 , segrd-d6zfr6 , segrd-d6za90 , segrd-d6za91 , segrd-d6zd15 , segrd-d6zcg9 , segrd-d6zb77

Title : Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034) - Glavina_2010_Stand.Genomic.Sci_2_87
Author(s) : Glavina Del Rio T , Abt B , Spring S , Lapidus A , Nolan M , Tice H , Copeland A , Cheng JF , Chen F , Bruce D , Goodwin L , Pitluck S , Ivanova N , Mavromatis K , Mikhailova N , Pati A , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Chain P , Saunders E , Detter JC , Brettin T , Rohde M , Goker M , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP , Lucas S
Ref : Stand Genomic Sci , 2 :87 , 2010
Abstract : Chitinophaga pinensis Sangkhobol and Skerman 1981 is the type strain of the species which is the type species of the rapidly growing genus Chitinophaga in the sphingobacterial family 'Chitinophagaceae'. Members of the genus Chitinophaga vary in shape between filaments and spherical bodies without the production of a fruiting body, produce myxospores, and are of special interest for their ability to degrade chitin. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the family 'Chitinophagaceae', and the 9,127,347 bp long single replicon genome with its 7,397 protein-coding and 95 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Glavina_2010_Stand.Genomic.Sci_2_87
PubMedSearch : Glavina_2010_Stand.Genomic.Sci_2_87
PubMedID: 21304681
Gene_locus related to this paper: chipd-c7pkc8

Title : Complete genome sequence of Sebaldella termitidis type strain (NCTC 11300) - Harmon-Smith_2010_Stand.Genomic.Sci_2_220
Author(s) : Harmon-Smith M , Celia L , Chertkov O , Lapidus A , Copeland A , Glavina Del Rio T , Nolan M , Lucas S , Tice H , Cheng JF , Han C , Detter JC , Bruce D , Goodwin L , Pitluck S , Pati A , Liolios K , Ivanova N , Mavromatis K , Mikhailova N , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Brettin T , Goker M , Beck B , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP , Chen F
Ref : Stand Genomic Sci , 2 :220 , 2010
Abstract : Sebaldella termitidis (Sebald 1962) Collins and Shah 1986, is the only species in the genus Sebaldella within the fusobacterial family 'Leptotrichiaceae'. The sole and type strain of the species was first isolated about 50 years ago from intestinal content of Mediterranean termites. The species is of interest for its very isolated phylogenetic position within the phylum Fusobacteria in the tree of life, with no other species sharing more than 90% 16S rRNA sequence similarity. The 4,486,650 bp long genome with its 4,210 protein-coding and 54 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Harmon-Smith_2010_Stand.Genomic.Sci_2_220
PubMedSearch : Harmon-Smith_2010_Stand.Genomic.Sci_2_220
PubMedID: 21304705
Gene_locus related to this paper: sebte-d1am65

Title : Complete genome sequence of Denitrovibrio acetiphilus type strain (N2460) - Kiss_2010_Stand.Genomic.Sci_2_270
Author(s) : Kiss H , Lang E , Lapidus A , Copeland A , Nolan M , Glavina Del Rio T , Chen F , Lucas S , Tice H , Cheng JF , Han C , Goodwin L , Pitluck S , Liolios K , Pati A , Ivanova N , Mavromatis K , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Detter JC , Brettin T , Spring S , Rohde M , Goker M , Woyke T , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP
Ref : Stand Genomic Sci , 2 :270 , 2010
Abstract : Denitrovibrio acetiphilus Myhr and Torsvik 2000 is the type species of the genus Denitrovibrio in the bacterial family Deferribacteraceae. It is of phylogenetic interest because there are only six genera described in the family Deferribacteraceae. D. acetiphilus was isolated as a representative of a population reducing nitrate to ammonia in a laboratory column simulating the conditions in off-shore oil recovery fields. When nitrate was added to this column undesirable hydrogen sulfide production was stopped because the sulfate reducing populations were superseded by these nitrate reducing bacteria. Here we describe the features of this marine, mesophilic, obligately anaerobic organism respiring by nitrate reduction, together with the complete genome sequence, and annotation. This is the second complete genome sequence of the order Deferribacterales and the class Deferribacteres, which is the sole class in the phylum Deferribacteres. The 3,222,077 bp genome with its 3,034 protein-coding and 51 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Kiss_2010_Stand.Genomic.Sci_2_270
PubMedSearch : Kiss_2010_Stand.Genomic.Sci_2_270
PubMedID: 21304711
Gene_locus related to this paper: dena2-d4h2g2 , dena2-d4h260

Title : Complete genome sequence of Thermocrinis albus type strain (HI 11\/12) - Wirth_2010_Stand.Genomic.Sci_2_194
Author(s) : Wirth R , Sikorski J , Brambilla E , Misra M , Lapidus A , Copeland A , Nolan M , Lucas S , Chen F , Tice H , Cheng JF , Han C , Detter JC , Tapia R , Bruce D , Goodwin L , Pitluck S , Pati A , Anderson I , Ivanova N , Mavromatis K , Mikhailova N , Chen A , Palaniappan K , Bilek Y , Hader T , Land M , Hauser L , Chang YJ , Jeffries CD , Tindall BJ , Rohde M , Goker M , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP
Ref : Stand Genomic Sci , 2 :194 , 2010
Abstract : Thermocrinis albus Eder and Huber 2002 is one of three species in the genus Thermocrinis in the family Aquificaceae. Members of this family have become of significant interest because of their involvement in global biogeochemical cycles in high-temperature ecosystems. This interest had already spurred several genome sequencing projects for members of the family. We here report the first completed genome sequence a member of the genus Thermocrinis and the first type strain genome from a member of the family Aquificaceae. The 1,500,577 bp long genome with its 1,603 protein-coding and 47 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Wirth_2010_Stand.Genomic.Sci_2_194
PubMedSearch : Wirth_2010_Stand.Genomic.Sci_2_194
PubMedID: 21304702
Gene_locus related to this paper: theah-d3smz6

Title : Complete genome sequence of Thermosphaera aggregans type strain (M11TL) - Spring_2010_Stand.Genomic.Sci_2_245
Author(s) : Spring S , Rachel R , Lapidus A , Davenport K , Tice H , Copeland A , Cheng JF , Lucas S , Chen F , Nolan M , Bruce D , Goodwin L , Pitluck S , Ivanova N , Mavromatis K , Ovchinnikova G , Pati A , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CC , Brettin T , Detter JC , Tapia R , Han C , Heimerl T , Weikl F , Brambilla E , Goker M , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP
Ref : Stand Genomic Sci , 2 :245 , 2010
Abstract : Thermosphaera aggregans Huber et al. 1998 is the type species of the genus Thermosphaera, which comprises at the time of writing only one species. This species represents archaea with a hyperthermophilic, heterotrophic, strictly anaerobic and fermentative phenotype. The type strain M11TL(T) was isolated from a water-sediment sample of a hot terrestrial spring (Obsidian Pool, Yellowstone National Park, Wyoming). Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1,316,595 bp long single replicon genome with its 1,410 protein-coding and 47 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Spring_2010_Stand.Genomic.Sci_2_245
PubMedSearch : Spring_2010_Stand.Genomic.Sci_2_245
PubMedID: 21304709
Gene_locus related to this paper: theam-d5u0z4

Title : Complete genome sequence of Kytococcus sedentarius type strain (541) - Sims_2009_Stand.Genomic.Sci_1_12
Author(s) : Sims D , Brettin T , Detter JC , Han C , Lapidus A , Copeland A , Glavina Del Rio T , Nolan M , Chen F , Lucas S , Tice H , Cheng JF , Bruce D , Goodwin L , Pitluck S , Ovchinnikova G , Pati A , Ivanova N , Mavrommatis K , Chen A , Palaniappan K , D'Haeseleer P , Chain P , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Schneider S , Goker M , Pukall R , Kyrpides NC , Klenk HP
Ref : Stand Genomic Sci , 1 :12 , 2009
Abstract : Kytococcus sedentarius (ZoBell and Upham 1944) Stackebrandt et al. 1995 is the type strain of the species, and is of phylogenetic interest because of its location in the Dermacoccaceae, a poorly studied family within the actinobacterial suborder Micrococcineae. Kytococcus sedentarius is known for the production of oligoketide antibiotics as well as for its role as an opportunistic pathogen causing valve endocarditis, hemorrhagic pneumonia, and pitted keratolysis. It is strictly aerobic and can only grow when several amino acids are provided in the medium. The strain described in this report is a free-living, nonmotile, Gram-positive bacterium, originally isolated from a marine environment. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the family Dermacoccaceae and the 2,785,024 bp long single replicon genome with its 2639 protein-coding and 64 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Sims_2009_Stand.Genomic.Sci_1_12
PubMedSearch : Sims_2009_Stand.Genomic.Sci_1_12
PubMedID: 21304632
Gene_locus related to this paper: kytsd-c7nfq8 , kytsd-c7nib9 , kytsd-c7niy9 , kytsd-c7nl26 , kytsd-c7nj46 , kytsd-c7nig1

Title : Complete genome sequence of Desulfotomaculum acetoxidans type strain (5575) - Spring_2009_Stand.Genomic.Sci_1_242
Author(s) : Spring S , Lapidus A , Schroder M , Gleim D , Sims D , Meincke L , Glavina Del Rio T , Tice H , Copeland A , Cheng JF , Lucas S , Chen F , Nolan M , Bruce D , Goodwin L , Pitluck S , Ivanova N , Mavromatis K , Mikhailova N , Pati A , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Chain P , Saunders E , Brettin T , Detter JC , Goker M , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP , Han C
Ref : Stand Genomic Sci , 1 :242 , 2009
Abstract : Desulfotomaculum acetoxidans Widdel and Pfennig 1977 was one of the first sulfate-reducing bacteria known to grow with acetate as sole energy and carbon source. It is able to oxidize substrates completely to carbon dioxide with sulfate as the electron acceptor, which is reduced to hydrogen sulfide. All available data about this species are based on strain 5575(T), isolated from piggery waste in Germany. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a Desulfotomaculum species with validly published name. The 4,545,624 bp long single replicon genome with its 4370 protein-coding and 100 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Spring_2009_Stand.Genomic.Sci_1_242
PubMedSearch : Spring_2009_Stand.Genomic.Sci_1_242
PubMedID: 21304664
Gene_locus related to this paper: desas-c8vw82 , desas-c8vxd2

Title : Complete genome sequence of Desulfomicrobium baculatum type strain (X) - Copeland_2009_Stand.Genomic.Sci_1_29
Author(s) : Copeland A , Spring S , Goker M , Schneider S , Lapidus A , Del Rio TG , Tice H , Cheng JF , Chen F , Nolan M , Bruce D , Goodwin L , Pitluck S , Ivanova N , Mavrommatis K , Ovchinnikova G , Pati A , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CC , Meincke L , Sims D , Brettin T , Detter JC , Han C , Chain P , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP , Lucas S
Ref : Stand Genomic Sci , 1 :29 , 2009
Abstract : Desulfomicrobium baculatum is the type species of the genus Desulfomicrobium, which is the type genus of the family Desulfomicrobiaceae. It is of phylogenetic interest because of the isolated location of the family Desulfomicrobiaceae within the order Desulfovibrionales. D. baculatum strain X(T) is a Gram-negative, motile, sulfate-reducing bacterium isolated from water-saturated manganese carbonate ore. It is strictly anaerobic and does not require NaCl for growth, although NaCl concentrations up to 6% (w/v) are tolerated. The metabolism is respiratory or fermentative. In the presence of sulfate, pyruvate and lactate are incompletely oxidized to acetate and CO(2). Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the deltaproteobacterial family Desulfomicrobiaceae, and this 3,942,657 bp long single replicon genome with its 3494 protein-coding and 72 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Copeland_2009_Stand.Genomic.Sci_1_29
PubMedSearch : Copeland_2009_Stand.Genomic.Sci_1_29
PubMedID: 21304634
Gene_locus related to this paper: desbd-c7ln23 , desbd-c7lrc0 , desbd-c7lw38 , desbd-c7ls17

Title : Complete genome sequence of Halomicrobium mukohataei type strain (arg-2) - Tindall_2009_Stand.Genomic.Sci_1_270
Author(s) : Tindall BJ , Schneider S , Lapidus A , Copeland A , Glavina Del Rio T , Nolan M , Lucas S , Chen F , Tice H , Cheng JF , Saunders E , Bruce D , Goodwin L , Pitluck S , Mikhailova N , Pati A , Ivanova N , Mavrommatis K , Chen A , Palaniappan K , Chain P , Land M , Hauser L , Chang YJ , Jeffries CD , Brettin T , Han C , Rohde M , Goker M , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Klenk HP , Kyrpides NC , Detter JC
Ref : Stand Genomic Sci , 1 :270 , 2009
Abstract : Halomicrobium mukohataei (Ihara et al. 1997) Oren et al. 2002 is the type species of the genus Halomicrobium. It is of phylogenetic interest because of its isolated location within the large euryarchaeal family Halobacteriaceae. H. mukohataei is an extreme halophile that grows essentially aerobically, but can also grow anaerobically under a change of morphology and with nitrate as electron acceptor. The strain, whose genome is described in this report, is a free-living, motile, Gram-negative euryarchaeon, originally isolated from Salinas Grandes in Jujuy, Andes highlands, Argentina. Its genome contains three genes for the 16S rRNA that differ from each other by up to 9%. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence from the poorly populated genus Halomicrobium, and the 3,332,349 bp long genome (chromosome and one plasmid) with its 3416 protein-coding and 56 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Tindall_2009_Stand.Genomic.Sci_1_270
PubMedSearch : Tindall_2009_Stand.Genomic.Sci_1_270
PubMedID: 21304667
Gene_locus related to this paper: halmd-c7nwe5 , halmd-c7nwh2 , halmd-c7p0c0 , halmd-c7p2d1 , halmd-c7p3m9

Title : Complete genome sequence of Pirellula staleyi type strain (ATCC 27377) - Clum_2009_Stand.Genomic.Sci_1_308
Author(s) : Clum A , Tindall BJ , Sikorski J , Ivanova N , Mavrommatis K , Lucas S , Glavina T , Del R , Nolan M , Chen F , Tice H , Pitluck S , Cheng JF , Chertkov O , Brettin T , Han C , Detter JC , Kuske C , Bruce D , Goodwin L , Ovchinikova G , Pati A , Mikhailova N , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Chain P , Rohde M , Goker M , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP , Lapidus A
Ref : Stand Genomic Sci , 1 :308 , 2009
Abstract : Pirellula staleyi Schlesner and Hirsch 1987 is the type species of the genus Pirellula of the family Planctomycetaceae. Members of this pear- or teardrop-shaped bacterium show a clearly visible pointed attachment pole and can be distinguished from other Planctomycetes by a lack of true stalks. Strains closely related to the species have been isolated from fresh and brackish water, as well as from hypersaline lakes. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the order Planctomyces and only the second sequence from the phylum Planctobacteria/Planctomycetes. The 6,196,199 bp long genome with its 4773 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Clum_2009_Stand.Genomic.Sci_1_308
PubMedSearch : Clum_2009_Stand.Genomic.Sci_1_308
PubMedID: 21304671
Gene_locus related to this paper: pirsd-d2qwf7 , pirsd-d2qya4 , pirsd-d2qyh4 , pirsd-d2qyx7 , pirsd-d2r0n7 , pirsd-d2r1w6 , pirsd-d2r2c5 , pirsd-d2r2f7 , pirsd-d2r3w0 , pirsd-d2r4c3 , pirsd-d2r5t1 , pirsd-d2r9d5 , pirsd-d2r496 , pirsd-d2r881 , pirsd-d2r024

Title : Complete genome sequence of Streptobacillus moniliformis type strain (9901) - Nolan_2009_Stand.Genomic.Sci_1_300
Author(s) : Nolan M , Gronow S , Lapidus A , Ivanova N , Copeland A , Lucas S , Del Rio TG , Chen F , Tice H , Pitluck S , Cheng JF , Sims D , Meincke L , Bruce D , Goodwin L , Brettin T , Han C , Detter JC , Ovchinikova G , Pati A , Mavromatis K , Mikhailova N , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Rohde M , Sproer C , Goker M , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP , Chain P
Ref : Stand Genomic Sci , 1 :300 , 2009
Abstract : Streptobacillus moniliformis Levaditi et al. 1925 is the type and sole species of the genus Streptobacillus, and is of phylogenetic interest because of its isolated location in the sparsely populated and neither taxonomically nor genomically much accessed family 'Leptotrichiaceae' within the phylum Fusobacteria. The 'Leptotrichiaceae' have not been well characterized, genomically or taxonomically. S. moniliformis,is a Gram-negative, non-motile, pleomorphic bacterium and is the etiologic agent of rat bite fever and Haverhill fever. Strain 9901(T), the type strain of the species, was isolated from a patient with rat bite fever. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is only the second completed genome sequence of the order Fusobacteriales and no more than the third sequence from the phylum Fusobacteria. The 1,662,578 bp long chromosome and the 10,702 bp plasmid with a total of 1511 protein-coding and 55 RNA genes are part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Nolan_2009_Stand.Genomic.Sci_1_300
PubMedSearch : Nolan_2009_Stand.Genomic.Sci_1_300
PubMedID: 21304670
Gene_locus related to this paper: strm9-d1ayq9 , strm9-d1avt1

Title : Complete genome sequence of Halorhabdus utahensis type strain (AX-2) - Anderson_2009_Stand.Genomic.Sci_1_218
Author(s) : Anderson I , Tindall BJ , Pomrenke H , Goker M , Lapidus A , Nolan M , Copeland A , Glavina Del Rio T , Chen F , Tice H , Cheng JF , Lucas S , Chertkov O , Bruce D , Brettin T , Detter JC , Han C , Goodwin L , Land M , Hauser L , Chang YJ , Jeffries CD , Pitluck S , Pati A , Mavromatis K , Ivanova N , Ovchinnikova G , Chen A , Palaniappan K , Chain P , Rohde M , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP
Ref : Stand Genomic Sci , 1 :218 , 2009
Abstract : Halorhabdus utahensis Waino et al. 2000 is the type species of the genus, which is of phylogenetic interest because of its location on one of the deepest branches within the very extensive euryarchaeal family Halobacteriaceae. H. utahensis is a free-living, motile, rod shaped to pleomorphic, Gram-negative archaeon, which was originally isolated from a sediment sample collected from the southern arm of Great Salt Lake, Utah, USA. When grown on appropriate media, H. utahensis can form polyhydroxybutyrate (PHB). Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the a member of halobacterial genus Halorhabdus, and the 3,116,795 bp long single replicon genome with its 3027 protein-coding and 48 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Anderson_2009_Stand.Genomic.Sci_1_218
PubMedSearch : Anderson_2009_Stand.Genomic.Sci_1_218
PubMedID: 21304660
Gene_locus related to this paper: halud-c7npq6 , halud-c7npw0 , halud-c7nsl4 , halud-c7nut6 , halud-c7npw2

Title : Complete genome sequence of Halogeometricum borinquense type strain (PR3) - Malfatti_2009_Stand.Genomic.Sci_1_150
Author(s) : Malfatti S , Tindall BJ , Schneider S , Fahnrich R , Lapidus A , Labuttii K , Copeland A , Glavina Del Rio T , Nolan M , Chen F , Lucas S , Tice H , Cheng JF , Bruce D , Goodwin L , Pitluck S , Anderson I , Pati A , Ivanova N , Mavromatis K , Chen A , Palaniappan K , D'Haeseleer P , Goker M , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP , Chain P
Ref : Stand Genomic Sci , 1 :150 , 2009
Abstract : Halogeometricum borinquense Montalvo-Rodriguez et al. 1998 is the type species of the genus, and is of phylogenetic interest because of its distinct location between the halobacterial genera Haloquadratum and Halosarcina. H. borinquense requires extremely high salt (NaCl) concentrations for growth. It can not only grow aerobically but also anaerobically using nitrate as electron acceptor. The strain described in this report is a free-living, motile, pleomorphic, euryarchaeon, which was originally isolated from the solar salterns of Cabo Rojo, Puerto Rico. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the halobacterial genus Halogeometricum, and this 3,944,467 bp long six replicon genome with its 3937 protein-coding and 57 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Malfatti_2009_Stand.Genomic.Sci_1_150
PubMedSearch : Malfatti_2009_Stand.Genomic.Sci_1_150
PubMedID: 21304651
Gene_locus related to this paper: 9eury-c1v4h6 , 9eury-c1v4p7 , 9eury-c1v4w8 , 9eury-c1v5h9 , 9eury-c1v5q3 , 9eury-c1v5t3 , 9eury-c1v7y6 , 9eury-c1v8n9 , 9eury-c1v568 , 9eury-c1vb62 , 9eury-c1vc42 , 9eury-c1vcz1 , 9eury-c1vd75 , 9eury-c1vdd8 , 9eury-c1ve13 , 9eury-c1ve51 , 9eury-c1vei1 , 9eury-c1vet7 , halbp-e4nkx5 , halbp-e4nra7 , halbp-e4nub0 , halbp-e4nmr3

Title : Complete genome sequence of Acidimicrobium ferrooxidans type strain (ICP) - Clum_2009_Stand.Genomic.Sci_1_38
Author(s) : Clum A , Nolan M , Lang E , Glavina Del Rio T , Tice H , Copeland A , Cheng JF , Lucas S , Chen F , Bruce D , Goodwin L , Pitluck S , Ivanova N , Mavrommatis K , Mikhailova N , Pati A , Chen A , Palaniappan K , Goker M , Spring S , Land M , Hauser L , Chang YJ , Jeffries CC , Chain P , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP , Lapidus A
Ref : Stand Genomic Sci , 1 :38 , 2009
Abstract : Acidimicrobium ferrooxidans (Clark and Norris 1996) is the sole and type species of the genus, which until recently was the only genus within the actinobacterial family Acidimicrobiaceae and in the order Acidomicrobiales. Rapid oxidation of iron pyrite during autotrophic growth in the absence of an enhanced CO(2) concentration is characteristic for A. ferrooxidans. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the order Acidomicrobiales, and the 2,158,157 bp long single replicon genome with its 2038 protein coding and 54 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Clum_2009_Stand.Genomic.Sci_1_38
PubMedSearch : Clum_2009_Stand.Genomic.Sci_1_38
PubMedID: 21304635
Gene_locus related to this paper: acifd-c7m0l6 , acifd-c7m0z1 , acifd-c7m1g1 , acifd-c7m1p7

Title : Complete genome sequence of Eggerthella lenta type strain (IPP VPI 0255) - Saunders_2009_Stand.Genomic.Sci_1_174
Author(s) : Saunders E , Pukall R , Abt B , Lapidus A , Glavina Del Rio T , Copeland A , Tice H , Cheng JF , Lucas S , Chen F , Nolan M , Bruce D , Goodwin L , Pitluck S , Ivanova N , Mavromatis K , Ovchinnikova G , Pati A , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Chain P , Meincke L , Sims D , Brettin T , Detter JC , Goker M , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP , Han C
Ref : Stand Genomic Sci , 1 :174 , 2009
Abstract : Eggerthella lenta (Eggerth 1935) Wade et al. 1999, emended Wurdemann et al. 2009 is the type species of the genus Eggerthella, which belongs to the actinobacterial family Coriobacteriaceae. E. lenta is a Gram-positive, non-motile, non-sporulating pathogenic bacterium that can cause severe bacteremia. The strain described in this study has been isolated from a rectal tumor in 1935. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the genus Eggerthella, and the 3,632,260 bp long single replicon genome with its 3123 protein-coding and 58 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Saunders_2009_Stand.Genomic.Sci_1_174
PubMedSearch : Saunders_2009_Stand.Genomic.Sci_1_174
PubMedID: 21304654
Gene_locus related to this paper: eggle-c8wmc6 , eggle-c8wpb6

Title : Complete genome sequence of Slackia heliotrinireducens type strain (RHS 1) - Pukall_2009_Stand.Genomic.Sci_1_234
Author(s) : Pukall R , Lapidus A , Nolan M , Copeland A , Glavina Del Rio T , Lucas S , Chen F , Tice H , Cheng JF , Chertkov O , Bruce D , Goodwin L , Kuske C , Brettin T , Detter JC , Han C , Pitluck S , Pati A , Mavrommatis K , Ivanova N , Ovchinnikova G , Chen A , Palaniappan K , Schneider S , Rohde M , Chain P , D'Haeseleer P , Goker M , Bristow J , Eisen JA , Markowitz V , Kyrpides NC , Klenk HP , Hugenholtz P
Ref : Stand Genomic Sci , 1 :234 , 2009
Abstract : Slackia heliotrinireducens (Lanigan 1983) Wade et al. 1999 is of phylogenetic interest because of its location in a genomically yet uncharted section of the family Coriobacteriaceae, within the deep branching Actinobacteria. Strain RHS 1(T) was originally isolated from the ruminal flora of a sheep. It is a proteolytic anaerobic coccus, able to reductively cleave pyrrolizidine alkaloids. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the genus Slackia, and the 3,165,038 bp long single replicon genome with its 2798 protein-coding and 60 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Pukall_2009_Stand.Genomic.Sci_1_234
PubMedSearch : Pukall_2009_Stand.Genomic.Sci_1_234
PubMedID: 21304663
Gene_locus related to this paper: slahd-c7n2q9 , slahd-c7n5g8 , slahd-c7n8d3 , slahd-c7n116 , slahd-c7n1y7 , slahd-c7n5i5 , slahd-c7n6x8 , slahd-c7n8a4 , slahd-c7n2t9

Title : Complete genome sequence of Rhodothermus marinus type strain (R-10) - Nolan_2009_Stand.Genomic.Sci_1_283
Author(s) : Nolan M , Tindall BJ , Pomrenke H , Lapidus A , Copeland A , Glavina Del Rio T , Lucas S , Chen F , Tice H , Cheng JF , Saunders E , Han C , Bruce D , Goodwin L , Chain P , Pitluck S , Ovchinikova G , Pati A , Ivanova N , Mavromatis K , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Brettin T , Goker M , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP , Detter JC
Ref : Stand Genomic Sci , 1 :283 , 2009
Abstract : Rhodothermus marinus Alfredsson et al. 1995 is the type species of the genus and is of phylogenetic interest because the Rhodothermaceae represent the deepest lineage in the phylum Bacteroidetes. R. marinus R-10(T) is a Gram-negative, non-motile, non-spore-forming bacterium isolated from marine hot springs off the coast of Iceland. Strain R-10(T) is strictly aerobic and requires slightly halophilic conditions for growth. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the genus Rhodothermus, and only the second sequence from members of the family Rhodothermaceae. The 3,386,737 bp genome (including a 125 kb plasmid) with its 2914 protein-coding and 48 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Nolan_2009_Stand.Genomic.Sci_1_283
PubMedSearch : Nolan_2009_Stand.Genomic.Sci_1_283
PubMedID: 21304669
Gene_locus related to this paper: rhom4-d0mhy8 , rhom4-d0mg25 , rhom4-d0mhd2 , rhom4-d0mhw6

Title : Complete genome sequence of Sanguibacter keddieii type strain (ST-74) - Ivanova_2009_Stand.Genomic.Sci_1_110
Author(s) : Ivanova N , Sikorski J , Sims D , Brettin T , Detter JC , Han C , Lapidus A , Copeland A , Glavina Del Rio T , Nolan M , Chen F , Lucas S , Tice H , Cheng JF , Bruce D , Goodwin L , Pitluck S , Pati A , Mavromatis K , Chen A , Palaniappan K , D'Haeseleer P , Chain P , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Goker M , Pukall R , Klenk HP , Kyrpides NC
Ref : Stand Genomic Sci , 1 :110 , 2009
Abstract : Sanguibacter keddieii is the type species of the genus Sanguibacter, the only genus within the family of Sanguibacteraceae. Phylogenetically, this family is located in the neighborhood of the genus Oerskovia and the family Cellulomonadaceae within the actinobacterial suborder Micrococcineae. The strain described in this report was isolated from blood of apparently healthy cows. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the family Sanguibacteraceae, and the 4,253,413 bp long single replicon genome with its 3735 protein-coding and 70 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Ivanova_2009_Stand.Genomic.Sci_1_110
PubMedSearch : Ivanova_2009_Stand.Genomic.Sci_1_110
PubMedID: 21304646
Gene_locus related to this paper: sanks-d1bag5 , sanks-d1bah5 , sanks-d1bah6 , sanks-d1bat1 , sanks-d1bay1 , sanks-d1bb04 , sanks-d1bbg6 , sanks-d1bbs4 , sanks-d1bdb3 , sanks-d1bdq0 , sanks-d1bdy6 , sanks-d1bec0 , sanks-d1bes6 , sanks-d1bf19 , sanks-d1bfc5 , sanks-d1bfe7 , sanks-d1bfs7 , sanks-d1bg53 , sanks-d1bgd3 , sanks-d1bgi7 , sanks-d1bhh0 , sanks-d1biq2 , sanks-d1bjg2 , sanks-d1bkh6 , sanks-d1bb73

Title : Complete genome sequence of Atopobium parvulum type strain (IPP 1246) - Copeland_2009_Stand.Genomic.Sci_1_166
Author(s) : Copeland A , Sikorski J , Lapidus A , Nolan M , Del Rio TG , Lucas S , Chen F , Tice H , Pitluck S , Cheng JF , Pukall R , Chertkov O , Brettin T , Han C , Detter JC , Kuske C , Bruce D , Goodwin L , Ivanova N , Mavromatis K , Mikhailova N , Chen A , Palaniappan K , Chain P , Rohde M , Goker M , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP
Ref : Stand Genomic Sci , 1 :166 , 2009
Abstract : Atopobium parvulum (Weinberg et al. 1937) Collins and Wallbanks 1993 comb. nov. is the type strain of the species and belongs to the genomically yet unstudied Atopobium/Olsenella branch of the family Coriobacteriaceae. The species A. parvulum is of interest because its members are frequently isolated from the human oral cavity and are found to be associated with halitosis (oral malodor) but not with periodontitis. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the genus Atopobium, and the 1,543,805 bp long single replicon genome with its 1369 protein-coding and 49 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Copeland_2009_Stand.Genomic.Sci_1_166
PubMedSearch : Copeland_2009_Stand.Genomic.Sci_1_166
PubMedID: 21304653
Gene_locus related to this paper: atopd-c8w7b9 , atopd-c8w7c0 , atopd-c8w7k9 , atopd-c8w886

Title : Complete genome sequence of Beutenbergia cavernae type strain (HKI 0122) - Land_2009_Stand.Genomic.Sci_1_21
Author(s) : Land M , Pukall R , Abt B , Goker M , Rohde M , Glavina Del Rio T , Tice H , Copeland A , Cheng JF , Lucas S , Chen F , Nolan M , Bruce D , Goodwin L , Pitluck S , Ivanova N , Mavromatis K , Ovchinnikova G , Pati A , Chen A , Palaniappan K , Hauser L , Chang YJ , Jefferies CC , Saunders E , Brettin T , Detter JC , Han C , Chain P , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP , Lapidus A
Ref : Stand Genomic Sci , 1 :21 , 2009
Abstract : Beutenbergia cavernae (Groth et al. 1999) is the type species of the genus and is of phylogenetic interest because of its isolated location in the actinobacterial suborder Micrococcineae. B. cavernae HKI 0122(T) is a Gram-positive, non-motile, non-spore-forming bacterium isolated from a cave in Guangxi (China). B. cavernae grows best under aerobic conditions and shows a rod-coccus growth cycle. Its cell wall peptidoglycan contains the diagnostic L-lysine <-- L-glutamate interpeptide bridge. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first completed genome sequence from the poorly populated micrococcineal family Beutenbergiaceae, and this 4,669,183 bp long single replicon genome with its 4225 protein-coding and 53 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Land_2009_Stand.Genomic.Sci_1_21
PubMedSearch : Land_2009_Stand.Genomic.Sci_1_21
PubMedID: 21304633
Gene_locus related to this paper: beuc1-c5bux6 , beuc1-c5bve3 , beuc1-c5bvg4 , beuc1-c5bvm8 , beuc1-c5bwz5 , beuc1-c5bx55 , beuc1-c5bxw8 , beuc1-c5bxx8 , beuc1-c5byj2 , beuc1-c5bzt8 , beuc1-c5c0d3 , beuc1-c5c0f9 , beuc1-c5c1b7 , beuc1-c5c4j9 , beuc1-c5c4m3 , beuc1-c5c5h5 , beuc1-c5c5t9 , beuc1-c5c6d1 , beuc1-c5c476 , beuc1-c5c478 , beuc1-c5c572 , beuc1-c5c4i4 , beuc1-c5bxv5

Title : Complete genome sequence of Jonesia denitrificans type strain (Prevot 55134) - Pukall_2009_Stand.Genomic.Sci_1_262
Author(s) : Pukall R , Gehrich-Schroter G , Lapidus A , Nolan M , Glavina Del Rio T , Lucas S , Chen F , Tice H , Pitluck S , Cheng JF , Copeland A , Saunders E , Brettin T , Detter JC , Bruce D , Goodwin L , Pati A , Ivanova N , Mavromatis K , Ovchinnikova G , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Chain P , Goker M , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP , Han C
Ref : Stand Genomic Sci , 1 :262 , 2009
Abstract : Jonesia denitrificans (Prevot 1961) Rocourt et al. 1987 is the type species of the genus Jonesia, and is of phylogenetic interest because of its isolated location in the actinobacterial suborder Micrococcineae. J. denitrificans is characterized by a typical coryneform morphology and is able to form irregular nonsporulating rods showing branched and club-like forms. Coccoid cells occur in older cultures. J. denitrificans is classified as a pathogenic organism for animals (vertebrates). The type strain whose genome is described here was originally isolated from cooked ox blood. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the genus for which a complete genome sequence is described. The 2,749,646 bp long genome with its 2558 protein-coding and 71 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Pukall_2009_Stand.Genomic.Sci_1_262
PubMedSearch : Pukall_2009_Stand.Genomic.Sci_1_262
PubMedID: 21304666
Gene_locus related to this paper: jondd-c7qz27 , jondd-c7qza6 , jondd-c7r0s6 , jondd-c7r2p4 , jondd-c7r2s4 , jondd-c7r5f7 , jondd-c7r044 , jondd-c7r128 , jondd-c7r357

Title : Complete genome sequence of Cryptobacterium curtum type strain (12-3) - Mavrommatis_2009_Stand.Genomic.Sci_1_93
Author(s) : Mavrommatis K , Pukall R , Rohde C , Chen F , Sims D , Brettin T , Kuske C , Detter JC , Han C , Lapidus A , Copeland A , Glavina Del Rio T , Nolan M , Lucas S , Tice H , Cheng JF , Bruce D , Goodwin L , Pitluck S , Ovchinnikova G , Pati A , Ivanova N , Chen A , Palaniappan K , Chain P , D'Haeseleer P , Goker M , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Rohde M , Klenk HP , Kyrpides NC
Ref : Stand Genomic Sci , 1 :93 , 2009
Abstract : Cryptobacterium curtum Nakazawa etal. 1999 is the type species of the genus, and is of phylogenetic interest because of its very distant and isolated position within the family Coriobacteriaceae. C. curtum is an asaccharolytic, opportunistic pathogen with a typical occurrence in the oral cavity, involved in dental and oral infections like periodontitis, inflammations and abscesses. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the actinobacterial family Coriobacteriaceae, and this 1,617,804 bp long single replicon genome with its 1364 protein-coding and 58 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Mavrommatis_2009_Stand.Genomic.Sci_1_93
PubMedSearch : Mavrommatis_2009_Stand.Genomic.Sci_1_93
PubMedID: 21304644

Title : Complete genome sequence of Kangiella koreensis type strain (SW-125) - Han_2009_Stand.Genomic.Sci_1_226
Author(s) : Han C , Sikorski J , Lapidus A , Nolan M , Glavina Del Rio T , Tice H , Cheng JF , Lucas S , Chen F , Copeland A , Ivanova N , Mavromatis K , Ovchinnikova G , Pati A , Bruce D , Goodwin L , Pitluck S , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Chain P , Saunders E , Brettin T , Goker M , Tindall BJ , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP , Detter JC
Ref : Stand Genomic Sci , 1 :226 , 2009
Abstract : Kangiella koreensis (Yoon et al. 2004) is the type species of the genus and is of phylogenetic interest because of the very isolated location of the genus Kangiella in the gammaproteobacterial order Oceanospirillales. K. koreensis SW-125(T) is a Gram-negative, non-motile, non-spore-forming bacterium isolated from tidal flat sediments at Daepo Beach, Yellow Sea, Korea. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first completed genome sequence from the genus Kangiella and only the fourth genome from the order Oceanospirillales. This 2,852,073 bp long single replicon genome with its 2647 protein-coding and 48 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Han_2009_Stand.Genomic.Sci_1_226
PubMedSearch : Han_2009_Stand.Genomic.Sci_1_226
PubMedID: 21304661
Gene_locus related to this paper: kankd-c7r7f7 , kankd-c7r7w2 , kankd-c7r8t4 , kankd-c7r9y8 , kankd-c7r701 , kankd-c7r727 , kankd-c7r779 , kankd-c7r785 , kankd-c7ra17 , kankd-c7rc78

Title : Complete genome sequence of Saccharomonospora viridis type strain (P101) - Pati_2009_Stand.Genomic.Sci_1_141
Author(s) : Pati A , Sikorski J , Nolan M , Lapidus A , Copeland A , Glavina Del Rio T , Lucas S , Chen F , Tice H , Pitluck S , Cheng JF , Chertkov O , Brettin T , Han C , Detter JC , Kuske C , Bruce D , Goodwin L , Chain P , D'Haeseleer P , Chen A , Palaniappan K , Ivanova N , Mavromatis K , Mikhailova N , Rohde M , Tindall BJ , Goker M , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP
Ref : Stand Genomic Sci , 1 :141 , 2009
Abstract : Saccharomonospora viridis (Schuurmans et al. 1956) Nonomurea and Ohara 1971 is the type species of the genus Saccharomonospora which belongs to the family Pseudonocardiaceae. S. viridis is of interest because it is a Gram-negative organism classified among the usually Gram-positive actinomycetes. Members of the species are frequently found in hot compost and hay, and its spores can cause farmer's lung disease, bagassosis, and humidifier fever. Strains of the species S. viridis have been found to metabolize the xenobiotic pentachlorophenol (PCP). The strain described in this study has been isolated from peat-bog in Ireland. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the family Pseudonocardiaceae, and the 4,308,349 bp long single replicon genome with its 3906 protein-coding and 64 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Pati_2009_Stand.Genomic.Sci_1_141
PubMedSearch : Pati_2009_Stand.Genomic.Sci_1_141
PubMedID: 21304650
Gene_locus related to this paper: sacvd-DsvA , sacvd-c7mpm7 , sacvd-c7mpv6 , sacvd-c7mqn5 , sacvd-c7mrh9 , sacvd-c7mrj7 , sacvd-c7msh1 , sacvd-c7mss4 , sacvd-c7msy5 , sacvd-c7mua8 , sacvd-c7mv20 , sacvd-c7mvm9 , sacvd-c7mx36 , sacvd-c7my02 , sacvd-c7myf1 , sacvd-c7myf2 , sacvd-c7myh3 , sacvd-c7myv3 , sacvd-c7mzb0 , sacvd-c7n0e5 , sacvd-c7mxx2 , sacvd-c7mwe5 , sacvd-c7mve8 , sacvd-c7mu02 , sacvd-c7myq6

Title : Complete genome sequence of Brachybacterium faecium type strain (Schefferle 6-10) - Lapidus_2009_Stand.Genomic.Sci_1_3
Author(s) : Lapidus A , Pukall R , Labuttii K , Copeland A , Del Rio TG , Nolan M , Chen F , Lucas S , Tice H , Cheng JF , Bruce D , Goodwin L , Pitluck S , Rohde M , Goker M , Pati A , Ivanova N , Mavrommatis K , Chen A , Palaniappan K , D'Haeseleer P , Chain P , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP
Ref : Stand Genomic Sci , 1 :3 , 2009
Abstract : Brachybacterium faecium Collins et al. 1988 is the type species of the genus, and is of phylogenetic interest because of its location in the Dermabacteraceae, a rather isolated family within the actinobacterial suborder Micrococcineae. B. faecium is known for its rod-coccus growth cycle and the ability to degrade uric acid. It grows aerobically or weakly anaerobically. The strain described in this report is a free-living, nonmotile, Gram-positive bacterium, originally isolated from poultry deep litter. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the actinobacterial family Dermabacteraceae, and the 3,614,992 bp long single replicon genome with its 3129 protein-coding and 69 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Lapidus_2009_Stand.Genomic.Sci_1_3
PubMedSearch : Lapidus_2009_Stand.Genomic.Sci_1_3
PubMedID: 21304631
Gene_locus related to this paper: brafd-c7maj6 , brafd-c7mb43 , brafd-c7mc54 , brafd-c7mcf0 , brafd-c7mfs9 , brafd-c7mfx9 , brafd-c7mg22 , brafd-c7mbr0 , brafd-c7mi27 , brafd-c7mhn6

Title : Complete genome sequence of Actinosynnema mirum type strain (101) - Land_2009_Stand.Genomic.Sci_1_46
Author(s) : Land M , Lapidus A , Mayilraj S , Chen F , Copeland A , Del Rio TG , Nolan M , Lucas S , Tice H , Cheng JF , Chertkov O , Bruce D , Goodwin L , Pitluck S , Rohde M , Goker M , Pati A , Ivanova N , Mavromatis K , Chen A , Palaniappan K , Hauser L , Chang YJ , Jeffries CC , Brettin T , Detter JC , Han C , Chain P , Tindall BJ , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP
Ref : Stand Genomic Sci , 1 :46 , 2009
Abstract : Actinosynnema mirum Hasegawa et al. 1978 is the type species of the genus, and is of phylogenetic interest because of its central phylogenetic location in the Actino-synnemataceae, a rapidly growing family within the actinobacterial suborder Pseudo-nocardineae. A. mirum is characterized by its motile spores borne on synnemata and as a producer of nocardicin antibiotics. It is capable of growing aerobically and under a moderate CO(2) atmosphere. The strain is a Gram-positive, aerial and substrate mycelium producing bacterium, originally isolated from a grass blade collected from the Raritan River, New Jersey. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first complete genome sequence of a member of the family Actinosynnemataceae, and only the second sequence from the actinobacterial suborder Pseudonocardineae. The 8,248,144 bp long single replicon genome with its 7100 protein-coding and 77 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Land_2009_Stand.Genomic.Sci_1_46
PubMedSearch : Land_2009_Stand.Genomic.Sci_1_46
PubMedID: 21304636
Gene_locus related to this paper: actmd-c6w9l3 , actmd-c6w9n7 , actmd-c6w9s6 , actmd-c6w9w6 , actmd-c6w881 , actmd-c6w899 , actmd-c6waq3 , actmd-c6wbu4 , actmd-c6wc84 , actmd-c6we33 , actmd-c6wed0 , actmd-c6wee7 , actmd-c6weq5 , actmd-c6wer8 , actmd-c6wf96 , actmd-c6wfj7 , actmd-c6wg08 , actmd-c6wgs1 , actmd-c6wh70 , actmd-c6wh84 , actmd-c6whc5 , actmd-c6whm5 , actmd-c6wi63 , actmd-c6wiw2 , actmd-c6wl14 , actmd-c6wla7 , actmd-c6wlp6 , actmd-c6wnr8 , actmd-c6wnv1 , actmd-c6wq55 , actmd-c6wqd1 , actmd-c6wqs5 , actmd-c6wqw5 , actmd-c6wrs4 , actmd-c6ws01 , actmd-c6ws38 , actmd-c6wre6 , actmd-c6wj22 , actmd-c6wmc1 , actmd-c6wn31 , actmd-c6wqv1 , actmd-c6wlx3 , actmd-c6wmy9

Title : The complete genome of Teredinibacter turnerae T7901: an intracellular endosymbiont of marine wood-boring bivalves (shipworms) - Yang_2009_PLoS.One_4_e6085
Author(s) : Yang JC , Madupu R , Durkin AS , Ekborg NA , Pedamallu CS , Hostetler JB , Radune D , Toms BS , Henrissat B , Coutinho PM , Schwarz S , Field L , Trindade-Silva AE , Soares CA , Elshahawi S , Hanora A , Schmidt EW , Haygood MG , Posfai J , Benner J , Madinger C , Nove J , Anton B , Chaudhary K , Foster J , Holman A , Kumar S , Lessard PA , Luyten YA , Slatko B , Wood N , Wu B , Teplitski M , Mougous JD , Ward N , Eisen JA , Badger JH , Distel DL
Ref : PLoS ONE , 4 :e6085 , 2009
Abstract : Here we report the complete genome sequence of Teredinibacter turnerae T7901. T. turnerae is a marine gamma proteobacterium that occurs as an intracellular endosymbiont in the gills of wood-boring marine bivalves of the family Teredinidae (shipworms). This species is the sole cultivated member of an endosymbiotic consortium thought to provide the host with enzymes, including cellulases and nitrogenase, critical for digestion of wood and supplementation of the host's nitrogen-deficient diet. T. turnerae is closely related to the free-living marine polysaccharide degrading bacterium Saccharophagus degradans str. 2-40 and to as yet uncultivated endosymbionts with which it coexists in shipworm cells. Like S. degradans, the T. turnerae genome encodes a large number of enzymes predicted to be involved in complex polysaccharide degradation (>100). However, unlike S. degradans, which degrades a broad spectrum (>10 classes) of complex plant, fungal and algal polysaccharides, T. turnerae primarily encodes enzymes associated with deconstruction of terrestrial woody plant material. Also unlike S. degradans and many other eubacteria, T. turnerae dedicates a large proportion of its genome to genes predicted to function in secondary metabolism. Despite its intracellular niche, the T. turnerae genome lacks many features associated with obligate intracellular existence (e.g. reduced genome size, reduced %G+C, loss of genes of core metabolism) and displays evidence of adaptations common to free-living bacteria (e.g. defense against bacteriophage infection). These results suggest that T. turnerae is likely a facultative intracellular ensosymbiont whose niche presently includes, or recently included, free-living existence. As such, the T. turnerae genome provides insights into the range of genomic adaptations associated with intracellular endosymbiosis as well as enzymatic mechanisms relevant to the recycling of plant materials in marine environments and the production of cellulose-derived biofuels.
ESTHER : Yang_2009_PLoS.One_4_e6085
PubMedSearch : Yang_2009_PLoS.One_4_e6085
PubMedID: 19568419
Gene_locus related to this paper: tertt-c5bif5 , tertt-c5bkb0 , tertt-c5bkv2 , tertt-c5bmq4 , tertt-c5bmw5 , tertt-c5bmx1 , tertt-c5bmz8 , tertt-c5bn23 , tertt-c5bn62 , tertt-c5bpb2 , tertt-c5bpu2 , tertt-c5bru8 , tertt-c5btp6 , tertt-c5buc2 , tertt-metx , tertt-c5br42 , tertt-c5bpt0 , tertt-c5btk3

Title : Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum - Wu_2009_PLoS.One_4_e4207
Author(s) : Wu D , Raymond J , Wu M , Chatterji S , Ren Q , Graham JE , Bryant DA , Robb F , Colman A , Tallon LJ , Badger JH , Madupu R , Ward NL , Eisen JA
Ref : PLoS ONE , 4 :e4207 , 2009
Abstract : In order to enrich the phylogenetic diversity represented in the available sequenced bacterial genomes and as part of an "Assembling the Tree of Life" project, we determined the genome sequence of Thermomicrobium roseum DSM 5159. T. roseum DSM 5159 is a red-pigmented, rod-shaped, Gram-negative extreme thermophile isolated from a hot spring that possesses both an atypical cell wall composition and an unusual cell membrane that is composed entirely of long-chain 1,2-diols. Its genome is composed of two circular DNA elements, one of 2,006,217 bp (referred to as the chromosome) and one of 919,596 bp (referred to as the megaplasmid). Strikingly, though few standard housekeeping genes are found on the megaplasmid, it does encode a complete system for chemotaxis including both chemosensory components and an entire flagellar apparatus. This is the first known example of a complete flagellar system being encoded on a plasmid and suggests a straightforward means for lateral transfer of flagellum-based motility. Phylogenomic analyses support the recent rRNA-based analyses that led to T. roseum being removed from the phylum Thermomicrobia and assigned to the phylum Chloroflexi. Because T. roseum is a deep-branching member of this phylum, analysis of its genome provides insights into the evolution of the Chloroflexi. In addition, even though this species is not photosynthetic, analysis of the genome provides some insight into the origins of photosynthesis in the Chloroflexi. Metabolic pathway reconstructions and experimental studies revealed new aspects of the biology of this species. For example, we present evidence that T. roseum oxidizes CO aerobically, making it the first thermophile known to do so. In addition, we propose that glycosylation of its carotenoids plays a crucial role in the adaptation of the cell membrane to this bacterium's thermophilic lifestyle. Analyses of published metagenomic sequences from two hot springs similar to the one from which this strain was isolated, show that close relatives of T. roseum DSM 5159 are present but have some key differences from the strain sequenced.
ESTHER : Wu_2009_PLoS.One_4_e4207
PubMedSearch : Wu_2009_PLoS.One_4_e4207
PubMedID: 19148287
Gene_locus related to this paper: therp-b9kxz7 , therp-b9l2i8 , therp-b9l396

Title : Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3) - Han_2009_Stand.Genomic.Sci_1_54
Author(s) : Han C , Spring S , Lapidus A , Del Rio TG , Tice H , Copeland A , Cheng JF , Lucas S , Chen F , Nolan M , Bruce D , Goodwin L , Pitluck S , Ivanova N , Mavromatis K , Mikhailova N , Pati A , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CC , Saunders E , Chertkov O , Brettin T , Goker M , Rohde M , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP , Detter JC
Ref : Stand Genomic Sci , 1 :54 , 2009
Abstract : Pedobacter heparinus (Payza and Korn 1956) Steyn et al. 1998 comb. nov. is the type species of the rapidly growing genus Pedobacter within the family Sphingobacteriaceae of the phylum 'Bacteroidetes'. P. heparinus is of interest, because it was the first isolated strain shown to grow with heparin as sole carbon and nitrogen source and because it produces several enzymes involved in the degradation of mucopolysaccharides. All available data about this species are based on a sole strain that was isolated from dry soil. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first report on a complete genome sequence of a member of the genus Pedobacter, and the 5,167,383 bp long single replicon genome with its 4287 protein-coding and 54 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Han_2009_Stand.Genomic.Sci_1_54
PubMedSearch : Han_2009_Stand.Genomic.Sci_1_54
PubMedID: 21304637
Gene_locus related to this paper: pedhd-c6xsb2 , pedhd-c6xtc2 , pedhd-c6xtt3 , pedhd-c6xwf3 , pedhd-c6xzk8 , pedhd-c6y3i4 , pedhd-c6y3z2 , pedhd-c6y041 , pedhd-c6y150 , pedhd-c6xze4 , pedhd-c6xze5 , pedhd-c6y111

Title : Complete genome sequence of Anaerococcus prevotii type strain (PC1) - Labutti_2009_Stand.Genomic.Sci_1_159
Author(s) : LaButti K , Pukall R , Steenblock K , Glavina Del Rio T , Tice H , Copeland A , Cheng JF , Lucas S , Chen F , Nolan M , Bruce D , Goodwin L , Pitluck S , Ivanova N , Mavromatis K , Ovchinnikova G , Pati A , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Chain P , Saunders E , Brettin T , Detter JC , Han C , Goker M , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP , Lapidus A
Ref : Stand Genomic Sci , 1 :159 , 2009
Abstract : Anaerococcus prevotii (Foubert and Douglas 1948) Ezaki et al. 2001 is the type species of the genus, and is of phylogenetic interest because of its arguable assignment to the provisionally arranged family 'Peptostreptococcaceae'. A. prevotii is an obligate anaerobic coccus, usually arranged in clumps or tetrads. The strain, whose genome is described here, was originally isolated from human plasma; other strains of the species were also isolated from clinical specimen. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the genus. Next to Finegoldia magna, A. prevotii is only the second species from the family 'Peptostreptococcaceae' for which a complete genome sequence is described. The 1,998,633 bp long genome (chromosome and one plasmid) with its 1852 protein-coding and 61 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Labutti_2009_Stand.Genomic.Sci_1_159
PubMedSearch : Labutti_2009_Stand.Genomic.Sci_1_159
PubMedID: 21304652
Gene_locus related to this paper: anapd-c7ri43

Title : Adaptations to submarine hydrothermal environments exemplified by the genome of Nautilia profundicola - Campbell_2009_PLoS.Genet_5_e1000362
Author(s) : Campbell BJ , Smith JL , Hanson TE , Klotz MG , Stein LY , Lee CK , Wu D , Robinson JM , Khouri HM , Eisen JA , Cary SC
Ref : PLoS Genet , 5 :e1000362 , 2009
Abstract : Submarine hydrothermal vents are model systems for the Archaean Earth environment, and some sites maintain conditions that may have favored the formation and evolution of cellular life. Vents are typified by rapid fluctuations in temperature and redox potential that impose a strong selective pressure on resident microbial communities. Nautilia profundicola strain Am-H is a moderately thermophilic, deeply-branching Epsilonproteobacterium found free-living at hydrothermal vents and is a member of the microbial mass on the dorsal surface of vent polychaete, Alvinella pompejana. Analysis of the 1.7-Mbp genome of N. profundicola uncovered adaptations to the vent environment--some unique and some shared with other Epsilonproteobacterial genomes. The major findings included: (1) a diverse suite of hydrogenases coupled to a relatively simple electron transport chain, (2) numerous stress response systems, (3) a novel predicted nitrate assimilation pathway with hydroxylamine as a key intermediate, and (4) a gene (rgy) encoding the hallmark protein for hyperthermophilic growth, reverse gyrase. Additional experiments indicated that expression of rgy in strain Am-H was induced over 100-fold with a 20 degrees C increase above the optimal growth temperature of this bacterium and that closely related rgy genes are present and expressed in bacterial communities residing in geographically distinct thermophilic environments. N. profundicola, therefore, is a model Epsilonproteobacterium that contains all the genes necessary for life in the extreme conditions widely believed to reflect those in the Archaean biosphere--anaerobic, sulfur, H2- and CO2-rich, with fluctuating redox potentials and temperatures. In addition, reverse gyrase appears to be an important and common adaptation for mesophiles and moderate thermophiles that inhabit ecological niches characterized by rapid and frequent temperature fluctuations and, as such, can no longer be considered a unique feature of hyperthermophiles.
ESTHER : Campbell_2009_PLoS.Genet_5_e1000362
PubMedSearch : Campbell_2009_PLoS.Genet_5_e1000362
PubMedID: 19197347
Gene_locus related to this paper: naupa-b9l8q7 , naupa-b9l9g8 , naupa-metxa

Title : Complete genome sequence of Stackebrandtia nassauensis type strain (LLR-40K-21) - Munk_2009_Stand.Genomic.Sci_1_234
Author(s) : Munk C , Lapidus A , Copeland A , Jando M , Mayilraj S , Glavina Del Rio T , Nolan M , Chen F , Lucas S , Tice H , Cheng JF , Han C , Detter JC , Bruce D , Goodwin L , Chain P , Pitluck S , Goker M , Ovchinikova G , Pati A , Ivanova N , Mavromatis K , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP
Ref : Stand Genomic Sci , 1 :234 , 2009
Abstract : Stackebrandtia nassauensis Labeda and Kroppenstedt (2005) is the type species of the genus Stackebrandtia, and a member of the actinobacterial family Glycomycetaceae. Stackebrandtia currently contains two species, which are differentiated from Glycomyces spp. by cellular fatty acid and menaquinone composition. Strain LLR-40K-21(T) is Gram-positive, aerobic, and nonmotile, with a branched substrate mycelium and on some media an aerial mycelium. The strain was originally isolated from a soil sample collected from a road side in Nassau, Bahamas. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first complete genome sequence of the actinobacterial suborder Glycomycineae. The 6,841,557 bp long single replicon genome with its 6487 protein-coding and 53 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Munk_2009_Stand.Genomic.Sci_1_234
PubMedSearch : Munk_2009_Stand.Genomic.Sci_1_234
PubMedID: 21304662
Gene_locus related to this paper: stanl-d3pu17 , stanl-d3pum9 , stanl-d3puq6 , stanl-d3pv31 , stanl-d3pve8 , stanl-d3px28 , stanl-d3pxd2 , stanl-d3pxk8 , stanl-d3pxp3 , stanl-d3pxu2 , stanl-d3py25 , stanl-d3py33 , stanl-d3pzi4 , stanl-d3q2d8 , stanl-d3q2s1 , stanl-d3q2z9 , stanl-d3q3r4 , stanl-d3q3u7 , stanl-d3q4g9 , stanl-d3q4i5 , stanl-d3q4i6 , stanl-d3q5k1 , stanl-d3q5x3 , stanl-d3q6b0 , stanl-d3q6y1 , stanl-d3q7h0 , stanl-d3q8a8 , stanl-d3q8h5 , stanl-d3q8k0 , stanl-d3q8m9 , stanl-d3q8q0 , stanl-d3q8y3 , stanl-d3q9n2 , stanl-d3q9n8 , stanl-d3q9v6 , stanl-d3q028 , stanl-d3q293 , stanl-d3q721 , stanl-d3q784 , stanl-d3q912 , stanl-d3q956 , stanl-d3qak3 , stanl-d3qas4 , stanl-d3qb03 , stanl-d3qbc6 , stanl-d3q1i5 , stanl-d3pws8 , stanl-d3py92 , stanl-d3qbx6

Title : Complete genome sequence of Leptotrichia buccalis type strain (C-1013-b) - Ivanova_2009_Stand.Genomic.Sci_1_126
Author(s) : Ivanova N , Gronow S , Lapidus A , Copeland A , Glavina Del Rio T , Nolan M , Lucas S , Chen F , Tice H , Cheng JF , Saunders E , Bruce D , Goodwin L , Brettin T , Detter JC , Han C , Pitluck S , Mikhailova N , Pati A , Mavrommatis K , Chen A , Palaniappan K , Land M , Hauser L , Chang YJ , Jeffries CD , Chain P , Rohde C , Goker M , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP
Ref : Stand Genomic Sci , 1 :126 , 2009
Abstract : Leptotrichia buccalis (Robin 1853) Trevisan 1879 is the type species of the genus, and is of phylogenetic interest because of its isolated location in the sparsely populated and neither taxonomically nor genomically adequately accessed family 'Leptotrichiaceae' within the phylum 'Fusobacteria'. Species of Leptotrichia are large, fusiform, non-motile, non-sporulating rods, which often populate the human oral flora. L. buccalis is anaerobic to aerotolerant, and saccharolytic. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first complete genome sequence of the order 'Fusobacteriales' and no more than the second sequence from the phylum 'Fusobacteria'. The 2,465,610 bp long single replicon genome with its 2306 protein-coding and 61 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Ivanova_2009_Stand.Genomic.Sci_1_126
PubMedSearch : Ivanova_2009_Stand.Genomic.Sci_1_126
PubMedID: 21304648
Gene_locus related to this paper: lepbd-c7naa9 , lepbd-c7nay1 , lepbd-c7ncm7

Title : Complete genome sequence of Capnocytophaga ochracea type strain (VPI 2845) - Mavrommatis_2009_Stand.Genomic.Sci_1_101
Author(s) : Mavrommatis K , Gronow S , Saunders E , Land M , Lapidus A , Copeland A , Glavina Del Rio T , Nolan M , Lucas S , Chen F , Tice H , Cheng JF , Bruce D , Goodwin L , Pitluck S , Pati A , Ivanova N , Chen A , Palaniappan K , Chain P , Hauser L , Chang YJ , Jeffries CD , Brettin T , Detter JC , Han C , Bristow J , Goker M , Rohde M , Eisen JA , Markowitz V , Kyrpides NC , Klenk HP , Hugenholtz P
Ref : Stand Genomic Sci , 1 :101 , 2009
Abstract : Capnocytophaga ochracea (Prevot et al. 1956) Leadbetter et al. 1982 is the type species of the genus Capnocytophaga. It is of interest because of its location in the Flavobacteriaceae, a genomically not yet charted family within the order Flavobacteriales. The species grows as fusiform to rod shaped cells which tend to form clumps and are able to move by gliding. C. ochracea is known as a capnophilic (CO(2)-requiring) organism with the ability to grow under anaerobic as well as aerobic conditions (oxygen concentration larger than 15%), here only in the presence of 5% CO(2). Strain VPI 2845(T), the type strain of the species, is portrayed in this report as a gliding, Gram-negative bacterium, originally isolated from a human oral cavity. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first completed genome sequence from the flavobacterial genus Capnocytophaga, and the 2,612,925 bp long single replicon genome with its 2193 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Mavrommatis_2009_Stand.Genomic.Sci_1_101
PubMedSearch : Mavrommatis_2009_Stand.Genomic.Sci_1_101
PubMedID: 21304645
Gene_locus related to this paper: capgi-c2m6q0 , capod-c7m434 , capod-c7m7m0 , capod-c7m8e1 , capod-c7m590 , capoc-e4mus7

Title : Complete genome sequence of Catenulispora acidiphila type strain (ID 139908) - Copeland_2009_Stand.Genomic.Sci_1_119
Author(s) : Copeland A , Lapidus A , Glavina Del Rio T , Nolan M , Lucas S , Chen F , Tice H , Cheng JF , Bruce D , Goodwin L , Pitluck S , Mikhailova N , Pati A , Ivanova N , Mavromatis K , Chen A , Palaniappan K , Chain P , Land M , Hauser L , Chang YJ , Jeffries CD , Chertkov O , Brettin T , Detter JC , Han C , Ali Z , Tindall BJ , Goker M , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Kyrpides NC , Klenk HP
Ref : Stand Genomic Sci , 1 :119 , 2009
Abstract : Catenulispora acidiphila Busti et al. 2006 is the type species of the genus Catenulispora, and is of interest because of the rather isolated phylogenetic location it occupies within the scarcely explored suborder Catenulisporineae of the order Actinomycetales. C. acidiphilia is known for its acidophilic, aerobic lifestyle, but can also grow scantly under anaerobic conditions. Under regular conditions, C. acidiphilia grows in long filaments of relatively short aerial hyphae with marked septation. It is a free living, non motile, Gram-positive bacterium isolated from a forest soil sample taken from a wooded area in Gerenzano, Italy. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first complete genome sequence of the actinobacterial family Catenulisporaceae, and the 10,467,782 bp long single replicon genome with its 9056 protein-coding and 69 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Copeland_2009_Stand.Genomic.Sci_1_119
PubMedSearch : Copeland_2009_Stand.Genomic.Sci_1_119
PubMedID: 21304647
Gene_locus related to this paper: catad-c7pvc2 , catad-c7pvf9 , catad-c7pwm0 , catad-c7pwp0 , catad-c7pws9 , catad-c7pxh4 , catad-c7py99 , catad-c7pyw2 , catad-c7pz32 , catad-c7pz91 , catad-c7pze9 , catad-c7pzn0 , catad-c7q0c0 , catad-c7q0r2 , catad-c7q1d2 , catad-c7q1l8 , catad-c7q3r3 , catad-c7q3t4 , catad-c7q4e4 , catad-c7q5v1 , catad-c7q6u5 , catad-c7q6u8 , catad-c7q7m3 , catad-c7q7s8 , catad-c7q8l0 , catad-c7q8u5 , catad-c7q8y2 , catad-c7q9c0 , catad-c7q209 , catad-c7q740 , catad-c7q940 , catad-c7q983 , catad-c7qam3 , catad-c7qam5 , catad-c7qam7 , catad-c7qat2 , catad-c7qav4 , catad-c7qc64 , catad-c7qdc4 , catad-c7qds2 , catad-c7qdv2 , catad-c7qe72 , catad-c7qed5 , catad-c7qfj4 , catad-c7qfu6 , catad-c7qg26 , catad-c7qgn7 , catad-c7qh87 , catad-c7qh95 , catad-c7qi49 , catad-c7qi50 , catad-c7qib3 , catad-c7qju9 , catad-c7q631 , catad-c7pzc9 , catad-c7pw02 , catad-c7pvj4 , catad-c7q6w1 , catad-c7q7k2 , catad-c7q329

Title : Complete genome sequence of Dyadobacter fermentans type strain (NS114) - Lang_2009_Stand.Genomic.Sci_1_133
Author(s) : Lang E , Lapidus A , Chertkov O , Brettin T , Detter JC , Han C , Copeland A , Glavina Del Rio T , Nolan M , Chen F , Lucas S , Tice H , Cheng JF , Land M , Hauser L , Chang YJ , Jeffries CD , Kopitz M , Bruce D , Goodwin L , Pitluck S , Ovchinnikova G , Pati A , Ivanova N , Mavrommatis K , Chen A , Palaniappan K , Chain P , Bristow J , Eisen JA , Markowitz V , Hugenholtz P , Goker M , Rohde M , Kyrpides NC , Klenk HP
Ref : Stand Genomic Sci , 1 :133 , 2009
Abstract : Dyadobacter fermentans (Chelius and Triplett, 2000) is the type species of the genus Dyadobacter. It is of phylogenetic interest because of its location in the Cytophagaceae, a very diverse family within the order 'Sphingobacteriales'. D. fermentans has a mainly respiratory metabolism, stains Gram-negative, is non-motile and oxidase and catalase positive. It is characterized by the production of cell filaments in aging cultures, a flexirubin-like pigment and its ability to ferment glucose, which is almost unique in the aerobically living members of this taxonomically difficult family. Here we describe the features of this organism, together with the complete genome sequence, and its annotation. This is the first complete genome sequence of the sphingobacterial genus Dyadobacter, and this 6,967,790 bp long single replicon genome with its 5804 protein-coding and 50 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ESTHER : Lang_2009_Stand.Genomic.Sci_1_133
PubMedSearch : Lang_2009_Stand.Genomic.Sci_1_133
PubMedID: 21304649
Gene_locus related to this paper: dyafd-c6vtl2 , dyafd-c6vtn9 , dyafd-c6vuf1 , dyafd-c6vv37 , dyafd-c6vw49 , dyafd-c6vx42 , dyafd-c6vx54 , dyafd-c6vx95 , dyafd-c6vy00 , dyafd-c6vy01 , dyafd-c6vy05 , dyafd-c6vy98 , dyafd-c6vyc2 , dyafd-c6vyy9 , dyafd-c6vz95 , dyafd-c6vz96 , dyafd-c6w0j7 , dyafd-c6w1q5 , dyafd-c6w3h8 , dyafd-c6w4r6 , dyafd-c6w5n0 , dyafd-c6w5s2 , dyafd-c6w6a8 , dyafd-c6w6k0 , dyafd-c6w6z4 , dyafd-c6w7f1 , dyafd-c6w7i5 , dyafd-c6w325 , dyafd-c6w605 , dyafd-c6w743 , dyafd-c6w773 , dyafd-c6vux0 , dyafd-c6vux5 , dyafd-c6w724 , dyafd-c6w248

Title : Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications - Valdes_2008_BMC.Genomics_9_597
Author(s) : Valdes J , Pedroso I , Quatrini R , Dodson RJ , Tettelin H , Blake R, 2nd , Eisen JA , Holmes DS
Ref : BMC Genomics , 9 :597 , 2008
Abstract : BACKGROUND: Acidithiobacillus ferrooxidans is a major participant in consortia of microorganisms used for the industrial recovery of copper (bioleaching or biomining). It is a chemolithoautrophic, gamma-proteobacterium using energy from the oxidation of iron- and sulfur-containing minerals for growth. It thrives at extremely low pH (pH 1-2) and fixes both carbon and nitrogen from the atmosphere. It solubilizes copper and other metals from rocks and plays an important role in nutrient and metal biogeochemical cycling in acid environments. The lack of a well-developed system for genetic manipulation has prevented thorough exploration of its physiology. Also, confusion has been caused by prior metabolic models constructed based upon the examination of multiple, and sometimes distantly related, strains of the microorganism. RESULTS: The genome of the type strain A. ferrooxidans ATCC 23270 was sequenced and annotated to identify general features and provide a framework for in silico metabolic reconstruction. Earlier models of iron and sulfur oxidation, biofilm formation, quorum sensing, inorganic ion uptake, and amino acid metabolism are confirmed and extended. Initial models are presented for central carbon metabolism, anaerobic metabolism (including sulfur reduction, hydrogen metabolism and nitrogen fixation), stress responses, DNA repair, and metal and toxic compound fluxes. CONCLUSION: Bioinformatics analysis provides a valuable platform for gene discovery and functional prediction that helps explain the activity of A. ferrooxidans in industrial bioleaching and its role as a primary producer in acidic environments. An analysis of the genome of the type strain provides a coherent view of its gene content and metabolic potential.
ESTHER : Valdes_2008_BMC.Genomics_9_597
PubMedSearch : Valdes_2008_BMC.Genomics_9_597
PubMedID: 19077236
Gene_locus related to this paper: acif2-b7j3y8 , acif2-b7j4u5 , acif2-b7j5z4 , acif2-b7j620 , acif2-metx

Title : The Calyptogena magnifica chemoautotrophic symbiont genome - Newton_2007_Science_315_998
Author(s) : Newton IL , Woyke T , Auchtung TA , Dilly GF , Dutton RJ , Fisher MC , Fontanez KM , Lau E , Stewart FJ , Richardson PM , Barry KW , Saunders E , Detter JC , Wu D , Eisen JA , Cavanaugh CM
Ref : Science , 315 :998 , 2007
Abstract : Chemoautotrophic endosymbionts are the metabolic cornerstone of hydrothermal vent communities, providing invertebrate hosts with nearly all of their nutrition. The Calyptogena magnifica (Bivalvia: Vesicomyidae) symbiont, Candidatus Ruthia magnifica, is the first intracellular sulfur-oxidizing endosymbiont to have its genome sequenced, revealing a suite of metabolic capabilities. The genome encodes major chemoautotrophic pathways as well as pathways for biosynthesis of vitamins, cofactors, and all 20 amino acids required by the clam.
ESTHER : Newton_2007_Science_315_998
PubMedSearch : Newton_2007_Science_315_998
PubMedID: 17303757
Gene_locus related to this paper: rutmc-a1aw39 , rutmc-a1ax96

Title : Evolution of sensory complexity recorded in a myxobacterial genome - Goldman_2006_Proc.Natl.Acad.Sci.U.S.A_103_15200
Author(s) : Goldman BS , Nierman WC , Kaiser D , Slater SC , Durkin AS , Eisen JA , Ronning CM , Barbazuk WB , Blanchard M , Field C , Halling C , Hinkle G , Iartchuk O , Kim HS , Mackenzie C , Madupu R , Miller N , Shvartsbeyn A , Sullivan SA , Vaudin M , Wiegand R , Kaplan HB
Ref : Proc Natl Acad Sci U S A , 103 :15200 , 2006
Abstract : Myxobacteria are single-celled, but social, eubacterial predators. Upon starvation they build multicellular fruiting bodies using a developmental program that progressively changes the pattern of cell movement and the repertoire of genes expressed. Development terminates with spore differentiation and is coordinated by both diffusible and cell-bound signals. The growth and development of Myxococcus xanthus is regulated by the integration of multiple signals from outside the cells with physiological signals from within. A collection of M. xanthus cells behaves, in many respects, like a multicellular organism. For these reasons M. xanthus offers unparalleled access to a regulatory network that controls development and that organizes cell movement on surfaces. The genome of M. xanthus is large (9.14 Mb), considerably larger than the other sequenced delta-proteobacteria. We suggest that gene duplication and divergence were major contributors to genomic expansion from its progenitor. More than 1,500 duplications specific to the myxobacterial lineage were identified, representing >15% of the total genes. Genes were not duplicated at random; rather, genes for cell-cell signaling, small molecule sensing, and integrative transcription control were amplified selectively. Families of genes encoding the production of secondary metabolites are overrepresented in the genome but may have been received by horizontal gene transfer and are likely to be important for predation.
ESTHER : Goldman_2006_Proc.Natl.Acad.Sci.U.S.A_103_15200
PubMedSearch : Goldman_2006_Proc.Natl.Acad.Sci.U.S.A_103_15200
PubMedID: 17015832
Gene_locus related to this paper: myxxa-q4vps9 , myxxa-Q8VQX5 , myxxa-Q84FB1 , myxxa-Q84FE8 , myxxd-q1cvh4 , myxxd-q1cvn3 , myxxd-q1cvz5 , myxxd-q1cw78 , myxxd-q1cwf6 , myxxd-q1cwl7 , myxxd-q1cwt9 , myxxd-q1cxe9 , myxxd-q1cxf0 , myxxd-q1cxj1 , myxxd-q1cze1 , myxxd-q1czi2 , myxxd-q1czk0 , myxxd-q1czr4 , myxxd-q1czy4 , myxxd-q1d0l8 , myxxd-q1d0y6 , myxxd-q1d1c9 , myxxd-q1d2h6 , myxxd-q1d2h8 , myxxd-q1d2m8 , myxxd-q1d2n2 , myxxd-q1d3m2 , myxxd-q1d5c1 , myxxd-q1d6k0 , myxxd-q1d6z6 , myxxd-q1d8v0 , myxxd-q1d145 , myxxd-q1d167 , myxxd-q1d458 , myxxd-q1d796 , myxxd-q1da49 , myxxd-q1dbk1 , myxxd-q1dbn0 , myxxd-q1dbn1 , myxxd-q1dbn9 , myxxd-q1dbp0 , myxxd-q1dbs7 , myxxd-q1dcd0 , myxxd-q1dcj1 , myxxd-q1ddx1 , myxxd-q1ddx8 , myxxd-q1de36 , myxxd-q1det8 , myxxd-q1dey9 , myxxd-q1df33 , myxxd-q1dfs1 , myxxd-q1dfu0 , myxxd-q1dfy2 , myxxd-q1ddu9 , myxxd-q1d1h0 , myxxd-q1cwu7 , myxxd-q1d790

Title : Metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters - Wu_2006_PLoS.Biol_4_e188
Author(s) : Wu D , Daugherty SC , Van Aken SE , Pai GH , Watkins KL , Khouri H , Tallon LJ , Zaborsky JM , Dunbar HE , Tran PL , Moran NA , Eisen JA
Ref : PLoS Biol , 4 :e188 , 2006
Abstract : Mutualistic intracellular symbiosis between bacteria and insects is a widespread phenomenon that has contributed to the global success of insects. The symbionts, by provisioning nutrients lacking from diets, allow various insects to occupy or dominate ecological niches that might otherwise be unavailable. One such insect is the glassy-winged sharpshooter (Homalodisca coagulata), which feeds on xylem fluid, a diet exceptionally poor in organic nutrients. Phylogenetic studies based on rRNA have shown two types of bacterial symbionts to be coevolving with sharpshooters: the gamma-proteobacterium Baumannia cicadellinicola and the Bacteroidetes species Sulcia muelleri. We report here the sequencing and analysis of the 686,192-base pair genome of B. cicadellinicola and approximately 150 kilobase pairs of the small genome of S. muelleri, both isolated from H. coagulata. Our study, which to our knowledge is the first genomic analysis of an obligate symbiosis involving multiple partners, suggests striking complementarity in the biosynthetic capabilities of the two symbionts: B. cicadellinicola devotes a substantial portion of its genome to the biosynthesis of vitamins and cofactors required by animals and lacks most amino acid biosynthetic pathways, whereas S. muelleri apparently produces most or all of the essential amino acids needed by its host. This finding, along with other results of our genome analysis, suggests the existence of metabolic codependency among the two unrelated endosymbionts and their insect host. This dual symbiosis provides a model case for studying correlated genome evolution and genome reduction involving multiple organisms in an intimate, obligate mutualistic relationship. In addition, our analysis provides insight for the first time into the differences in symbionts between insects (e.g., aphids) that feed on phloem versus those like H. coagulata that feed on xylem. Finally, the genomes of these two symbionts provide potential targets for controlling plant pathogens such as Xylella fastidiosa, a major agroeconomic problem, for which H. coagulata and other sharpshooters serve as vectors of transmission.
ESTHER : Wu_2006_PLoS.Biol_4_e188
PubMedSearch : Wu_2006_PLoS.Biol_4_e188
PubMedID: 16729848
Gene_locus related to this paper: bauch-q1lsz2

Title : Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote - Eisen_2006_PLoS.Biol_4_e286
Author(s) : Eisen JA , Coyne RS , Wu M , Wu D , Thiagarajan M , Wortman JR , Badger JH , Ren Q , Amedeo P , Jones KM , Tallon LJ , Delcher AL , Salzberg SL , Silva JC , Haas BJ , Majoros WH , Farzad M , Carlton JM , Smith RK, Jr. , Garg J , Pearlman RE , Karrer KM , Sun L , Manning G , Elde NC , Turkewitz AP , Asai DJ , Wilkes DE , Wang Y , Cai H , Collins K , Stewart BA , Lee SR , Wilamowska K , Weinberg Z , Ruzzo WL , Wloga D , Gaertig J , Frankel J , Tsao CC , Gorovsky MA , Keeling PJ , Waller RF , Patron NJ , Cherry JM , Stover NA , Krieger CJ , del Toro C , Ryder HF , Williamson SC , Barbeau RA , Hamilton EP , Orias E
Ref : PLoS Biol , 4 :e286 , 2006
Abstract : The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct nuclei within a single cell. The germline-like micronucleus (MIC) has its genome held in reserve for sexual reproduction. The soma-like macronucleus (MAC), which possesses a genome processed from that of the MIC, is the center of gene expression and does not directly contribute DNA to sexual progeny. We report here the shotgun sequencing, assembly, and analysis of the MAC genome of T. thermophila, which is approximately 104 Mb in length and composed of approximately 225 chromosomes. Overall, the gene set is robust, with more than 27,000 predicted protein-coding genes, 15,000 of which have strong matches to genes in other organisms. The functional diversity encoded by these genes is substantial and reflects the complexity of processes required for a free-living, predatory, single-celled organism. This is highlighted by the abundance of lineage-specific duplications of genes with predicted roles in sensing and responding to environmental conditions (e.g., kinases), using diverse resources (e.g., proteases and transporters), and generating structural complexity (e.g., kinesins and dyneins). In contrast to the other lineages of alveolates (apicomplexans and dinoflagellates), no compelling evidence could be found for plastid-derived genes in the genome. UGA, the only T. thermophila stop codon, is used in some genes to encode selenocysteine, thus making this organism the first known with the potential to translate all 64 codons in nuclear genes into amino acids. We present genomic evidence supporting the hypothesis that the excision of DNA from the MIC to generate the MAC specifically targets foreign DNA as a form of genome self-defense. The combination of the genome sequence, the functional diversity encoded therein, and the presence of some pathways missing from other model organisms makes T. thermophila an ideal model for functional genomic studies to address biological, biomedical, and biotechnological questions of fundamental importance.
ESTHER : Eisen_2006_PLoS.Biol_4_e286
PubMedSearch : Eisen_2006_PLoS.Biol_4_e286
PubMedID: 16933976
Gene_locus related to this paper: tetts-i7mam3 , tetts-i7ml33

Title : Comparative genomics of emerging human ehrlichiosis agents - Dunning Hotopp_2006_PLoS.Genet_2_e21
Author(s) : Dunning Hotopp JC , Lin M , Madupu R , Crabtree J , Angiuoli SV , Eisen JA , Seshadri R , Ren Q , Wu M , Utterback TR , Smith S , Lewis M , Khouri H , Zhang C , Niu H , Lin Q , Ohashi N , Zhi N , Nelson W , Brinkac LM , Dodson RJ , Rosovitz MJ , Sundaram J , Daugherty SC , Davidsen T , Durkin AS , Gwinn M , Haft DH , Selengut JD , Sullivan SA , Zafar N , Zhou L , Benahmed F , Forberger H , Halpin R , Mulligan S , Robinson J , White O , Rikihisa Y , Tettelin H
Ref : PLoS Genet , 2 :e21 , 2006
Abstract : Anaplasma (formerly Ehrlichia) phagocytophilum, Ehrlichia chaffeensis, and Neorickettsia (formerly Ehrlichia) sennetsu are intracellular vector-borne pathogens that cause human ehrlichiosis, an emerging infectious disease. We present the complete genome sequences of these organisms along with comparisons to other organisms in the Rickettsiales order. Ehrlichia spp. and Anaplasma spp. display a unique large expansion of immunodominant outer membrane proteins facilitating antigenic variation. All Rickettsiales have a diminished ability to synthesize amino acids compared to their closest free-living relatives. Unlike members of the Rickettsiaceae family, these pathogenic Anaplasmataceae are capable of making all major vitamins, cofactors, and nucleotides, which could confer a beneficial role in the invertebrate vector or the vertebrate host. Further analysis identified proteins potentially involved in vacuole confinement of the Anaplasmataceae, a life cycle involving a hematophagous vector, vertebrate pathogenesis, human pathogenesis, and lack of transovarial transmission. These discoveries provide significant insights into the biology of these obligate intracellular pathogens.
ESTHER : Dunning Hotopp_2006_PLoS.Genet_2_e21
PubMedSearch : Dunning Hotopp_2006_PLoS.Genet_2_e21
PubMedID: 16482227
Gene_locus related to this paper: anapz-q2gj80 , anapz-q2gle9 , anapz-q2glf0 , anapz-q2gln7 , ehrch-q40iu0 , ehrch-q40jj7 , ehrcr-q2gfq9 , neosm-q2gcq8 , neosm-q2gdf2 , neosm-q2gcn8 , anapz-q2gk48 , ehrcr-q2ggj6

Title : Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes - Seshadri_2005_Science_307_105
Author(s) : Seshadri R , Adrian L , Fouts DE , Eisen JA , Phillippy AM , Methe BA , Ward NL , Nelson WC , DeBoy RT , Khouri HM , Kolonay JF , Dodson RJ , Daugherty SC , Brinkac LM , Sullivan SA , Madupu R , Nelson KE , Kang KH , Impraim M , Tran K , Robinson JM , Forberger HA , Fraser CM , Zinder SH , Heidelberg JF
Ref : Science , 307 :105 , 2005
Abstract : Dehalococcoides ethenogenes is the only bacterium known to reductively dechlorinate the groundwater pollutants, tetrachloroethene (PCE) and trichloroethene, to ethene. Its 1,469,720-base pair chromosome contains large dynamic duplicated regions and integrated elements. Genes encoding 17 putative reductive dehalogenases, nearly all of which were adjacent to genes for transcription regulators, and five hydrogenase complexes were identified. These findings, plus a limited repertoire of other metabolic modes, indicate that D. ethenogenes is highly evolved to utilize halogenated organic compounds and H2. Diversification of reductive dehalogenase functions appears to have been mediated by recent genetic exchange and amplification. Genome analysis provides insights into the organism's complex nutrient requirements and suggests that an ancestor was a nitrogen-fixing autotroph.
ESTHER : Seshadri_2005_Science_307_105
PubMedSearch : Seshadri_2005_Science_307_105
PubMedID: 15637277
Gene_locus related to this paper: dehm1-q3z6q3 , dehm1-q3z6x9 , dehm1-q3z6z2 , dehm1-q3z8f3 , dehm1-q3za50

Title : Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901 - Wu_2005_PLoS.Genet_1_e65
Author(s) : Wu M , Ren Q , Durkin AS , Daugherty SC , Brinkac LM , Dodson RJ , Madupu R , Sullivan SA , Kolonay JF , Haft DH , Nelson WC , Tallon LJ , Jones KM , Ulrich LE , Gonzalez JM , Zhulin IB , Robb FT , Eisen JA
Ref : PLoS Genet , 1 :e65 , 2005
Abstract : We report here the sequencing and analysis of the genome of the thermophilic bacterium Carboxydothermus hydrogenoformans Z-2901. This species is a model for studies of hydrogenogens, which are diverse bacteria and archaea that grow anaerobically utilizing carbon monoxide (CO) as their sole carbon source and water as an electron acceptor, producing carbon dioxide and hydrogen as waste products. Organisms that make use of CO do so through carbon monoxide dehydrogenase complexes. Remarkably, analysis of the genome of C. hydrogenoformans reveals the presence of at least five highly differentiated anaerobic carbon monoxide dehydrogenase complexes, which may in part explain how this species is able to grow so much more rapidly on CO than many other species. Analysis of the genome also has provided many general insights into the metabolism of this organism which should make it easier to use it as a source of biologically produced hydrogen gas. One surprising finding is the presence of many genes previously found only in sporulating species in the Firmicutes Phylum. Although this species is also a Firmicutes, it was not known to sporulate previously. Here we show that it does sporulate and because it is missing many of the genes involved in sporulation in other species, this organism may serve as a "minimal" model for sporulation studies. In addition, using phylogenetic profile analysis, we have identified many uncharacterized gene families found in all known sporulating Firmicutes, but not in any non-sporulating bacteria, including a sigma factor not known to be involved in sporulation previously.
ESTHER : Wu_2005_PLoS.Genet_1_e65
PubMedSearch : Wu_2005_PLoS.Genet_1_e65
PubMedID: 16311624
Gene_locus related to this paper: carhz-metx , carhz-q3abd5 , carhz-q3adp4

Title : The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough - Heidelberg_2004_Nat.Biotechnol_22_554
Author(s) : Heidelberg JF , Seshadri R , Haveman SA , Hemme CL , Paulsen IT , Kolonay JF , Eisen JA , Ward N , Methe B , Brinkac LM , Daugherty SC , DeBoy RT , Dodson RJ , Durkin AS , Madupu R , Nelson WC , Sullivan SA , Fouts D , Haft DH , Selengut J , Peterson JD , Davidsen TM , Zafar N , Zhou L , Radune D , Dimitrov G , Hance M , Tran K , Khouri H , Gill J , Utterback TR , Feldblyum TV , Wall JD , Voordouw G , Fraser CM
Ref : Nat Biotechnol , 22 :554 , 2004
Abstract : Desulfovibrio vulgaris Hildenborough is a model organism for studying the energy metabolism of sulfate-reducing bacteria (SRB) and for understanding the economic impacts of SRB, including biocorrosion of metal infrastructure and bioremediation of toxic metal ions. The 3,570,858 base pair (bp) genome sequence reveals a network of novel c-type cytochromes, connecting multiple periplasmic hydrogenases and formate dehydrogenases, as a key feature of its energy metabolism. The relative arrangement of genes encoding enzymes for energy transduction, together with inferred cellular location of the enzymes, provides a basis for proposing an expansion to the 'hydrogen-cycling' model for increasing energy efficiency in this bacterium. Plasmid-encoded functions include modification of cell surface components, nitrogen fixation and a type-III protein secretion system. This genome sequence represents a substantial step toward the elucidation of pathways for reduction (and bioremediation) of pollutants such as uranium and chromium and offers a new starting point for defining this organism's complex anaerobic respiration.
ESTHER : Heidelberg_2004_Nat.Biotechnol_22_554
PubMedSearch : Heidelberg_2004_Nat.Biotechnol_22_554
PubMedID: 15077118
Gene_locus related to this paper: desvh-q72b36 , desvh-q72ed6 , desvh-q728i3 , desvh-q729w4 , desvh-q72b15

Title : Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment - Moran_2004_Nature_432_910
Author(s) : Moran MA , Buchan A , Gonzalez JM , Heidelberg JF , Whitman WB , Kiene RP , Henriksen JR , King GM , Belas R , Fuqua C , Brinkac L , Lewis M , Johri S , Weaver B , Pai G , Eisen JA , Rahe E , Sheldon WM , Ye W , Miller TR , Carlton J , Rasko DA , Paulsen IT , Ren Q , Daugherty SC , DeBoy RT , Dodson RJ , Durkin AS , Madupu R , Nelson WC , Sullivan SA , Rosovitz MJ , Haft DH , Selengut J , Ward N
Ref : Nature , 432 :910 , 2004
Abstract : Since the recognition of prokaryotes as essential components of the oceanic food web, bacterioplankton have been acknowledged as catalysts of most major biogeochemical processes in the sea. Studying heterotrophic bacterioplankton has been challenging, however, as most major clades have never been cultured or have only been grown to low densities in sea water. Here we describe the genome sequence of Silicibacter pomeroyi, a member of the marine Roseobacter clade (Fig. 1), the relatives of which comprise approximately 10-20% of coastal and oceanic mixed-layer bacterioplankton. This first genome sequence from any major heterotrophic clade consists of a chromosome (4,109,442 base pairs) and megaplasmid (491,611 base pairs). Genome analysis indicates that this organism relies upon a lithoheterotrophic strategy that uses inorganic compounds (carbon monoxide and sulphide) to supplement heterotrophy. Silicibacter pomeroyi also has genes advantageous for associations with plankton and suspended particles, including genes for uptake of algal-derived compounds, use of metabolites from reducing microzones, rapid growth and cell-density-dependent regulation. This bacterium has a physiology distinct from that of marine oligotrophs, adding a new strategy to the recognized repertoire for coping with a nutrient-poor ocean.
ESTHER : Moran_2004_Nature_432_910
PubMedSearch : Moran_2004_Nature_432_910
PubMedID: 15602564
Gene_locus related to this paper: silpo-q5lke5 , silpo-q5lke7 , silpo-q5lke8 , silpo-q5lkk5 , silpo-q5lkv2 , silpo-q5lln9 , silpo-q5llu0 , silpo-q5llu2 , silpo-q5llx5 , silpo-q5lm66 , silpo-q5lmb9 , silpo-q5lml9 , silpo-q5lnp6 , silpo-q5lp28 , silpo-q5lp48 , silpo-q5lp56 , silpo-q5lpa5 , silpo-q5lpf7 , silpo-q5lpy6 , silpo-q5lrk1 , silpo-q5lsn7 , silpo-q5ltb5 , silpo-q5ltk0 , silpo-q5ltm5 , silpo-q5ltw8 , silpo-q5ltw9 , silpo-q5ltx1 , silpo-q5ltx5 , silpo-q5lu02 , silpo-q5lv12 , silpo-q5lv17 , silpo-q5lv53 , silpo-q5lvg9 , silpo-q5lw35 , silpo-q5lwk9 , silpo-q5lws0

Title : Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements - Wu_2004_PLoS.Biol_2_E69
Author(s) : Wu M , Sun LV , Vamathevan J , Riegler M , Deboy R , Brownlie JC , McGraw EA , Martin W , Esser C , Ahmadinejad N , Wiegand C , Madupu R , Beanan MJ , Brinkac LM , Daugherty SC , Durkin AS , Kolonay JF , Nelson WC , Mohamoud Y , Lee P , Berry K , Young MB , Utterback T , Weidman J , Nierman WC , Paulsen IT , Nelson KE , Tettelin H , O'Neill SL , Eisen JA
Ref : PLoS Biol , 2 :E69 , 2004
Abstract : The complete sequence of the 1,267,782 bp genome of Wolbachia pipientis wMel, an obligate intracellular bacteria of Drosophila melanogaster, has been determined. Wolbachia, which are found in a variety of invertebrate species, are of great interest due to their diverse interactions with different hosts, which range from many forms of reproductive parasitism to mutualistic symbioses. Analysis of the wMel genome, in particular phylogenomic comparisons with other intracellular bacteria, has revealed many insights into the biology and evolution of wMel and Wolbachia in general. For example, the wMel genome is unique among sequenced obligate intracellular species in both being highly streamlined and containing very high levels of repetitive DNA and mobile DNA elements. This observation, coupled with multiple evolutionary reconstructions, suggests that natural selection is somewhat inefficient in wMel, most likely owing to the occurrence of repeated population bottlenecks. Genome analysis predicts many metabolic differences with the closely related Rickettsia species, including the presence of intact glycolysis and purine synthesis, which may compensate for an inability to obtain ATP directly from its host, as Rickettsia can. Other discoveries include the apparent inability of wMel to synthesize lipopolysaccharide and the presence of the most genes encoding proteins with ankyrin repeat domains of any prokaryotic genome yet sequenced. Despite the ability of wMel to infect the germline of its host, we find no evidence for either recent lateral gene transfer between wMel and D. melanogaster or older transfers between Wolbachia and any host. Evolutionary analysis further supports the hypothesis that mitochondria share a common ancestor with the alpha-Proteobacteria, but shows little support for the grouping of mitochondria with species in the order Rickettsiales. With the availability of the complete genomes of both species and excellent genetic tools for the host, the wMel-D. melanogaster symbiosis is now an ideal system for studying the biology and evolution of Wolbachia infections.
ESTHER : Wu_2004_PLoS.Biol_2_E69
PubMedSearch : Wu_2004_PLoS.Biol_2_E69
PubMedID: 15024419
Gene_locus related to this paper: wolpm-q73gf0 , wolpm-q73gx7

Title : Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes - Seshadri_2004_Proc.Natl.Acad.Sci.U.S.A_101_5646
Author(s) : Seshadri R , Myers GS , Tettelin H , Eisen JA , Heidelberg JF , Dodson RJ , Davidsen TM , DeBoy RT , Fouts DE , Haft DH , Selengut J , Ren Q , Brinkac LM , Madupu R , Kolonay J , Durkin SA , Daugherty SC , Shetty J , Shvartsbeyn A , Gebregeorgis E , Geer K , Tsegaye G , Malek J , Ayodeji B , Shatsman S , McLeod MP , Smajs D , Howell JK , Pal S , Amin A , Vashisth P , McNeill TZ , Xiang Q , Sodergren E , Baca E , Weinstock GM , Norris SJ , Fraser CM , Paulsen IT
Ref : Proc Natl Acad Sci U S A , 101 :5646 , 2004
Abstract : We present the complete 2,843,201-bp genome sequence of Treponema denticola (ATCC 35405) an oral spirochete associated with periodontal disease. Analysis of the T. denticola genome reveals factors mediating coaggregation, cell signaling, stress protection, and other competitive and cooperative measures, consistent with its pathogenic nature and lifestyle within the mixed-species environment of subgingival dental plaque. Comparisons with previously sequenced spirochete genomes revealed specific factors contributing to differences and similarities in spirochete physiology as well as pathogenic potential. The T. denticola genome is considerably larger in size than the genome of the related syphilis-causing spirochete Treponema pallidum. The differences in gene content appear to be attributable to a combination of three phenomena: genome reduction, lineage-specific expansions, and horizontal gene transfer. Genes lost due to reductive evolution appear to be largely involved in metabolism and transport, whereas some of the genes that have arisen due to lineage-specific expansions are implicated in various pathogenic interactions, and genes acquired via horizontal gene transfer are largely phage-related or of unknown function.
ESTHER : Seshadri_2004_Proc.Natl.Acad.Sci.U.S.A_101_5646
PubMedSearch : Seshadri_2004_Proc.Natl.Acad.Sci.U.S.A_101_5646
PubMedID: 15064399
Gene_locus related to this paper: trede-q73j01 , trede-q73kf5 , trede-q73kp3 , trede-q73ks1 , trede-q73nf8 , trede-q73qt5 , trede-q73qv0 , trede-q73ra4 , trede-q73ri8 , trede-Q93EK3 , trede-TDE0521

Title : Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath) - Ward_2004_PLoS.Biol_2_e303
Author(s) : Ward N , Larsen O , Sakwa J , Bruseth L , Khouri H , Durkin AS , Dimitrov G , Jiang L , Scanlan D , Kang KH , Lewis M , Nelson KE , Methe B , Wu M , Heidelberg JF , Paulsen IT , Fouts D , Ravel J , Tettelin H , Ren Q , Read T , DeBoy RT , Seshadri R , Salzberg SL , Jensen HB , Birkeland NK , Nelson WC , Dodson RJ , Grindhaug SH , Holt I , Eidhammer I , Jonasen I , Vanaken S , Utterback T , Feldblyum TV , Fraser CM , Lillehaug JR , Eisen JA
Ref : PLoS Biol , 2 :e303 , 2004
Abstract : Methanotrophs are ubiquitous bacteria that can use the greenhouse gas methane as a sole carbon and energy source for growth, thus playing major roles in global carbon cycles, and in particular, substantially reducing emissions of biologically generated methane to the atmosphere. Despite their importance, and in contrast to organisms that play roles in other major parts of the carbon cycle such as photosynthesis, no genome-level studies have been published on the biology of methanotrophs. We report the first complete genome sequence to our knowledge from an obligate methanotroph, Methylococcus capsulatus (Bath), obtained by the shotgun sequencing approach. Analysis revealed a 3.3-Mb genome highly specialized for a methanotrophic lifestyle, including redundant pathways predicted to be involved in methanotrophy and duplicated genes for essential enzymes such as the methane monooxygenases. We used phylogenomic analysis, gene order information, and comparative analysis with the partially sequenced methylotroph Methylobacterium extorquens to detect genes of unknown function likely to be involved in methanotrophy and methylotrophy. Genome analysis suggests the ability of M. capsulatus to scavenge copper (including a previously unreported nonribosomal peptide synthetase) and to use copper in regulation of methanotrophy, but the exact regulatory mechanisms remain unclear. One of the most surprising outcomes of the project is evidence suggesting the existence of previously unsuspected metabolic flexibility in M. capsulatus, including an ability to grow on sugars, oxidize chemolithotrophic hydrogen and sulfur, and live under reduced oxygen tension, all of which have implications for methanotroph ecology. The availability of the complete genome of M. capsulatus (Bath) deepens our understanding of methanotroph biology and its relationship to global carbon cycles. We have gained evidence for greater metabolic flexibility than was previously known, and for genetic components that may have biotechnological potential.
ESTHER : Ward_2004_PLoS.Biol_2_e303
PubMedSearch : Ward_2004_PLoS.Biol_2_e303
PubMedID: 15383840
Gene_locus related to this paper: metca-q60a38 , metca-q60bu6 , metca-q60cn0 , metca-q605j8 , metca-q606x9 , metca-q607f7 , metca-q607m2 , metca-q609v0

Title : The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria - Read_2003_Nature_423_81
Author(s) : Read TD , Peterson SN , Tourasse N , Baillie LW , Paulsen IT , Nelson KE , Tettelin H , Fouts DE , Eisen JA , Gill SR , Holtzapple EK , Okstad OA , Helgason E , Rilstone J , Wu M , Kolonay JF , Beanan MJ , Dodson RJ , Brinkac LM , Gwinn M , DeBoy RT , Madpu R , Daugherty SC , Durkin AS , Haft DH , Nelson WC , Peterson JD , Pop M , Khouri HM , Radune D , Benton JL , Mahamoud Y , Jiang L , Hance IR , Weidman JF , Berry KJ , Plaut RD , Wolf AM , Watkins KL , Nierman WC , Hazen A , Cline R , Redmond C , Thwaite JE , White O , Salzberg SL , Thomason B , Friedlander AM , Koehler TM , Hanna PC , Kolsto AB , Fraser CM
Ref : Nature , 423 :81 , 2003
Abstract : Bacillus anthracis is an endospore-forming bacterium that causes inhalational anthrax. Key virulence genes are found on plasmids (extra-chromosomal, circular, double-stranded DNA molecules) pXO1 (ref. 2) and pXO2 (ref. 3). To identify additional genes that might contribute to virulence, we analysed the complete sequence of the chromosome of B. anthracis Ames (about 5.23 megabases). We found several chromosomally encoded proteins that may contribute to pathogenicity--including haemolysins, phospholipases and iron acquisition functions--and identified numerous surface proteins that might be important targets for vaccines and drugs. Almost all these putative chromosomal virulence and surface proteins have homologues in Bacillus cereus, highlighting the similarity of B. anthracis to near-neighbours that are not associated with anthrax. By performing a comparative genome hybridization of 19 B. cereus and Bacillus thuringiensis strains against a B. anthracis DNA microarray, we confirmed the general similarity of chromosomal genes among this group of close relatives. However, we found that the gene sequences of pXO1 and pXO2 were more variable between strains, suggesting plasmid mobility in the group. The complete sequence of B. anthracis is a step towards a better understanding of anthrax pathogenesis.
ESTHER : Read_2003_Nature_423_81
PubMedSearch : Read_2003_Nature_423_81
PubMedID: 12721629
Gene_locus related to this paper: bacan-BA0160 , bacan-BA0950 , bacan-BA0954 , bacan-BA1019 , bacan-BA1242 , bacan-BA1727 , bacan-BA1747 , bacan-BA1866 , bacan-BA1914 , bacan-BA2015 , bacan-BA2392 , bacan-BA2417 , bacan-BA2557 , bacan-BA2607 , bacan-BA2687 , bacan-BA2694 , bacan-BA2738 , bacan-BA2865 , bacan-BA3068 , bacan-BA3165 , bacan-BA3178 , bacan-BA3187 , bacan-BA3343 , bacan-BA3372 , bacan-BA3703 , bacan-BA3805 , bacan-BA3863 , bacan-BA3877 , bacan-BA3887 , bacan-BA4324 , bacan-BA4328 , bacan-BA4338 , bacan-BA4577 , bacan-BA4983 , bacan-BA5009 , bacan-BA5110 , bacan-BA5136 , bacan-DHBF , bacan-q81tt2 , bacce-BC0192 , bacce-BC1788 , bacce-BC1954 , bacce-BC2141 , bacce-BC2171 , bacce-BC4730 , bacce-BC4862 , bacce-BC5130 , bacce-PHAC , bacce-q72yu1 , baccr-pepx

Title : Genome of Geobacter sulfurreducens: metal reduction in subsurface environments - Methe_2003_Science_302_1967
Author(s) : Methe BA , Nelson KE , Eisen JA , Paulsen IT , Nelson W , Heidelberg JF , Wu D , Wu M , Ward N , Beanan MJ , Dodson RJ , Madupu R , Brinkac LM , Daugherty SC , DeBoy RT , Durkin AS , Gwinn M , Kolonay JF , Sullivan SA , Haft DH , Selengut J , Davidsen TM , Zafar N , White O , Tran B , Romero C , Forberger HA , Weidman J , Khouri H , Feldblyum TV , Utterback TR , Van Aken SE , Lovley DR , Fraser CM
Ref : Science , 302 :1967 , 2003
Abstract : The complete genome sequence of Geobacter sulfurreducens, a delta-proteobacterium, reveals unsuspected capabilities, including evidence of aerobic metabolism, one-carbon and complex carbon metabolism, motility, and chemotactic behavior. These characteristics, coupled with the possession of many two-component sensors and many c-type cytochromes, reveal an ability to create alternative, redundant, electron transport networks and offer insights into the process of metal ion reduction in subsurface environments. As well as playing roles in the global cycling of metals and carbon, this organism clearly has the potential for use in bioremediation of radioactive metals and in the generation of electricity.
ESTHER : Methe_2003_Science_302_1967
PubMedSearch : Methe_2003_Science_302_1967
PubMedID: 14671304
Gene_locus related to this paper: geosl-q74a54 , geosl-q74ac8 , geosl-q74eb1 , geosl-q747u4 , geosl-q747v8 , geosl-q749w4

Title : Complete genome sequence of the oral pathogenic Bacterium porphyromonas gingivalis strain W83 - Nelson_2003_J.Bacteriol_185_5591
Author(s) : Nelson KE , Fleischmann RD , DeBoy RT , Paulsen IT , Fouts DE , Eisen JA , Daugherty SC , Dodson RJ , Durkin AS , Gwinn M , Haft DH , Kolonay JF , Nelson WC , Mason T , Tallon L , Gray J , Granger D , Tettelin H , Dong H , Galvin JL , Duncan MJ , Dewhirst FE , Fraser CM
Ref : Journal of Bacteriology , 185 :5591 , 2003
Abstract : The complete 2,343,479-bp genome sequence of the gram-negative, pathogenic oral bacterium Porphyromonas gingivalis strain W83, a major contributor to periodontal disease, was determined. Whole-genome comparative analysis with other available complete genome sequences confirms the close relationship between the Cytophaga-Flavobacteria-Bacteroides (CFB) phylum and the green-sulfur bacteria. Within the CFB phyla, the genomes most similar to that of P. gingivalis are those of Bacteroides thetaiotaomicron and B. fragilis. Outside of the CFB phyla the most similar genome to P. gingivalis is that of Chlorobium tepidum, supporting the previous phylogenetic studies that indicated that the Chlorobia and CFB phyla are related, albeit distantly. Genome analysis of strain W83 reveals a range of pathways and virulence determinants that relate to the novel biology of this oral pathogen. Among these determinants are at least six putative hemagglutinin-like genes and 36 previously unidentified peptidases. Genome analysis also reveals that P. gingivalis can metabolize a range of amino acids and generate a number of metabolic end products that are toxic to the human host or human gingival tissue and contribute to the development of periodontal disease.
ESTHER : Nelson_2003_J.Bacteriol_185_5591
PubMedSearch : Nelson_2003_J.Bacteriol_185_5591
PubMedID: 12949112
Gene_locus related to this paper: 9gamm-q4a538 , porgi-DPP , porgi-q7mtk3 , porgi-q7mu18 , porgi-q7mub3 , porgi-q7muw6 , porgi-q7mvp4 , porgi-q7mwa7 , porgi-q7mx03

Title : Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis - Paulsen_2003_Science_299_2071
Author(s) : Paulsen IT , Banerjei L , Myers GS , Nelson KE , Seshadri R , Read TD , Fouts DE , Eisen JA , Gill SR , Heidelberg JF , Tettelin H , Dodson RJ , Umayam L , Brinkac L , Beanan M , Daugherty S , DeBoy RT , Durkin S , Kolonay J , Madupu R , Nelson W , Vamathevan J , Tran B , Upton J , Hansen T , Shetty J , Khouri H , Utterback T , Radune D , Ketchum KA , Dougherty BA , Fraser CM
Ref : Science , 299 :2071 , 2003
Abstract : The complete genome sequence of Enterococcus faecalis V583, a vancomycin-resistant clinical isolate, revealed that more than a quarter of the genome consists of probable mobile or foreign DNA. One of the predicted mobile elements is a previously unknown vanB vancomycin-resistance conjugative transposon. Three plasmids were identified, including two pheromone-sensing conjugative plasmids, one encoding a previously undescribed pheromone inhibitor. The apparent propensity for the incorporation of mobile elements probably contributed to the rapid acquisition and dissemination of drug resistance in the enterococci.
ESTHER : Paulsen_2003_Science_299_2071
PubMedSearch : Paulsen_2003_Science_299_2071
PubMedID: 12663927
Gene_locus related to this paper: entfa-EF0101 , entfa-EF0274 , entfa-EF0381 , entfa-EF0449 , entfa-EF0667 , entfa-EF0786 , entfa-EF1028 , entfa-EF1236 , entfa-EF1505 , entfa-EF1536 , entfa-EF1670 , entfa-EF2618 , entfa-EF2728 , entfa-EF2792 , entfa-EF2963 , entfa-EF3191

Title : Complete genome sequence of the Q-fever pathogen Coxiella burnetii - Seshadri_2003_Proc.Natl.Acad.Sci.U.S.A_100_5455
Author(s) : Seshadri R , Paulsen IT , Eisen JA , Read TD , Nelson KE , Nelson WC , Ward NL , Tettelin H , Davidsen TM , Beanan MJ , DeBoy RT , Daugherty SC , Brinkac LM , Madupu R , Dodson RJ , Khouri HM , Lee KH , Carty HA , Scanlan D , Heinzen RA , Thompson HA , Samuel JE , Fraser CM , Heidelberg JF
Ref : Proc Natl Acad Sci U S A , 100 :5455 , 2003
Abstract : The 1,995,275-bp genome of Coxiella burnetii, Nine Mile phase I RSA493, a highly virulent zoonotic pathogen and category B bioterrorism agent, was sequenced by the random shotgun method. This bacterium is an obligate intracellular acidophile that is highly adapted for life within the eukaryotic phagolysosome. Genome analysis revealed many genes with potential roles in adhesion, invasion, intracellular trafficking, host-cell modulation, and detoxification. A previously uncharacterized 13-member family of ankyrin repeat-containing proteins is implicated in the pathogenesis of this organism. Although the lifestyle and parasitic strategies of C. burnetii resemble that of Rickettsiae and Chlamydiae, their genome architectures differ considerably in terms of presence of mobile elements, extent of genome reduction, metabolic capabilities, and transporter profiles. The presence of 83 pseudogenes displays an ongoing process of gene degradation. Unlike other obligate intracellular bacteria, 32 insertion sequences are found dispersed in the chromosome, indicating some plasticity in the C. burnetii genome. These analyses suggest that the obligate intracellular lifestyle of C. burnetii may be a relatively recent innovation.
ESTHER : Seshadri_2003_Proc.Natl.Acad.Sci.U.S.A_100_5455
PubMedSearch : Seshadri_2003_Proc.Natl.Acad.Sci.U.S.A_100_5455
PubMedID: 12704232
Gene_locus related to this paper: coxbu-BIOH , coxbu-CBU0752 , coxbu-CBU1119 , coxbu-CBU1225 , coxbu-CBU1529 , coxbu-CBU1769 , coxbu-CBU1975

Title : The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts - Paulsen_2002_Proc.Natl.Acad.Sci.U.S.A_99_13148
Author(s) : Paulsen IT , Seshadri R , Nelson KE ,