Saunders E

References (32)

Title : Complete genome sequence of Parvibaculum lavamentivorans type strain (DS-1(T)) - Schleheck_2011_Stand.Genomic.Sci_5_298
Author(s) : Schleheck D , Weiss M , Pitluck S , Bruce D , Land ML , Han S , Saunders E , Tapia R , Detter C , Brettin T , Han J , Woyke T , Goodwin L , Pennacchio L , Nolan M , Cook AM , Kjelleberg S , Thomas T
Ref : Stand Genomic Sci , 5 :298 , 2011
Abstract : Parvibaculum lavamentivorans DS-1(T) is the type species of the novel genus Parvibaculum in the novel family Rhodobiaceae (formerly Phyllobacteriaceae) of the order Rhizobiales of Alphaproteobacteria. Strain DS-1(T) is a non-pigmented, aerobic, heterotrophic bacterium and represents the first tier member of environmentally important bacterial communities that catalyze the complete degradation of synthetic laundry surfactants. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,914,745 bp long genome with its predicted 3,654 protein coding genes is the first completed genome sequence of the genus Parvibaculum, and the first genome sequence of a representative of the family Rhodobiaceae.
ESTHER : Schleheck_2011_Stand.Genomic.Sci_5_298
PubMedSearch : Schleheck_2011_Stand.Genomic.Sci_5_298
PubMedID: 22675581
Gene_locus related to this paper: parl1-a7hy87

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 : 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 : Genome sequence of the ethanol-producing Zymomonas mobilis subsp. mobilis lectotype strain ATCC 10988 - Pappas_2011_J.Bacteriol_193_5051
Author(s) : Pappas KM , Kouvelis VN , Saunders E , Brettin TS , Bruce D , Detter C , Balakireva M , Han CS , Savvakis G , Kyrpides NC , Typas MA
Ref : Journal of Bacteriology , 193 :5051 , 2011
Abstract : Zymomonas mobilis ATCC 10988 is the type strain of the Z. mobilis subsp. mobilis taxon, members of which are some of the most rigorous ethanol-producing bacteria. Isolated from Agave cactus fermentations in Mexico, ATCC 10988 is one of the first Z. mobilis strains to be described and studied. Its robustness in sucrose-substrate fermentations, physiological characteristics, large number of plasmids, and overall genomic plasticity render this strain important to the study of the species. Here we report the finishing and annotation of the ATCC 10988 chromosomal and plasmid genome.
ESTHER : Pappas_2011_J.Bacteriol_193_5051
PubMedSearch : Pappas_2011_J.Bacteriol_193_5051
PubMedID: 21725006
Gene_locus related to this paper: zymmo-q5nmh0 , zymma-a0a0h3g4v2

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 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 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 : Genome sequence of the dioxin-mineralizing bacterium Sphingomonas wittichii RW1 - Miller_2010_J.Bacteriol_192_6101
Author(s) : Miller TR , Delcher AL , Salzberg SL , Saunders E , Detter JC , Halden RU
Ref : Journal of Bacteriology , 192 :6101 , 2010
Abstract : Pollutants such as polychlorinated biphenyls and dioxins pose a serious threat to human and environmental health. Natural attenuation of these compounds by microorganisms provides one promising avenue for their removal from contaminated areas. Over the past 2 decades, studies of the bacterium Sphingomonas wittichii RW1 have provided a wealth of knowledge about how bacteria metabolize chlorinated aromatic hydrocarbons. Here we describe the finished genome sequence of S. wittichii RW1 and major findings from its annotation.
ESTHER : Miller_2010_J.Bacteriol_192_6101
PubMedSearch : Miller_2010_J.Bacteriol_192_6101
PubMedID: 20833805
Gene_locus related to this paper: 9sphn-a0a0f5pa67 , sphww-a5ve07

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 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 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 : Comparative genomics of clinical and environmental Vibrio mimicus - Hasan_2010_Proc.Natl.Acad.Sci.U.S.A_107_21134
Author(s) : Hasan NA , Grim CJ , Haley BJ , Chun J , Alam M , Taviani E , Hoq M , Munk AC , Saunders E , Brettin TS , Bruce DC , Challacombe JF , Detter JC , Han CS , Xie G , Nair GB , Huq A , Colwell RR
Ref : Proc Natl Acad Sci U S A , 107 :21134 , 2010
Abstract : Whether Vibrio mimicus is a variant of Vibrio cholerae or a separate species has been the subject of taxonomic controversy. A genomic analysis was undertaken to resolve the issue. The genomes of V. mimicus MB451, a clinical isolate, and VM223, an environmental isolate, comprise ca. 4,347,971 and 4,313,453 bp and encode 3,802 and 3,290 ORFs, respectively. As in other vibrios, chromosome I (C-I) predominantly contains genes necessary for growth and viability, whereas chromosome II (C-II) bears genes for adaptation to environmental change. C-I harbors many virulence genes, including some not previously reported in V. mimicus, such as mannose-sensitive hemagglutinin (MSHA), and enterotoxigenic hemolysin (HlyA); C-II encodes a variant of Vibrio pathogenicity island 2 (VPI-2), and Vibrio seventh pandemic island II (VSP-II) cluster of genes. Extensive genomic rearrangement in C-II indicates it is a hot spot for evolution and genesis of speciation for the genus Vibrio. The number of virulence regions discovered in this study (VSP-II, MSHA, HlyA, type IV pilin, PilE, and integron integrase, IntI4) with no notable difference in potential virulence genes between clinical and environmental strains suggests these genes also may play a role in the environment and that pathogenic strains may arise in the environment. Significant genome synteny with prototypic pre-seventh pandemic strains of V. cholerae was observed, and the results of phylogenetic analysis support the hypothesis that, in the course of evolution, V. mimicus and V. cholerae diverged from a common ancestor with a prototypic sixth pandemic genomic backbone.
ESTHER : Hasan_2010_Proc.Natl.Acad.Sci.U.S.A_107_21134
PubMedSearch : Hasan_2010_Proc.Natl.Acad.Sci.U.S.A_107_21134
PubMedID: 21078967
Gene_locus related to this paper: vibch-VC2610 , vibch-VC2718 , vibch-VCA0688 , vibch-y1892 , vibch-y2276 , vibmi-d0gt41 , vibmi-u4zh77

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 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 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 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 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 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 : Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens - Silby_2009_Genome.Biol_10_R51
Author(s) : Silby MW , Cerdeno-Tarraga AM , Vernikos GS , Giddens SR , Jackson RW , Preston GM , Zhang XX , Moon CD , Gehrig SM , Godfrey SA , Knight CG , Malone JG , Robinson Z , Spiers AJ , Harris S , Challis GL , Yaxley AM , Harris D , Seeger K , Murphy L , Rutter S , Squares R , Quail MA , Saunders E , Mavromatis K , Brettin TS , Bentley SD , Hothersall J , Stephens E , Thomas CM , Parkhill J , Levy SB , Rainey PB , Thomson NR
Ref : Genome Biol , 10 :R51 , 2009
Abstract : BACKGROUND: Pseudomonas fluorescens are common soil bacteria that can improve plant health through nutrient cycling, pathogen antagonism and induction of plant defenses. The genome sequences of strains SBW25 and Pf0-1 were determined and compared to each other and with P. fluorescens Pf-5. A functional genomic in vivo expression technology (IVET) screen provided insight into genes used by P. fluorescens in its natural environment and an improved understanding of the ecological significance of diversity within this species. RESULTS: Comparisons of three P. fluorescens genomes (SBW25, Pf0-1, Pf-5) revealed considerable divergence: 61% of genes are shared, the majority located near the replication origin. Phylogenetic and average amino acid identity analyses showed a low overall relationship. A functional screen of SBW25 defined 125 plant-induced genes including a range of functions specific to the plant environment. Orthologues of 83 of these exist in Pf0-1 and Pf-5, with 73 shared by both strains. The P. fluorescens genomes carry numerous complex repetitive DNA sequences, some resembling Miniature Inverted-repeat Transposable Elements (MITEs). In SBW25, repeat density and distribution revealed 'repeat deserts' lacking repeats, covering approximately 40% of the genome. CONCLUSIONS: P. fluorescens genomes are highly diverse. Strain-specific regions around the replication terminus suggest genome compartmentalization. The genomic heterogeneity among the three strains is reminiscent of a species complex rather than a single species. That 42% of plant-inducible genes were not shared by all strains reinforces this conclusion and shows that ecological success requires specialized and core functions. The diversity also indicates the significant size of genetic information within the Pseudomonas pan genome.
ESTHER : Silby_2009_Genome.Biol_10_R51
PubMedSearch : Silby_2009_Genome.Biol_10_R51
PubMedID: 19432983
Gene_locus related to this paper: psef5-metx , psefl-este , psefs-c3jz63 , psefs-c3jzq8 , psefs-c3k1v7 , psefs-c3k3d6 , psefs-c3k3m8 , psefs-c3k3s9 , psefs-c3k5q5 , psefs-c3k6c6 , psefs-c3k7v4 , psefs-c3k8m7 , psefs-c3k8y7 , psefs-c3k9z2 , psefs-c3k032 , psefs-c3k320 , psefs-c3k362 , psefs-c3k632 , psefs-c3k927 , psefs-c3kan9 , psefs-c3kbe5 , psefs-c3kdh9 , psefs-c3ke34 , psefs-laaa , psepf-q3k5t9 , psepf-q3k6f3 , psepf-q3k524 , psepf-q3kcu9 , psepf-q3kd07 , psepf-q3kf33 , psepf-q3kh87 , psefs-c3jxp6 , psepf-q3kf85 , psefs-c3k813 , psefs-c3keb8 , psefl-e2xkc8 , psefs-c3k9x6

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 : Comparative genomics reveals mechanism for short-term and long-term clonal transitions in pandemic Vibrio cholerae - Chun_2009_Proc.Natl.Acad.Sci.U.S.A_106_15442
Author(s) : Chun J , Grim CJ , Hasan NA , Lee JH , Choi SY , Haley BJ , Taviani E , Jeon YS , Kim DW , Brettin TS , Bruce DC , Challacombe JF , Detter JC , Han CS , Munk AC , Chertkov O , Meincke L , Saunders E , Walters RA , Huq A , Nair GB , Colwell RR
Ref : Proc Natl Acad Sci U S A , 106 :15442 , 2009
Abstract : Vibrio cholerae, the causative agent of cholera, is a bacterium autochthonous to the aquatic environment, and a serious public health threat. V. cholerae serogroup O1 is responsible for the previous two cholera pandemics, in which classical and El Tor biotypes were dominant in the sixth and the current seventh pandemics, respectively. Cholera researchers continually face newly emerging and reemerging pathogenic clones carrying diverse combinations of phenotypic and genotypic properties, which significantly hampered control of the disease. To elucidate evolutionary mechanisms governing genetic diversity of pandemic V. cholerae, we compared the genome sequences of 23 V. cholerae strains isolated from a variety of sources over the past 98 years. The genome-based phylogeny revealed 12 distinct V. cholerae lineages, of which one comprises both O1 classical and El Tor biotypes. All seventh pandemic clones share nearly identical gene content. Using analogy to influenza virology, we define the transition from sixth to seventh pandemic strains as a "shift" between pathogenic clones belonging to the same O1 serogroup, but from significantly different phyletic lineages. In contrast, transition among clones during the present pandemic period is characterized as a "drift" between clones, differentiated mainly by varying composition of laterally transferred genomic islands, resulting in emergence of variants, exemplified by V. cholerae O139 and V. cholerae O1 El Tor hybrid clones. Based on the comparative genomics it is concluded that V. cholerae undergoes extensive genetic recombination via lateral gene transfer, and, therefore, genome assortment, not serogroup, should be used to define pathogenic V. cholerae clones.
ESTHER : Chun_2009_Proc.Natl.Acad.Sci.U.S.A_106_15442
PubMedSearch : Chun_2009_Proc.Natl.Acad.Sci.U.S.A_106_15442
PubMedID: 19720995
Gene_locus related to this paper: vibch-lipas , vibch-VC0135 , vibch-VC1418 , vibch-VC1974 , vibch-VC2432 , vibch-VC2718 , vibch-VCA0063 , vibch-VCA0490 , vibch-VCA0688 , vibch-VCA0754 , vibch-y1892 , vibch-y2276

Title : Complete genome sequence of the ethanol producer Zymomonas mobilis NCIMB 11163 - Kouvelis_2009_J.Bacteriol_191_7140
Author(s) : Kouvelis VN , Saunders E , Brettin TS , Bruce D , Detter C , Han C , Typas MA , Pappas KM
Ref : Journal of Bacteriology , 191 :7140 , 2009
Abstract : Zymomonas mobilis is an ethanol-producing alphaproteobacterium currently considered a major candidate organism for bioethanol production. Here we report the finished and annotated genome sequence of Z. mobilis subsp. mobilis strain NCIMB 11163, a British ale-infecting isolate. This is the first Z. mobilis strain whose genome, chromosomal and plasmid, is presented in its entirety.
ESTHER : Kouvelis_2009_J.Bacteriol_191_7140
PubMedSearch : Kouvelis_2009_J.Bacteriol_191_7140
PubMedID: 19767433
Gene_locus related to this paper: zymmo-DLH , zymmo-GAA , zymmo-q5nmh0 , zymmo-q5nmm8 , zymmo-Q8GF33 , zymmo-Q8GF53

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 Methanoculleus marisnigri Romesser et al. 1981 type strain JR1 - Anderson_2009_Stand.Genomic.Sci_1_189
Author(s) : Anderson IJ , Sieprawska-Lupa M , Lapidus A , Nolan M , Copeland A , Glavina Del Rio T , Tice H , Dalin E , Barry K , Saunders E , Han C , Brettin T , Detter JC , Bruce D , Mikhailova N , Pitluck S , Hauser L , Land M , Lucas S , Richardson P , Whitman WB , Kyrpides NC
Ref : Stand Genomic Sci , 1 :189 , 2009
Abstract : Methanoculleus marisnigri Romesser et al. 1981 is a methanogen belonging to the order Methanomicrobiales within the archaeal phylum Euryarchaeota. The type strain, JR1, was isolated from anoxic sediments of the Black Sea. M. marisnigri is of phylogenetic interest because at the time the sequencing project began only one genome had previously been sequenced from the order Methanomicrobiales. We report here the complete genome sequence of M. marisnigri type strain JR1 and its annotation. This is part of a Joint Genome Institute 2006 Community Sequencing Program to sequence genomes of diverse Archaea.
ESTHER : Anderson_2009_Stand.Genomic.Sci_1_189
PubMedSearch : Anderson_2009_Stand.Genomic.Sci_1_189
PubMedID: 21304656

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 : The complete genome sequence of Bacillus thuringiensis Al Hakam - Challacombe_2007_J.Bacteriol_189_3680
Author(s) : Challacombe JF , Altherr MR , Xie G , Bhotika SS , Brown N , Bruce D , Campbell CS , Campbell ML , Chen J , Chertkov O , Cleland C , Dimitrijevic M , Doggett NA , Fawcett JJ , Glavina T , Goodwin LA , Green LD , Han CS , Hill KK , Hitchcock P , Jackson PJ , Keim P , Kewalramani AR , Longmire J , Lucas S , Malfatti S , Martinez D , McMurry K , Meincke LJ , Misra M , Moseman BL , Mundt M , Munk AC , Okinaka RT , Parson-Quintana B , Reilly LP , Richardson P , Robinson DL , Saunders E , Tapia R , Tesmer JG , Thayer N , Thompson LS , Tice H , Ticknor LO , Wills PL , Gilna P , Brettin TS
Ref : Journal of Bacteriology , 189 :3680 , 2007
Abstract : Bacillus thuringiensis is an insect pathogen that is widely used as a biopesticide (E. Schnepf, N. Crickmore, J. Van Rie, D. Lereclus, J. Baum, J. Feitelson, D. R. Zeigler, and D. H. Dean, Microbiol. Mol. Biol. Rev. 62:775-806, 1998). Here we report the finished, annotated genome sequence of B. thuringiensis Al Hakam, which was collected in Iraq by the United Nations Special Commission (L. Radnedge, P. Agron, K. Hill, P. Jackson, L. Ticknor, P. Keim, and G. Andersen, Appl. Environ. Microbiol. 69:2755-2764, 2003).
ESTHER : Challacombe_2007_J.Bacteriol_189_3680
PubMedSearch : Challacombe_2007_J.Bacteriol_189_3680
PubMedID: 17337577
Gene_locus related to this paper: bacah-a0rcd1 , bacah-a0rer5 , bacah-a0rev7 , bacan-BA1019 , bacan-BA1242 , bacan-BA2392 , bacan-BA2607 , bacan-BA3343 , bacan-BA3863 , bacan-BA3877 , bacan-BA4324 , bacan-BA4338 , bacan-BA4577 , bacan-BA5009 , bacan-BA5110 , bacan-BA5136 , bacan-DHBF , bacc1-q73a27 , bacc1-q73c93 , bacce-BC0192 , bacce-BC1788 , bacce-BC1954 , bacce-BC2141 , bacce-BC2171 , bacce-BC4730 , bacce-BC4862 , bacce-BC5130 , bacce-PHAC , bacce-q72yu1 , baccr-pepx , bachk-q6hcl3 , bachk-q6hgn4 , bachk-q6hgp9 , bachk-q6hig3 , bachk-q6hit8

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 : Legumes symbioses: absence of Nod genes in photosynthetic bradyrhizobia - Giraud_2007_Science_316_1307
Author(s) : Giraud E , Moulin L , Vallenet D , Barbe V , Cytryn E , Avarre JC , Jaubert M , Simon D , Cartieaux F , Prin Y , Bena G , Hannibal L , Fardoux J , Kojadinovic M , Vuillet L , Lajus A , Cruveiller S , Rouy Z , Mangenot S , Segurens B , Dossat C , Franck WL , Chang WS , Saunders E , Bruce D , Richardson P , Normand P , Dreyfus B , Pignol D , Stacey G , Emerich D , Vermeglio A , Medigue C , Sadowsky M
Ref : Science , 316 :1307 , 2007
Abstract : Leguminous plants (such as peas and soybeans) and rhizobial soil bacteria are symbiotic partners that communicate through molecular signaling pathways, resulting in the formation of nodules on legume roots and occasionally stems that house nitrogen-fixing bacteria. Nodule formation has been assumed to be exclusively initiated by the binding of bacterial, host-specific lipochito-oligosaccharidic Nod factors, encoded by the nodABC genes, to kinase-like receptors of the plant. Here we show by complete genome sequencing of two symbiotic, photosynthetic, Bradyrhizobium strains, BTAi1 and ORS278, that canonical nodABC genes and typical lipochito-oligosaccharidic Nod factors are not required for symbiosis in some legumes. Mutational analyses indicated that these unique rhizobia use an alternative pathway to initiate symbioses, where a purine derivative may play a key role in triggering nodule formation.
ESTHER : Giraud_2007_Science_316_1307
PubMedSearch : Giraud_2007_Science_316_1307
PubMedID: 17540897
Gene_locus related to this paper: brasb-a5e8s7 , brasb-a5e9h9 , brasb-a5e9x2 , brasb-a5eac3 , brasb-a5eb24 , brasb-a5ech6 , brasb-a5eck9 , brasb-a5ed44 , brasb-a5edz7 , brasb-a5ee62 , brasb-a5ees1 , brasb-a5ef53 , brasb-a5efp3 , brasb-a5efp4 , brasb-a5eg29 , brasb-a5eh09 , brasb-a5ei81 , brasb-a5eiy7 , brasb-a5ej26 , brasb-a5ek41 , brasb-a5elh0 , brasb-a5ema7 , brasb-a5emc8 , brasb-a5eml7 , brasb-a5ene5 , brasb-a5ent6 , brasb-a5eny8 , brasb-a5ep81 , brasb-a5eph8 , brasb-a5epv4 , brasb-a5epx9 , brasb-a5eqb3 , brasb-a5erc8 , brasb-a5esb1 , brasb-a5ese9 , brasb-a5esl7 , brasb-a5esv5 , brasb-a5esw6 , brasb-a5etk7 , brasb-a5eul1 , braso-a4yk16 , braso-a4yl66 , braso-a4ylm4 , braso-a4ylr9 , braso-a4ylx7 , braso-a4ymj8 , braso-a4ynl1 , braso-a4ypd9 , braso-a4yqh3 , braso-a4yr10 , braso-a4yri0 , braso-a4yt56 , braso-a4yul4 , braso-a4yw76 , braso-a4ywb6 , braso-a4yxg2 , braso-a4yy49 , braso-a4yyj6 , braso-a4yzd7 , braso-a4yzh0 , braso-a4z0q9 , braso-a4z0v7 , braso-a4z1h1 , braso-a4z1p1 , braso-a4z1p8 , braso-a4z1v6 , braso-a4z2a5 , braso-a4z152 , braso-a4yl32 , brasb-a5et63 , brasb-a5emr8 , braso-a4ynl2 , brasb-a5eqb2 , braso-a4yr63

Title : Pathogenomic sequence analysis of Bacillus cereus and Bacillus thuringiensis isolates closely related to Bacillus anthracis - Han_2006_J.Bacteriol_188_3382
Author(s) : Han CS , Xie G , Challacombe JF , Altherr MR , Bhotika SS , Brown N , Bruce D , Campbell CS , Campbell ML , Chen J , Chertkov O , Cleland C , Dimitrijevic M , Doggett NA , Fawcett JJ , Glavina T , Goodwin LA , Green LD , Hill KK , Hitchcock P , Jackson PJ , Keim P , Kewalramani AR , Longmire J , Lucas S , Malfatti S , McMurry K , Meincke LJ , Misra M , Moseman BL , Mundt M , Munk AC , Okinaka RT , Parson-Quintana B , Reilly LP , Richardson P , Robinson DL , Rubin E , Saunders E , Tapia R , Tesmer JG , Thayer N , Thompson LS , Tice H , Ticknor LO , Wills PL , Brettin TS , Gilna P
Ref : Journal of Bacteriology , 188 :3382 , 2006
Abstract : Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis are closely related gram-positive, spore-forming bacteria of the B. cereus sensu lato group. While independently derived strains of B. anthracis reveal conspicuous sequence homogeneity, environmental isolates of B. cereus and B. thuringiensis exhibit extensive genetic diversity. Here we report the sequencing and comparative analysis of the genomes of two members of the B. cereus group, B. thuringiensis 97-27 subsp. konkukian serotype H34, isolated from a necrotic human wound, and B. cereus E33L, which was isolated from a swab of a zebra carcass in Namibia. These two strains, when analyzed by amplified fragment length polymorphism within a collection of over 300 of B. cereus, B. thuringiensis, and B. anthracis isolates, appear closely related to B. anthracis. The B. cereus E33L isolate appears to be the nearest relative to B. anthracis identified thus far. Whole-genome sequencing of B. thuringiensis 97-27and B. cereus E33L was undertaken to identify shared and unique genes among these isolates in comparison to the genomes of pathogenic strains B. anthracis Ames and B. cereus G9241 and nonpathogenic strains B. cereus ATCC 10987 and B. cereus ATCC 14579. Comparison of these genomes revealed differences in terms of virulence, metabolic competence, structural components, and regulatory mechanisms.
ESTHER : Han_2006_J.Bacteriol_188_3382
PubMedSearch : Han_2006_J.Bacteriol_188_3382
PubMedID: 16621833
Gene_locus related to this paper: bacan-BA0954 , bacan-BA2607 , bacce-BC0968 , bacce-BC3133 , bacce-BC5130 , bacce-c2mr40 , baccz-q63gk2

Title : The Methanosarcina barkeri genome: comparative analysis with Methanosarcina acetivorans and Methanosarcina mazei reveals extensive rearrangement within methanosarcinal genomes - Maeder_2006_J.Bacteriol_188_7922
Author(s) : Maeder DL , Anderson I , Brettin TS , Bruce DC , Gilna P , Han CS , Lapidus A , Metcalf WW , Saunders E , Tapia R , Sowers KR
Ref : Journal of Bacteriology , 188 :7922 , 2006
Abstract : We report here a comparative analysis of the genome sequence of Methanosarcina barkeri with those of Methanosarcina acetivorans and Methanosarcina mazei. The genome of M. barkeri is distinguished by having an organization that is well conserved with respect to the other Methanosarcina spp. in the region proximal to the origin of replication, with interspecies gene similarities as high as 95%. However, it is disordered and marked by increased transposase frequency and decreased gene synteny and gene density in the distal semigenome. Of the 3,680 open reading frames (ORFs) in M. barkeri, 746 had homologs with better than 80% identity to both M. acetivorans and M. mazei, while 128 nonhypothetical ORFs were unique (nonorthologous) among these species, including a complete formate dehydrogenase operon, genes required for N-acetylmuramic acid synthesis, a 14-gene gas vesicle cluster, and a bacterial-like P450-specific ferredoxin reductase cluster not previously observed or characterized for this genus. A cryptic 36-kbp plasmid sequence that contains an orc1 gene flanked by a presumptive origin of replication consisting of 38 tandem repeats of a 143-nucleotide motif was detected in M. barkeri. Three-way comparison of these genomes reveals differing mechanisms for the accrual of changes. Elongation of the relatively large M. acetivorans genome is the result of uniformly distributed multiple gene scale insertions and duplications, while the M. barkeri genome is characterized by localized inversions associated with the loss of gene content. In contrast, the short M. mazei genome most closely approximates the putative ancestral organizational state of these species.
ESTHER : Maeder_2006_J.Bacteriol_188_7922
PubMedSearch : Maeder_2006_J.Bacteriol_188_7922
PubMedID: 16980466
Gene_locus related to this paper: metbf-q46ca9 , metbf-q469u5