Ussery DW

References (7)

Title : The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium - Kroger_2012_Proc.Natl.Acad.Sci.U.S.A_109_E1277
Author(s) : Kroger C , Dillon SC , Cameron AD , Papenfort K , Sivasankaran SK , Hokamp K , Chao Y , Sittka A , Hebrard M , Handler K , Colgan A , Leekitcharoenphon P , Langridge GC , Lohan AJ , Loftus B , Lucchini S , Ussery DW , Dorman CJ , Thomson NR , Vogel J , Hinton JC
Ref : Proc Natl Acad Sci U S A , 109 :E1277 , 2012
Abstract : More than 50 y of research have provided great insight into the physiology, metabolism, and molecular biology of Salmonella enterica serovar Typhimurium (S. Typhimurium), but important gaps in our knowledge remain. It is clear that a precise choreography of gene expression is required for Salmonella infection, but basic genetic information such as the global locations of transcription start sites (TSSs) has been lacking. We combined three RNA-sequencing techniques and two sequencing platforms to generate a robust picture of transcription in S. Typhimurium. Differential RNA sequencing identified 1,873 TSSs on the chromosome of S. Typhimurium SL1344 and 13% of these TSSs initiated antisense transcripts. Unique findings include the TSSs of the virulence regulators phoP, slyA, and invF. Chromatin immunoprecipitation revealed that RNA polymerase was bound to 70% of the TSSs, and two-thirds of these TSSs were associated with sigma(70) (including phoP, slyA, and invF) from which we identified the -10 and -35 motifs of sigma(70)-dependent S. Typhimurium gene promoters. Overall, we corrected the location of important genes and discovered 18 times more promoters than identified previously. S. Typhimurium expresses 140 small regulatory RNAs (sRNAs) at early stationary phase, including 60 newly identified sRNAs. Almost half of the experimentally verified sRNAs were found to be unique to the Salmonella genus, and <20% were found throughout the Enterobacteriaceae. This description of the transcriptional map of SL1344 advances our understanding of S. Typhimurium, arguably the most important bacterial infection model.
ESTHER : Kroger_2012_Proc.Natl.Acad.Sci.U.S.A_109_E1277
PubMedSearch : Kroger_2012_Proc.Natl.Acad.Sci.U.S.A_109_E1277
PubMedID: 22538806

Title : Genome sequences of two stress-tolerant Campylobacter jejuni poultry strains, 305 and DFVF1099 - Takamiya_2011_J.Bacteriol_193_5546
Author(s) : Takamiya M , Ozen A , Rasmussen M , Alter T , Gilbert T , Ussery DW , Knochel S
Ref : Journal of Bacteriology , 193 :5546 , 2011
Abstract : Campylobacter jejuni is a food-borne pathogen with a high prevalence in poultry meat, which in fresh unfrozen condition is the major source of campylobacteriosis. C. jejuni strains DFVF1099 and 305 are considered tolerant to several environmental stresses (T. Birk et al., J. Food Prot. 73:258-265, 2010; S. L. On et al., Int. J. Med. Microbiol. 296:353-363, 2006). Here, we report the genome sequences of C. jejuni 305 and DFVF1099, a turkey and a chicken isolate, respectively.
ESTHER : Takamiya_2011_J.Bacteriol_193_5546
PubMedSearch : Takamiya_2011_J.Bacteriol_193_5546
PubMedID: 21914871
Gene_locus related to this paper: camco-e0qbj3 , camco-q4hhu5 , camjr-q5ht69 , camju-a3yll6 , camju-Q9ZF63

Title : Complete genome sequence of the commensal Enterococcus faecalis 62, isolated from a healthy Norwegian infant - Brede_2011_J.Bacteriol_193_2377
Author(s) : Brede DA , Snipen LG , Ussery DW , Nederbragt AJ , Nes IF
Ref : Journal of Bacteriology , 193 :2377 , 2011
Abstract : The genome of Enterococcus faecalis 62, a commensal isolate from a healthy Norwegian infant, revealed multiple adaptive traits to the gastrointestinal tract (GIT) environment and the milk-containing diet of breast-fed infants. Adaptation to a commensal existence was emphasized by lactose and other carbohydrate metabolism genes within genomic islands, accompanied by the absence of virulence traits.
ESTHER : Brede_2011_J.Bacteriol_193_2377
PubMedSearch : Brede_2011_J.Bacteriol_193_2377
PubMedID: 21398545
Gene_locus related to this paper: entfa-c7yea6 , entfa-EF0101 , entfa-EF0381 , entfa-EF0449 , entfa-EF0786 , entfa-EF1236 , entfa-EF1670 , entfa-EF2618 , entfa-EF2728 , entfa-EF2963 , entfa-EF3191 , entfa-q5j1l4 , entfl-e2z7d4

Title : Genome Sequence of Campylobacter jejuni strain 327, a strain isolated from a turkey slaughterhouse - Takamiya_2011_Stand.Genomic.Sci_4_113
Author(s) : Takamiya M , Ozen A , Rasmussen M , Alter T , Gilbert T , Ussery DW , Knochel S
Ref : Stand Genomic Sci , 4 :113 , 2011
Abstract : Campylobacter is one of the leading causes of food-borne gastroenteritis and has a high prevalence in poultry. Campylobacter jejuni subsp. jejuni 327 is a subspecies of the genus Campylobacter of the family Campylobacteraceae in the phylum Proteobacteria. The microaerophilic, spiral shaped, catalase positive bacterium obtains energy from the metabolism of amino acids and Krebs cycle intermediates. Strain 327 was isolated from a turkey slaughter production line and is considered environmentally sensitive to food processing (cold, heat, drying) and storage conditions. The 327 whole genome shotgun sequence of 1,618,613 bp long consists of 1,740 protein-coding genes, 46 tRNA genes and 3 rRNA operons. A protein based BLAST analysis places the turkey isolate 327 close to the human clinical strain 81116 (NCTC 11828).
ESTHER : Takamiya_2011_Stand.Genomic.Sci_4_113
PubMedSearch : Takamiya_2011_Stand.Genomic.Sci_4_113
PubMedID: 21677848
Gene_locus related to this paper: camjr-q5ht69

Title : Genomic characterization of Campylobacter jejuni strain M1 - Friis_2010_PLoS.One_5_e12253
Author(s) : Friis C , Wassenaar TM , Javed MA , Snipen L , Lagesen K , Hallin PF , Newell DG , Toszeghy M , Ridley A , Manning G , Ussery DW
Ref : PLoS ONE , 5 :e12253 , 2010
Abstract : Campylobacter jejuni strain M1 (laboratory designation 99/308) is a rarely documented case of direct transmission of C. jejuni from chicken to a person, resulting in enteritis. We have sequenced the genome of C. jejuni strain M1, and compared this to 12 other C. jejuni sequenced genomes currently publicly available. Compared to these, M1 is closest to strain 81116. Based on the 13 genome sequences, we have identified the C. jejuni pan-genome, as well as the core genome, the auxiliary genes, and genes unique between strains M1 and 81116. The pan-genome contains 2,427 gene families, whilst the core genome comprised 1,295 gene families, or about two-thirds of the gene content of the average of the sequenced C. jejuni genomes. Various comparison and visualization tools were applied to the 13 C. jejuni genome sequences, including a species pan- and core genome plot, a BLAST Matrix and a BLAST Atlas. Trees based on 16S rRNA sequences and on the total gene families in each genome are presented. The findings are discussed in the background of the proven virulence potential of M1.
ESTHER : Friis_2010_PLoS.One_5_e12253
PubMedSearch : Friis_2010_PLoS.One_5_e12253
PubMedID: 20865039
Gene_locus related to this paper: camjr-q5ht69

Title : Genomic taxonomy of Vibrios - Thompson_2009_BMC.Evol.Biol_9_258
Author(s) : Thompson CC , Vicente AC , Souza RC , Vasconcelos AT , Vesth T , Alves N, Jr. , Ussery DW , Iida T , Thompson FL
Ref : BMC Evol Biol , 9 :258 , 2009
Abstract : BACKGROUND: Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i.e. data that can be used to distinguish different taxonomic levels, such as species and genera) from 32 genome sequences of different vibrio species. We use a variety of tools to explore the taxonomic relationship between the sequenced genomes, including Multilocus Sequence Analysis (MLSA), supertrees, Average Amino Acid Identity (AAI), genomic signatures, and Genome BLAST atlases. Our aim is to analyse the usefulness of these tools for species identification in vibrios. RESULTS: We have generated four new genome sequences of three Vibrio species, i.e., V. alginolyticus 40B, V. harveyi-like 1DA3, and V. mimicus strains VM573 and VM603, and present a broad analyses of these genomes along with other sequenced Vibrio species. The genome atlas and pangenome plots provide a tantalizing image of the genomic differences that occur between closely related sister species, e.g. V. cholerae and V. mimicus. The vibrio pangenome contains around 26504 genes. The V. cholerae core genome and pangenome consist of 1520 and 6923 genes, respectively. Pangenomes might allow different strains of V. cholerae to occupy different niches. MLSA and supertree analyses resulted in a similar phylogenetic picture, with a clear distinction of four groups (Vibrio core group, V. cholerae-V. mimicus, Aliivibrio spp., and Photobacterium spp.). A Vibrio species is defined as a group of strains that share > 95% DNA identity in MLSA and supertree analysis, > 96% AAI, < or = 10 genome signature dissimilarity, and > 61% proteome identity. Strains of the same species and species of the same genus will form monophyletic groups on the basis of MLSA and supertree. CONCLUSION: The combination of different analytical and bioinformatics tools will enable the most accurate species identification through genomic computational analysis. This endeavour will culminate in the birth of the online genomic taxonomy whereby researchers and end-users of taxonomy will be able to identify their isolates through a web-based server. This novel approach to microbial systematics will result in a tremendous advance concerning biodiversity discovery, description, and understanding.
ESTHER : Thompson_2009_BMC.Evol.Biol_9_258
PubMedSearch : Thompson_2009_BMC.Evol.Biol_9_258
PubMedID: 19860885
Gene_locus related to this paper: vibal-q1v7b5 , vibal-q1v7d0 , vibal-q1v463 , vibal-q1v627 , vibal-q1v697 , vibal-q1va42 , vibal-q1vai8 , vibal-q1vap1 , vibal-q1vbx2 , vibal-q1vfw6 , vibch-a6xrz3 , vibch-VC2718 , vibch-VCA0688 , vibch-y1892 , vibch-y2276 , vibha-d0x5c8 , vibha-d0x7p9 , vibha-d0xb11 , vibha-d0xgc5 , vibcb-a7mwv0 , vibhb-a7mzs1 , vibhb-a7n5i4 , vibhb-bioh , vibmi-d2y908 , vibmi-d2ygk2 , vibpa-PHAC , vibpa-VPA0468 , vibpa-VPA1467 , vibpa-VPA1496 , vibpa-VPA1595 , vibal-d0wu09 , vibha-d0xda8 , vibmi-u4zh77 , 9vibr-k5u9q4 , vibmi-g0sil5

Title : The complete genome sequence and analysis of the epsilonproteobacterium Arcobacter butzleri - Miller_2007_PLoS.One_2_e1358
Author(s) : Miller WG , Parker CT , Rubenfield M , Mendz GL , Wosten MM , Ussery DW , Stolz JF , Binnewies TT , Hallin PF , Wang G , Malek JA , Rogosin A , Stanker LH , Mandrell RE
Ref : PLoS ONE , 2 :e1358 , 2007
Abstract : BACKGROUND: Arcobacter butzleri is a member of the epsilon subdivision of the Proteobacteria and a close taxonomic relative of established pathogens, such as Campylobacter jejuni and Helicobacter pylori. Here we present the complete genome sequence of the human clinical isolate, A. butzleri strain RM4018. METHODOLOGY/PRINCIPAL FINDINGS: Arcobacter butzleri is a member of the Campylobacteraceae, but the majority of its proteome is most similar to those of Sulfuromonas denitrificans and Wolinella succinogenes, both members of the Helicobacteraceae, and those of the deep-sea vent Epsilonproteobacteria Sulfurovum and Nitratiruptor. In addition, many of the genes and pathways described here, e.g. those involved in signal transduction and sulfur metabolism, have been identified previously within the epsilon subdivision only in S. denitrificans, W. succinogenes, Sulfurovum, and/or Nitratiruptor, or are unique to the subdivision. In addition, the analyses indicated also that a substantial proportion of the A. butzleri genome is devoted to growth and survival under diverse environmental conditions, with a large number of respiration-associated proteins, signal transduction and chemotaxis proteins and proteins involved in DNA repair and adaptation. To investigate the genomic diversity of A. butzleri strains, we constructed an A. butzleri DNA microarray comprising 2238 genes from strain RM4018. Comparative genomic indexing analysis of 12 additional A. butzleri strains identified both the core genes of A. butzleri and intraspecies hypervariable regions, where <70% of the genes were present in at least two strains. CONCLUSION/SIGNIFICANCE: The presence of pathways and loci associated often with non-host-associated organisms, as well as genes associated with virulence, suggests that A. butzleri is a free-living, water-borne organism that might be classified rightfully as an emerging pathogen. The genome sequence and analyses presented in this study are an important first step in understanding the physiology and genetics of this organism, which constitutes a bridge between the environment and mammalian hosts.
ESTHER : Miller_2007_PLoS.One_2_e1358
PubMedSearch : Miller_2007_PLoS.One_2_e1358
PubMedID: 18159241
Gene_locus related to this paper: arcb4-a8esr8 , arcb4-a8ety0 , arcb4-a8euk7 , 9prot-e6l4v2 , 9prot-a0a0g9kwp1