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41.
Carsten Friis Trudy M. Wassenaar Muhammad A. Javed Lars Snipen Karin Lagesen Peter F. Hallin Diane G. Newell Monique Toszeghy Anne Ridley Georgina Manning David W. Ussery 《PloS one》2010,5(8)
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. 相似文献
42.
Tammi Vesth Trudy M. Wassenaar Peter F. Hallin Lars Snipen Karin Lagesen David W. Ussery 《Microbial ecology》2010,59(1):1-13
Thirty-two genome sequences of various Vibrionaceae members are compared, with emphasis on what makes V. cholerae unique. As few as 1,000 gene families are conserved across all the Vibrionaceae genomes analysed; this fraction roughly doubles for gene families conserved within the species V. cholerae. Of these, approximately 200 gene families that cluster on various locations of the genome are not found in other sequenced
Vibrionaceae; these are possibly unique to the V. cholerae species. By comparing gene family content of the analysed genomes, the relatedness to a particular species is identified
for two unspeciated genomes. Conversely, two genomes presumably belonging to the same species have suspiciously dissimilar
gene family content. We are able to identify a number of genes that are conserved in, and unique to, V. cholerae. Some of these genes may be crucial to the niche adaptation of this species. 相似文献
43.
Binnewies TT Motro Y Hallin PF Lund O Dunn D La T Hampson DJ Bellgard M Wassenaar TM Ussery DW 《Functional & integrative genomics》2006,6(3):165-185
It has been more than 10 years since the first bacterial genome sequence was published. Hundreds of bacterial genome sequences are now available for comparative genomics, and searching a given protein against more than a thousand genomes will soon be possible. The subject of this review will address a relatively straightforward question: “What have we learned from this vast amount of new genomic data?” Perhaps one of the most important lessons has been that genetic diversity, at the level of large-scale variation amongst even genomes of the same species, is far greater than was thought. The classical textbook view of evolution relying on the relatively slow accumulation of mutational events at the level of individual bases scattered throughout the genome has changed. One of the most obvious conclusions from examining the sequences from several hundred bacterial genomes is the enormous amount of diversity—even in different genomes from the same bacterial species. This diversity is generated by a variety of mechanisms, including mobile genetic elements and bacteriophages. An examination of the 20 Escherichia coli genomes sequenced so far dramatically illustrates this, with the genome size ranging from 4.6 to 5.5 Mbp; much of the variation appears to be of phage origin. This review also addresses mobile genetic elements, including pathogenicity islands and the structure of transposable elements. There are at least 20 different methods available to compare bacterial genomes. Metagenomics offers the chance to study genomic sequences found in ecosystems, including genomes of species that are difficult to culture. It has become clear that a genome sequence represents more than just a collection of gene sequences for an organism and that information concerning the environment and growth conditions for the organism are important for interpretation of the genomic data. The newly proposed Minimal Information about a Genome Sequence standard has been developed to obtain this information. 相似文献
44.
Takamiya M Ozen A Rasmussen M Alter T Gilbert T Ussery DW Knøchel S 《Journal of bacteriology》2011,193(19):5546-5547
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. 相似文献
45.
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. 相似文献
46.
A Ali SC Soares AR Santos LC Guimarães E Barbosa SS Almeida VA Abreu AR Carneiro RT Ramos SM Bakhtiar SS Hassan DW Ussery S On A Silva MP Schneider AP Lage A Miyoshi V Azevedo 《Gene》2012,508(2):145-156
The genus Campylobacter contains pathogens causing a wide range of diseases, targeting both humans and animals. Among them, the Campylobacter fetus subspecies fetus and venerealis deserve special attention, as they are the etiological agents of human bacterial gastroenteritis and bovine genital campylobacteriosis, respectively. We compare the whole genomes of both subspecies to get insights into genomic architecture, phylogenetic relationships, genome conservation and core virulence factors. Pan-genomic approach was applied to identify the core- and pan-genome for both C. fetus subspecies and members of the genus. The C. fetus subspecies conserved (76%) proteome were then analyzed for their subcellular localization and protein functions in biological processes. Furthermore, with pathogenomic strategies, unique candidate regions in the genomes and several potential core-virulence factors were identified. The potential candidate factors identified for attenuation and/or subunit vaccine development against C. fetus subspecies contain: nucleoside diphosphate kinase (Ndk), type IV secretion systems (T4SS), outer membrane proteins (OMP), substrate binding proteins CjaA and CjaC, surface array proteins, sap gene, and cytolethal distending toxin (CDT). Significantly, many of those genes were found in genomic regions with signals of horizontal gene transfer and, therefore, predicted as putative pathogenicity islands. We found CRISPR loci and dam genes in an island specific for C. fetus subsp. fetus, and T4SS and sap genes in an island specific for C. fetus subsp. venerealis. The genomic variations and potential core and unique virulence factors characterized in this study would lead to better insight into the species virulence and to more efficient use of the candidates for antibiotic, drug and vaccine development. 相似文献
47.
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49.
E Fidelma Boyd Ana Luisa V Cohen Lynn M Naughton David W Ussery Tim T Binnewies O Colin Stine Michelle A Parent 《BMC microbiology》2008,8(1):110
Background
Vibrio parahaemolyticusis abundant in the aquatic environment particularly in warmer waters and is the leading cause of seafood borne gastroenteritis worldwide. Prior to 1995, numerousV. parahaemolyticusserogroups were associated with disease, however, in that year an O3:K6 serogroup emerged in Southeast Asia causing large outbreaks and rapid hospitalizations. This new highly virulent strain is now globally disseminated. 相似文献50.
Metagenomic based strategies have previously been successfully employed as powerful tools to isolate and identify enzymes
with novel biocatalytic activities from the unculturable component of microbial communities from various terrestrial environmental
niches. Both sequence based and function based screening approaches have been employed to identify genes encoding novel biocatalytic
activities and metabolic pathways from metagenomic libraries. While much of the focus to date has centred on terrestrial based
microbial ecosystems, it is clear that the marine environment has enormous microbial biodiversity that remains largely unstudied.
Marine microbes are both extremely abundant and diverse; the environments they occupy likewise consist of very diverse niches.
As culture-dependent methods have thus far resulted in the isolation of only a tiny percentage of the marine microbiota the
application of metagenomic strategies holds great potential to study and exploit the enormous microbial biodiversity which
is present within these marine environments. 相似文献