Abstract:
:Escherichia coli is the most abundant facultative anaerobic bacteria in the gastro-intestinal tract of mammals but can be responsible for intestinal infection due to acquisition of virulence factors. Genomes of pathogenic E. coli strains are widely described whereas those of bovine commensal E. coli strains are very scarce. Here, we report the genome sequence, annotation, and features of the commensal E. coli BG1 isolated from the gastro-intestinal tract of cattle. Whole genome sequencing analysis showed that BG1 has a chromosome of 4,782,107 bp coding for 4465 proteins and 97 RNAs. E. coli BG1 belonged to the serotype O159:H21, was classified in the phylogroup B1 and possessed the genetic information encoding "virulence factors" such as adherence systems, iron acquisition and flagella synthesis. A total of 12 adherence systems were detected reflecting the potential ability of BG1 to colonize different segments of the bovine gastro-intestinal tract. E. coli BG1 is unable to assimilate ethanolamine that confers a nutritional advantage to some pathogenic E. coli in the bovine gastro-intestinal tract. Genome analysis revealed the presence of i) 34 amino acids change due to non-synonymous SNPs among the genes encoding ethanolamine transport and assimilation, and ii) an additional predicted alpha helix inserted in cobalamin adenosyltransferase, a key enzyme required for ethanolamine assimilation. These modifications could explain the incapacity of BG1 to use ethanolamine. The BG1 genome can now be used as a reference (control strain) for subsequent evolution and comparative studies.
journal_name
Stand Genomic Scijournal_title
Standards in genomic sciencesauthors
Segura A,Auffret P,Klopp C,Bertin Y,Forano Edoi
10.1186/s40793-017-0272-0subject
Has Abstractpub_date
2017-10-10 00:00:00pages
61issn
1944-3277pii
272journal_volume
12pub_type
abstract::Thioalkalivibrio thiocyanoxidans strain ARh 2(T) is a sulfur-oxidizing bacterium isolated from haloalkaline soda lakes. It is a motile, Gram-negative member of the Gammaproteobacteria. Remarkable properties include the ability to grow on thiocyanate as the sole energy, sulfur and nitrogen source, and the capability of...
journal_title:Standards in genomic sciences
pub_type:
doi:10.1186/s40793-015-0078-x
更新日期:2015-10-26 00:00:00
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journal_title:Standards in genomic sciences
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doi:10.1186/s40793-016-0174-6
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abstract::Thermosediminibacter oceani (Lee et al. 2006) is the type species of the genus Thermosediminibacter in the family Thermoanaerobacteraceae. The anaerobic, barophilic, chemoorganotrophic thermophile is characterized by straight to curved Gram-negative rods. The strain described in this study was isolated from a core sam...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.4056/sigs.1133078
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abstract::The family Hyphomonadaceae within the Alphaproteobacteria is largely comprised of bacteria isolated from marine environments with striking morphologies and an unusual mode of cell growth. Here, we report the complete genome sequence Hirschia baltica, which is only the second a member of the Hyphomonadaceae with a publ...
journal_title:Standards in genomic sciences
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abstract::The genus Porphyrobacter belongs to aerobic anoxygenic phototrophic bacteria cluster. Porphyrobacter neustonensis DSM 9434 was isolated from a eutrophic freshwater pond in Australia, and is able to synthesize Bacteriochlorophyll a as well as grow under aerobic conditions. It is the type species of the genus Porphyroba...
journal_title:Standards in genomic sciences
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doi:10.1186/s40793-017-0243-5
更新日期:2017-05-10 00:00:00
abstract::Mucilaginibacter pedocola TBZ30T (= CCTCC AB 2015301T = KCTC 42833T) is a Gram- negative, rod-shaped, non-motile and non-spore-forming bacterium isolated from a heavy metal contaminated paddy field. It shows resistance to multiple heavy metals and can adsorb/remove Zn2+ and Cd2+ during cultivation. In addition, strain...
journal_title:Standards in genomic sciences
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doi:10.1186/s40793-018-0337-8
更新日期:2018-11-28 00:00:00
abstract::Halorhabdus utahensis Wainø 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, wh...
journal_title:Standards in genomic sciences
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更新日期:2009-11-22 00:00:00
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journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.4056/sigs.2705996
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journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.4056/sigs.5649756
更新日期:2014-03-15 00:00:00
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journal_title:Standards in genomic sciences
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doi:10.1186/s40793-015-0098-6
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journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.1186/s40793-015-0059-0
更新日期:2015-09-21 00:00:00
abstract::Methylibium sp. strain T29 was isolated from a gasoline-contaminated aquifer and proved to have excellent capabilities in degrading some common fuel oxygenates like methyl tert-butyl ether, tert-amyl methyl ether and tert-butyl alcohol along with other organic compounds. Here, we report the draft genome sequence of M....
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.1186/s40793-015-0023-z
更新日期:2015-07-19 00:00:00
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 '...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.4056/sigs.48727
更新日期:2009-12-30 00:00:00
abstract::Hydrogenobacter thermophilus Kawasumi et al. 1984 is the type species of the genus Hydrogenobacter. H. thermophilus was the first obligate autotrophic organism reported among aerobic hydrogen-oxidizing bacteria. Strain TK-6(T) is of interest because of the unusually efficient hydrogen-oxidizing ability of this strain,...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.4056/sigs.1463589
更新日期:2011-04-29 00:00:00
abstract::Phage ST0 lysing Escherichia coli H8 was isolated from wastewater and sequenced using an Illumina HiSeq system. Genomic analyses revealed that it was virulent phages and contained a circular double-stranded DNA genome, consisting of 170,496 nucleotides with an average G + C content of 37.67%. This study may provide po...
journal_title:Standards in genomic sciences
pub_type:
doi:10.1186/s40793-017-0304-9
更新日期:2017-12-19 00:00:00
abstract::Chryseobacterium bovis DSM 19482T (Hantsis-Zacharov et al., Int J Syst Evol Microbiol 58:1024-1028, 2008) is a Gram-negative, rod shaped, non-motile, facultative anaerobe, chemoorganotroph bacterium. C. bovis is a member of the Flavobacteriaceae, a family within the phylum Bacteroidetes. It was isolated when psychroto...
journal_title:Standards in genomic sciences
pub_type:
doi:10.1186/s40793-017-0242-6
更新日期:2017-05-08 00:00:00
abstract::Syntrophobacter fumaroxidans strain MPOB(T) is the best-studied species of the genus Syntrophobacter. The species is of interest because of its anaerobic syntrophic lifestyle, its involvement in the conversion of propionate to acetate, H2 and CO2 during the overall degradation of organic matter, and its release of pro...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.4056/sigs.2996379
更新日期:2012-10-10 00:00:00
abstract::Strain HIMB11 is a planktonic marine bacterium isolated from coastal seawater in Kaneohe Bay, Oahu, Hawaii belonging to the ubiquitous and versatile Roseobacter clade of the alphaproteobacterial family Rhodobacteraceae. Here we describe the preliminary characteristics of strain HIMB11, including annotation of the draf...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.4056/sigs.4998989
更新日期:2014-03-15 00:00:00
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journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.4056/sigs.1603927
更新日期:2011-02-22 00:00:00
abstract::Sphingomonas paucimobilis strain LCT-SP1 is a glucose-nonfermenting Gram-negative, chemoheterotrophic, strictly aerobic bacterium. The major feature of strain LCT-SP1, isolated from the Chinese spacecraft Shenzhou X, together with the genome draft and annotation are described in this paper. The total size of strain LC...
journal_title:Standards in genomic sciences
pub_type:
doi:10.1186/s40793-016-0136-z
更新日期:2016-02-24 00:00:00
abstract::Root nodule bacteria are free-living soil bacteria, belonging to diverse genera within the Alphaproteobacteria and Betaproteobacteria, that have the capacity to form nitrogen-fixing symbioses with legumes. The symbiosis is specific and is governed by signaling molecules produced from both host and bacteria. Sequencing...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.1186/1944-3277-10-14
更新日期:2015-02-09 00:00:00
abstract::Burkholderia sp. strain WSM2230 is an aerobic, motile, Gram-negative, non-spore-forming acid-tolerant rod isolated from acidic soil collected in 2001 from Karijini National Park, Western Australia, using Kennedia coccinea (Coral Vine) as a host. WSM2230 was initially effective in nitrogen-fixation with K. coccinea, bu...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
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abstract::Halomonas zhanjiangensis Chen et al. 2009 is a member of the genus Halomonas, family Halomonadaceae, class Gammaproteobacteria. Representatives of the genus Halomonas are a group of halophilic bacteria often isolated from salty environments. The type strain H. zhanjiangensis JSM 078169(T) was isolated from a sea urchi...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
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abstract::Spirosoma linguale Migula 1894 is the type species of the genus. S. linguale is a free-living and non-pathogenic organism, known for its peculiar ringlike and horseshoe-shaped cell morphology. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is only the th...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
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abstract::Mesotoga strain PhosAc3 was the first mesophilic cultivated member of the order Thermotogales. This genus currently contain two described species, M. prima and M. infera. Strain PhosAc3, isolated from a Tunisian digestor treating phosphogypsum, is phylogenetically closely related to M. prima strain MesG1.Ag.4.2(T). St...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.1186/1944-3277-10-12
更新日期:2015-05-01 00:00:00
abstract::The Roseophages, a group of marine viruses that uniquely infect the Roseobacter clade of bacteria, play a significant role in marine ecosystems. Here we present a complete genomic sequence of an N4 phage 'vB_DshP-R1', which infects Dinoroseobacter shibae DFL12, together with its structural and genomic features. vB_Dsh...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.1186/1944-3277-10-6
更新日期:2015-01-21 00:00:00
abstract::Strain 3.5.1 was isolated from soils of the Republic of Tatarstan, Russia, on the basis of presence of a high phytate-degrading activity. Strains with such activities attract special interest because of its potential use as feed additives and natural manures. Strain 3.5.1 harbors a 99 % 16S rRNA nucleotide sequence si...
journal_title:Standards in genomic sciences
pub_type:
doi:10.1186/s40793-015-0093-y
更新日期:2015-11-11 00:00:00
abstract::Although the hemipterans (Aphididae) are comprised of roughly 50,000 extant insect species, only four have sequenced genomes that are publically available, namely Acyrthosiphon pisum (pea aphid), Rhodnius prolixus (Kissing bug), Myzus persicae (Green peach aphid) and Diuraphis noxia (Russian wheat aphid). As a signifi...
journal_title:Standards in genomic sciences
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doi:10.1186/s40793-017-0307-6
更新日期:2017-12-28 00:00:00
abstract::Nereida ignava strain 2SM4(T) (= CECT 5292(T) = DSM 16309(T) = CIP 108404(T) = CCUG 49433(T)) is a marine bacterium belonging to the Roseobacter group of the family Rhodobacteraceae within the class Alphaproteobacteria. The strain was isolated from sea water surrounding cultivated oysters 2-3 miles off the Mediterrane...
journal_title:Standards in genomic sciences
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doi:10.1186/s40793-016-0141-2
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abstract::Candidatus Arsenophonus lipopteni (Enterobacteriaceae, Gammaproteobacteria) is an obligate intracellular symbiont of the blood feeding deer ked, Lipoptena cervi (Diptera: Hippoboscidae). The bacteria reside in specialized cells derived from host gut epithelia (bacteriocytes) forming a compact symbiotic organ (bacterio...
journal_title:Standards in genomic sciences
pub_type:
doi:10.1186/s40793-016-0195-1
更新日期:2016-09-17 00:00:00