Whole-Genome Shotgun Sequence of Rhodococcus Species Strain JVH1

Here we present a whole-genome shotgun sequence of Rhodococcus species strain JVH1, an organism capable of degrading a variety of organosulfur compounds. In particular, JVH1 is able to selectively cleave carbon-sulfur bonds within alkyl chains. A large number of oxygenases were identified, consistent with other members of the genus.     

Draft Genome Sequence of a Nonhemolytic Fish-Pathogenic Streptococcus agalactiae Strain

Streptococcus agalactiae is a significant Gram-positive bacterial pathogen of terrestrial and aquatic animals. A subpopulation of nonhemolytic strains which appear to be pathogenic only for poikilotherms exists. We report here the first draft genome sequence of a nonhemolytic S. agalactiae isolate recovered from a diseased fish.     

Whole-Genome Shotgun Sequence of the Sulfur-Oxidizing Chemoautotroph Pseudaminobacter salicylatoxidans KCT001

The facultatively sulfur-oxidizing chemolithoautotrophic alphaproteobacterium Pseudaminobacter salicylatoxidans KCT001 (MTCC 7265) belongs to the family Phyllobacteriaceae of the order Rhizobiales. Analysis of its genome offers valuable insight into the adaptive specializations and evolution of free-living soil bacteria that are phylogenetically closely related to symbiotic and invasive rhizobacteria.     

Whole-Genome Shotgun Sequencing of the Extremophile Alkalibacillus haloalkaliphilus C-5, of Indian Origin

Alkalibacillus haloalkaliphilus C-5 is a haloalkaliphilic bacterium that was isolated from a soil sample from the salty Sambhar Lake, Rajasthan, India. The organism is capable of alkaline protease production under conditions of pH 10 and 10% (wt/vol) salt. We sequenced and have reported the whole genome of Alkalibacillus haloalkaliphilus C-5, of Indian origin, for the first time.     

Whole-Genome Shotgun Optical Mapping of Rhodospirillum rubrum

Rhodospirillum rubrum is a phototrophic purple nonsulfur bacterium known for its unique and well-studied nitrogen fixation and carbon monoxide oxidation systems and as a source of hydrogen and biodegradable plastic production. To better understand this organism and to facilitate assembly of its sequence, three whole-genome restriction endonuclease maps (XbaI, NheI, and HindIII) of R. rubrum strain ATCC 11170 were created by optical mapping. Optical mapping is a system for creating whole-genome ordered restriction endonuclease maps from randomly sheared genomic DNA molecules extracted from cells. During the sequence finishing process, all three optical maps confirmed a putative error in sequence assembly, while the HindIII map acted as a scaffold for high-resolution alignment with sequence contigs spanning the whole genome. In addition to highlighting optical mapping's role in the assembly and confirmation of genome sequence, this work underscores the unique niche in resolution occupied by the optical mapping system. With a resolution ranging from 6.5 kb (previously published) to 45 kb (reported here), optical mapping advances a “molecular cytogenetics” approach to solving problems in genomic analysis.     

Whole-Genome Sequence of Cupriavidus sp. Strain BIS7, a Heavy-Metal-Resistant Bacterium

Cupriavidus sp. strain BIS7 is a Malaysian tropical soil bacterium that exhibits broad heavy-metal resistance [Co(II), Zn(II), Ni(II), Se(IV), Cu(II), chromate, Co(III), Fe(II), and Fe(III)]. It is particularly resistant to Fe(II), Fe(III), and Zn(II). Here we present the assembly and annotation of its genome.     

Identification of Streptococcus uberis Multilocus Sequence Types Highly Associated with Mastitis

Multilocus sequence typing analysis of Streptococcus uberis has identified a cluster of isolates associated with clinical and subclinical mastitis and a cluster associated with cows with low somatic cell counts in their milk. Specific groups of genotypes (global clonal complex [GCC] sequence type 5s [ST5s] and GCC ST143s) were highly associated (P = 0.006) with clinical and subclinical mastitis and may represent a lineage of virulent isolates, whereas isolates belonging to GCC ST86 were associated with low-cell-count cows. This study has, for the first time, demonstrated the occurrence of identical sequence types (ST60 and ST184) between different continents (Australasia and Europe) and different countries (Australia and New Zealand). The standardized index of association and the empirical estimation of the rate of recombination showed substantial recombination within the S. uberis population in Australia, consistent with previous multilocus sequence type analyses.     

Whole-Genome Sequence of Corynebacterium pseudotuberculosis Strain Cp162, Isolated from Camel

Corynebacterium pseudotuberculosis is a pathogen of great veterinary and economic importance, since it affects livestock, mainly sheep and goats, worldwide, together with reports of its presence in camels in several Arabic, Asiatic, and East and West African countries, as well as Australia. In this article, we report the genome sequence of Corynebacterium pseudotuberculosis strain Cp162, collected from the external neck abscess of a camel in the United Kingdom.     

Whole-Genome Sequence of N-Acylhomoserine Lactone-Synthesizing and -Degrading Acinetobacter sp. Strain GG2

Acinetobacter sp. strain GG2 is a quorum-sensing and quorum-quenching bacterium isolated from the ginger rhizosphere. It degrades a broad range of N-acylhomoserine lactone molecules via lactonase. The genome sequence of strain GG2 may provide insights on the regulation of quorum-sensing and quorum-quenching mechanisms in this bacterium.     

Whole-Genome Sequence of Nocardiopsis alba Strain ATCC BAA-2165, Associated with Honeybees

The actinomycete Nocardiopsis alba was reportedly associated with honeybees in separate occurrences. We report the complete genome of Nocardiopsis alba ATCC BAA-2165 isolated from honeybee guts. It will provide insights into the metabolism and genetic regulatory networks of this genus of bacteria that enable them to live in a range of environments.     

Complete Genome Sequence of Streptococcus agalactiae ZQ0910, a Pathogen Causing Meningoencephalitis in the GIFT Strain of Nile Tilapia (Oreochromis niloticus)

Streptococcus agalactiae (group B streptococcus [GBS]) is a pathogen that causes meningoencephalitis in Nile tilapia (Oreochromis niloticus). Here, we reported the complete genome sequence of S. agalactiae strain ZQ0910, which was isolated from the GIFT strain of Nile tilapia in Guangdong, China.     

Serotypes,Antibiotic Susceptibilities,and Multi-Locus Sequence Type Profiles of Streptococcus agalactiae Isolates Circulating in Beijing,China

Background

To investigate the serotypes, antibiotic susceptibilities, and multi-locus sequence type (MLST) profiles of Streptococcus agalactiae (S. agalactiae) in Beijing to provide references for the prevention and treatment of S. agalactiae infections.

Methods

All isolates were identified using the CAMP test and the latex-agglutination assay and serotyped using a Strep-B-Latex kit, after which they were assessed for antibiotic susceptibility, macrolide-resistance genes, and MLST profiles.

Results

In total, 56 S. agalactiae isolates were identified in 863 pregnant women (6.5%). Serotypes Ia, Ib, II, III, and V were identified, among which types III (32.1%), Ia (17.9%), Ib (16.1%), and V (14.3%) were the predominant serotypes. All isolates were susceptible to penicillin and ceftriaxone. The nonsusceptiblity rates measured for erythromycin, clarithromycin, azithromycin, telithromycin, clindamycin, tetracycline, and levofloxacin were 85.7%, 92.9%, 98.2%, 30.4%, 73.2%, 91%, and 39.3%, respectively. We identified 14 sequence types (STs) for the 56 isolates, among which ST19 (30.4%) was predominant. The rate of fluoroquinolone resistance was higher in serotype III than in the other serotypes. Among the 44 erythromycin-resistant isolates, 32 (72.7%) carried ermB.

Conclusion

S. agalactiae isolates of the serotypes Ia, Ib, III, and V are common in Beijing. Among the S. agalactiae isolates, the macrolide and clindamycin resistance rates are extremely high. Most of the erythromycin-resistant isolates carry ermB.     

Complete Genome Sequence of Streptococcus thermophilus Strain MN-ZLW-002

Streptococcus thermophilus MN-ZLW-002 was originally isolated from traditionally fermented Chinese dairy products. One of the strain-dependent characteristics of this bacterium is its ability to produce exopolysaccharides (EPSs). This study determined and analyzed the genome sequence of MN-ZLW-002. Its complete genome comprised 2,046 genes and 1,848,520 nucleotides with an average GC content of 39%. The EPS cluster of MN-ZLW-002 includes 25 open reading frames (ORFs), and some results indicate a horizontal gene transfer between MN-ZLW-002 and other lactic acid bacteria (LAB).     

美科学家首次完成一家四口全基因组测序

2010年3月10日,杂志在线发表了一篇关于一家四口(父母及其孩子)的全基因组测序的文章.通过测序,研究人员发现了影响人类自发性基因突变平均速度,以及一些与影响兄弟姐妹的疾病有关的基因.     

Whole-Genome Sequence Analysis and Genome-Wide Virulence Gene Identification of Riemerella anatipestifer Strain Yb2

Riemerella anatipestifer is a well-described pathogen of waterfowl and other avian species that can cause septicemic and exudative diseases. In this study, we sequenced the complete genome of R. anatipestifer strain Yb2 and analyzed it against the published genomic sequences of R. anatipestifer strains DSM15868, RA-GD, RA-CH-1, and RA-CH-2. The Yb2 genome contains one circular chromosome of 2,184,066 bp with a 35.73% GC content and no plasmid. The genome has 2,021 open reading frames that occupy 90.88% of the genome. A comparative genomic analysis revealed that genome organization is highly conserved among R. anatipestifer strains, except for four inversions of a sequence segment in Yb2. A phylogenetic analysis found that the closest neighbor of Yb2 is RA-GD. Furthermore, we constructed a library of 3,175 mutants by random transposon mutagenesis, and 100 mutants exhibiting more than 100-fold-attenuated virulence were obtained by animal screening experiments. Southern blot analysis and genetic characterization of the mutants led to the identification of 49 virulence genes. Of these, 25 encode cytoplasmic proteins, 6 encode cytoplasmic membrane proteins, 4 encode outer membrane proteins, and the subcellular localization of the remaining 14 gene products is unknown. The functional classification of orthologous-group clusters revealed that 16 genes are associated with metabolism, 6 are associated with cellular processing and signaling, and 4 are associated with information storage and processing. The functions of the other 23 genes are poorly characterized or unknown. This genome-wide study identified genes important to the virulence of R. anatipestifer.     

Whole-Genome Sequence of the Hypervirulent Clinical Strain Mycobacterium intracellulare M.i.198

We report herein the draft genome sequence of Mycobacterium intracellulare clinical strain M.i.198, which consistently exhibits hypervirulence in human patients, human macrophages in vitro, and immunocompetent mice.     

Whole-Genome Sequencing of Aspergillus terreus Species Complex

Mycopathologia - Aspergillus terreus species complex is an opportunistic fungal pathogen increasingly implicated in invasive infection, as well as chronic respiratory disease. Currently, an...     

Mobile Genetic Elements Provide Evidence for a Bovine Origin of Clonal Complex 17 of Streptococcus agalactiae

We sought an explanation for epidemiological changes in Streptococcus agalactiae infections by investigating the link between ecological niches of the bacterium by determining the prevalence of 11 mobile genetic elements. The prevalence of nine of these elements differed significantly according to the human or bovine origin of the isolate. Correlating this distribution with the phylogeny obtained by multilocus sequence analysis, we observed that human isolates harboring GBSi1, a clear marker of the bovine niche, clustered in clonal complex 17. Our results are thus consistent with the emergence of this virulent human clone from a bovine ancestor.