Comparative genomic analysis reveals evidence of two novel Vibrio species closely related to V. cholerae.
Comparative genomic analysis reveals evidence of two novel Vibrio species closely related to V. cholerae.
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DOI：
10.1186/1471-2180-10-154
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发表时间：
2010-05-27
期刊：
影响因子：
4.2
通讯作者：
Colwell RR
中科院分区：
文献类型：
--
作者：
Haley BJ;Grim CJ;Hasan NA;Choi SY;Chun J;Brettin TS;Bruce DC;Challacombe JF;Detter JC;Han CS;Huq A;Colwell RR
近年来，基因组测序已被用于表征新的细菌物种，这是一种由于改进了方法和降低了成本而可用的分析方法。在不断扩大的弧菌物种名单中，有几个已被重新归类为弧菌科的新成员。两个可能的弧菌新种--弧菌属RC341和弧菌属。RC586，我们建议将其分别命名为Metecus和V.parilis，以前被描述为霍乱弧菌的非产毒环境变异株。根据全基因组平均核苷酸同源性(ANI)、平均氨基酸同源性(AAI)、rpoB相似性、MLSA和系统发育分析结果，该新种与霍乱弧菌和拟态弧菌在系统发育上有较近的亲缘关系。弧菌属RC341和弧菌属。RC586具有霍乱弧菌和拟态弧菌的特征，但它们的基因组与霍乱弧菌和拟态弧菌基因组序列(ANI<；95%和AAI<；96%)相比有12%~15%的差异(88%~85%的ANI和92%~91%的AAI)。弧菌属RC341和弧菌属。RC586与霍乱弧菌核心基因组的同源性分别为2104个ORF(59%)和2058个ORF(56%)，与拟态霍乱弧菌MB-451的同源性分别为2956个(82%)和3048个(84%)。新种共有2926个开放阅读框(81%为弧菌属)。RC341和81%弧菌。RC586)。在这些环境弧菌中发现了霍乱弧菌和拟态弧菌的毒力相关因子和基因组岛，包括VSP-I和VSP-II。分析结果表明，这两个以前被描述为霍乱弧菌变异株的环境弧菌是从霍乱弧菌和拟态弧菌的祖先谱系进化而来的新物种。霍乱弧菌和拟态弧菌这两个新物种之间基因组岛的保守整合位点的存在以及水平基因转移的证据表明，基因组岛和毒力因子在这两个物种之间转移。
In recent years genome sequencing has been used to characterize new bacterial species, a method of analysis available as a result of improved methodology and reduced cost. Included in a constantly expanding list of Vibrio species are several that have been reclassified as novel members of the Vibrionaceae. The description of two putative new Vibrio species, Vibrio sp. RC341 and Vibrio sp. RC586 for which we propose the names V. metecus and V. parilis, respectively, previously characterized as non-toxigenic environmental variants of V. cholerae is presented in this study. Based on results of whole-genome average nucleotide identity (ANI), average amino acid identity (AAI), rpoB similarity, MLSA, and phylogenetic analysis, the new species are concluded to be phylogenetically closely related to V. cholerae and V. mimicus. Vibrio sp. RC341 and Vibrio sp. RC586 demonstrate features characteristic of V. cholerae and V. mimicus, respectively, on differential and selective media, but their genomes show a 12 to 15% divergence (88 to 85% ANI and 92 to 91% AAI) compared to the sequences of V. cholerae and V. mimicus genomes (ANI <95% and AAI <96% indicative of separate species). Vibrio sp. RC341 and Vibrio sp. RC586 share 2104 ORFs (59%) and 2058 ORFs (56%) with the published core genome of V. cholerae and 2956 (82%) and 3048 ORFs (84%) with V. mimicus MB-451, respectively. The novel species share 2926 ORFs with each other (81% Vibrio sp. RC341 and 81% Vibrio sp. RC586). Virulence-associated factors and genomic islands of V. cholerae and V. mimicus, including VSP-I and II, were found in these environmental Vibrio spp. Results of this analysis demonstrate these two environmental vibrios, previously characterized as variant V. cholerae strains, are new species which have evolved from ancestral lineages of the V. cholerae and V. mimicus clade. The presence of conserved integration loci for genomic islands as well as evidence of horizontal gene transfer between these two new species, V. cholerae, and V. mimicus suggests genomic islands and virulence factors are transferred between these species.
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DOI：
10.1098/rstb.2006.1920
发表时间：
2006-11-29
影响因子：
6.3
作者：
Konstantinidis, Konstantinos T.;Ramette, Alban;Tiedje, James M.
通讯作者：
Tiedje, James M.
DOI：
10.1073/pnas.0409727102
发表时间：
2005-02-15
影响因子：
11.1
作者：
Konstantinidis, KT;Tiedje, JM
通讯作者：
Tiedje, JM
影响因子：
3.2
作者：
Konstantinidis, KT;Tiedje, JM
通讯作者：
Tiedje, JM
DOI：
10.1099/00207713-51-4-1383
发表时间：
2001-07-01
影响因子：
2.8
作者：
Kushmaro, A;Banin, E;Rosenberg, E
通讯作者：
Rosenberg, E
影响因子：
5.8
作者：
Larkin, M. A.;Blackshields, G.;Higgins, D. G.
通讯作者：
Higgins, D. G.