Comparative genomic analysis reveals evidence of two novel Vibrio species closely related to V. cholerae

BMC Microbiology

Research Article

J Chris Detter¹  Cliff S Han¹  Jean F Challacombe¹  David C Bruce¹  Thomas S Brettin²  Anwar Huq³  Nur A Hasan³  Bradd J Haley³  Seon-Young Choi⁴  Rita R Colwell⁵  Christopher J Grim⁶  Jongsik Chun⁷ 

[1] DOE Joint Genome Institute, Bioscience Division, Los Alamos National Laboratory, 87545, Los Alamos, NM, USA;DOE Joint Genome Institute, Bioscience Division, Los Alamos National Laboratory, 87545, Los Alamos, NM, USA;Current address: Oak Ridge National Laboratory, Oak Ridge, TN, USA;Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, USA;Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, USA;School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 151-742, Republic of Korea, and International Vaccine Institute, 151-818, Seoul, Republic of Korea;Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, USA;University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, Maryland, USA;Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, USA;University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, Maryland, USA;Current address: Food and Drug Administration, Greenbelt, MD, USA;School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 151-742, Republic of Korea, and International Vaccine Institute, 151-818, Seoul, Republic of Korea;

关键词: Horizontal Gene Transfer;    Amino Acid Identity;    Genomic Island;    Vibrio Species;    Average Nucleotide Identity;   

DOI  :  10.1186/1471-2180-10-154

 received in 2009-11-18, accepted in 2010-05-27,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundIn 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.ResultsBased 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.ConclusionsResults 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.

【 授权许可】

Unknown   
© Haley et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.