Defining natural species of bacteria: clear-cut genomic boundaries revealed by a turning point in nucleotide sequence divergence

BMC Genomics

Research Article

Randal N Johnston¹  Xia Deng²  Yang Li²  Le Tang³  Gui-Rong Liu³  Shu-Lin Liu⁴ 

[1] Departments of Biochemistry and Molecular Biology, Calgary, Canada;Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin, China;Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin, China;HMU-UCFM Centre for Infection and Genomics, Harbin, China;Department of Biopharmaceutics, Harbin Medical University, 157 Baojian Road, Harbin, 150081, China;Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin, China;HMU-UCFM Centre for Infection and Genomics, Harbin, China;Department of Biopharmaceutics, Harbin Medical University, 157 Baojian Road, Harbin, 150081, China;Microbiology and Infectious Diseases, University of Calgary, Calgary, Canada;

关键词: Natural species;    Salmonella;    Genetic boundary;   

DOI  :  10.1186/1471-2164-14-489

 received in 2013-01-24, accepted in 2013-07-15,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundBacteria are currently classified into arbitrary species, but whether they actually exist as discrete natural species was unclear. To reveal genomic features that may unambiguously group bacteria into discrete genetic clusters, we carried out systematic genomic comparisons among representative bacteria.ResultsWe found that bacteria of Salmonella formed tight phylogenetic clusters separated by various genetic distances: whereas over 90% of the approximately four thousand shared genes had completely identical sequences among strains of the same lineage, the percentages dropped sharply to below 50% across the lineages, demonstrating the existence of clear-cut genetic boundaries by a steep turning point in nucleotide sequence divergence. Recombination assays supported the genetic boundary hypothesis, suggesting that genetic barriers had been formed between bacteria of even very closely related lineages. We found similar situations in bacteria of Yersinia and Staphylococcus.ConclusionsBacteria are genetically isolated into discrete clusters equivalent to natural species.

【 授权许可】

Unknown   
© Tang et al.; licensee BioMed Central Ltd. 2013. 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.