Open Access Open Badges Research article

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

Le Tang123, Yang Li1, Xia Deng1, Randal N Johnston4, Gui-Rong Liu123* and Shu-Lin Liu1235*

Author Affiliations

1 Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin, China

2 HMU-UCFM Centre for Infection and Genomics, Harbin, China

3 Department of Biopharmaceutics, Harbin Medical University, 157 Baojian Road, Harbin 150081, China

4 Departments of Biochemistry and Molecular Biology, Calgary, Canada

5 Microbiology and Infectious Diseases, University of Calgary, Calgary, Canada

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BMC Genomics 2013, 14:489  doi:10.1186/1471-2164-14-489

Published: 18 July 2013



Bacteria 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.


We 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.


Bacteria are genetically isolated into discrete clusters equivalent to natural species.

Natural species; Salmonella; Genetic boundary