Whole-genome sequence comparison as a method for improving bacterial species definition

The Journal of General and Applied Microbiology

Chen Chen¹  Li Wan¹  Wen Zhang¹  Han Zheng¹  Pengcheng Du¹  Weiwen Yu¹ 

[1] National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention/State Key Laboratory for Infectious Disease Prevention and Control

关键词: ANI;    bacteria;    definition;    genome;    species;   

DOI  :  10.2323/jgam.60.75

学科分类：微生物学和免疫学

来源: Applied Microbiology, Molecular and Cellulrar Biosciences Research Foundation

【 摘 要 】

We compared pairs of 1,226 bacterial strains with whole genome sequences and calculated their average nucleotide identity (ANI) between genomes to determine whether whole genome comparison can be directly used for bacterial species definition. We found that genome comparisons of two bacterial strains from the same species (SGC) have a significantly higher ANI than those of two strains from different species (DGC), and that the ANI between the query and the reference genomes can be used to determine whether two genomes come from the same species. Bacterial species definition based on ANI with a cut-off value of 0.92 matched well (81.5%) with the current bacterial species definition. The ANI value was shown to be consistent with the standard for traditional bacterial species definition, and it could be used in bacterial taxonomy for species definition. A new bioinformatics program (ANItools) was also provided in this study for users to obtain the ANI value of any two bacterial genome pairs (http://genome.bioinfo-icdc.org/). This program can match a query strain to all bacterial genomes, and identify the highest ANI value of the strain at the species, genus and family levels respectively, providing valuable insights for species definition.

【 授权许可】

Unknown