School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, India.
Genome. 2019 Feb;62(2):45-52. doi: 10.1139/gen-2018-0072. Epub 2019 Jan 16.
Bacterial populations are routinely characterized based on microscopic examination, colony formation, and biochemical tests. However, in the recent past, bacterial identification, classification, and nomenclature have been strongly influenced by genome sequence information. Advances in bioinformatics and growth in genome databases has placed genome-based metadata analysis in the hands of researchers who will require taxonomic experience to resolve intricacies. To achieve this, different tools are now available to quantitatively measure genome relatedness within members of the same species, and genome-wide average nucleotide identity (gANI) is one such reliable tool to measure genome similarity. A genome assembly with a gANI score of <95% at the intraspecies level is generally considered indicative of a separate species. In this study, we have analysed 300 whole-genome sequences belonging to 26 different bacterial species available in the NCBI Genome database and calculated their similarity at the intraspecies level based on gANI score. At the intraspecies level, nine bacterial species showed less than 90% gANI and more than 10% of unaligned regions. We suggest the appropriate use of available bioinformatics resources after genome assembly to arrive at the proper bacterial identification, classification, and nomenclature to avoid erroneous species assignments and disparity due to diversity at the intraspecies level.
细菌群体通常基于显微镜检查、菌落形成和生化测试进行特征描述。然而，在最近的过去，细菌的鉴定、分类和命名受到了基因组序列信息的强烈影响。生物信息学的进步和基因组数据库的增长使基于基因组的元数据分析掌握在需要分类学经验来解决复杂性的研究人员手中。为此，现在有不同的工具可用于定量测量同一物种成员之间的基因组相关性，而全基因组平均核苷酸同一性 (gANI) 就是一种可靠的测量基因组相似性的工具。在种内水平上，基因组组装的 gANI 评分<95%通常被认为是一个独立物种的指标。在这项研究中，我们分析了 NCBI 基因组数据库中属于 26 个不同细菌物种的 300 个全基因组序列，并根据 gANI 评分计算了它们在种内水平的相似性。在种内水平上，有 9 个细菌物种的 gANI 低于 90%，且未对齐区域超过 10%。我们建议在基因组组装后适当利用可用的生物信息学资源，以进行正确的细菌鉴定、分类和命名，避免由于种内水平的多样性而导致错误的物种分配和差异。
