Department of Zoology, University of Oxford, Oxford, UK.
Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
Microb Genom. 2022 Sep;8(9). doi: 10.1099/mgen.0.000849.
Bacterial genomics is making an increasing contribution to the fields of medicine and public health microbiology. Consequently, accurate species identification of bacterial genomes is an important task, particularly as the number of genomes stored in online databases increases rapidly and new species are frequently discovered. Existing database entries require regular re-evaluation to ensure that species annotations are consistent with the latest species definitions. We have developed an automated method for bacterial species identification that is an extension of ribosomal multilocus sequence typing (rMLST). The method calculates an 'rMLST nucleotide identity' (rMLST-NI) based on the nucleotides present in the protein-encoding ribosomal genes derived from bacterial genomes. rMLST-NI was used to validate the species annotations of 11839 publicly available and genomes based on a comparison with a library of type strain genomes. rMLST-NI was compared with two whole-genome average nucleotide identity methods (OrthoANIu and FastANI) and the -mer based Kleborate software. The results of the four methods agreed across a dataset of 11839 bacterial genomes and identified a small number of entries (=89) with species annotations that required updating. The rMLST-NI method was 3.5 times faster than Kleborate, 4.5 times faster than FastANI and 1600 times faster than OrthoANIu. rMLST-NI represents a fast and generic method for species identification using type strains as a reference.
细菌基因组学在医学和公共卫生微生物学领域做出了越来越多的贡献。因此，准确识别细菌基因组的物种是一项重要任务，尤其是随着在线数据库中存储的基因组数量迅速增加，并且经常发现新的物种。现有的数据库条目需要定期重新评估，以确保物种注释与最新的物种定义一致。我们开发了一种自动化的细菌物种鉴定方法，该方法是核糖体多位点序列分型（rMLST）的扩展。该方法基于从细菌基因组中衍生的蛋白质编码核糖体基因中的核苷酸计算出“rMLST 核苷酸同一性”（rMLST-NI）。rMLST-NI 用于基于与模式株基因组文库的比较来验证 11839 个公开可用的和基因组的物种注释。rMLST-NI 与两种全基因组平均核苷酸同一性方法（OrthoANIu 和 FastANI）和基于-mer 的 Kleborate 软件进行了比较。这四种方法在 11839 个细菌基因组数据集上的结果一致，并确定了少数需要更新的具有物种注释的条目（=89）。rMLST-NI 方法比 Kleborate 快 3.5 倍，比 FastANI 快 4.5 倍，比 OrthoANIu 快 1600 倍。rMLST-NI 代表了一种使用模式株作为参考的快速通用的物种鉴定方法。
