Laboratoire Microbiologie, Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli 1300, Lebanon.
Institut de Recherche pour le Développement (IRD), Microbes, Evolution, Phylogénie et Infection (MEPHI), Faculté de Médecine et de Pharmacie, Aix Marseille Université, 13005 Marseille, France.
Int J Mol Sci. 2022 Nov 3;23(21):13456. doi: 10.3390/ijms232113456.
Genome sequencing facilitates the study of bacterial taxonomy and allows the re-evaluation of the taxonomic relationships between species. Here, we aimed to analyze the draft genomes of four commensal clinical isolates from the semen of infertile Lebanese men. To determine the phylogenetic relationships among these strains and other spp. and to confirm their identity at the genomic level, we compared the genomes of these four isolates with the complete genome sequences of and and the draft genomes of , , , and that are available in the NCBI Genbank database. Our findings revealed that the WGS analysis accurately identified and corroborated the matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) species identities of the isolates. The combination of three well-established genome-based taxonomic tools (in silico DNA-DNA Hybridization, Ortho Average Nucleotide identity, and pangenomic studies) proved to be relatively the best identification approach. Notably, we also discovered that some strains that are deposited in databases contain many taxonomical errors. The latter is very important and must be addressed to prevent misdiagnosis and missing emerging etiologies. We also highlight the need for robust cut-offs to delineate the species using genomic tools.
基因组测序有助于研究细菌分类学，并允许重新评估物种之间的分类关系。在这里，我们旨在分析来自黎巴嫩不孕男性精液中的四个共生临床分离株的草图基因组。为了确定这些菌株与其他 spp.之间的系统发育关系，并在基因组水平上确认它们的身份，我们将这四个分离株的基因组与 和 的完整基因组序列以及可在 NCBI Genbank 数据库中获得的 、 、 和 的草图基因组进行了比较。我们的研究结果表明，WGS 分析准确地鉴定并证实了 MALDI-TOF 对分离株的物种身份。三种成熟的基于基因组的分类工具（核酸杂交、平均核苷酸一致性和泛基因组研究）的组合被证明是相对较好的鉴定方法。值得注意的是，我们还发现一些数据库中储存的 菌株存在许多分类学错误。这一点非常重要，必须加以解决，以防止误诊和遗漏新出现的病因。我们还强调需要使用基因组工具来建立稳健的截止值来划定物种界限。
