Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada.
Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Québec City, QC G1V 0A6, Canada.
FEMS Microbiol Lett. 2024 Jan 9;371. doi: 10.1093/femsle/fnae089.
The genus Flavobacterium comprises a diversity of species, including fish pathogens. Multiple techniques have been used to identify isolates of this genus, such as phenotyping, polymerase chain reaction genotyping, and in silico whole-genome taxonomy. In this study, we demonstrate that whole-genome-based taxonomy, using average nucleotide identity and molecular phylogeny, is the most accurate approach for Flavobacterium species. We obtained various isolated strains from official collections; these strains had been previously characterized by a third party using various identification methodologies. We analyzed isolates by PCR genotyping using previously published primers targeting gyrB and gyrA genes, which are supposedly specific to the genus Flavobacterium and Flavobacterium psychrophilum, respectively. After genomic analysis, nearly half of the isolates had their identities re-evaluated: around a quarter of them were re-assigned to other genera and two isolates are new species of flavobacteria. In retrospect, the phenotyping method was the least accurate. While gyrB genotyping was accurate with the isolates included in this study, bioinformatics analysis suggests that only 70% of the Flavobacterium species could be appropriately identified using this approach. We propose that whole-genome taxonomy should be used for accurate Flavobacterium identification, and we encourage bacterial collections to review the identification of isolates identified by phenotyping.
黄杆菌属包含多种物种，包括鱼类病原体。已经使用了多种技术来鉴定该属的分离株，例如表型分析、聚合酶链反应基因分型和基于全基因组的计算分类学。在这项研究中，我们证明了基于全基因组的分类学，使用平均核苷酸同一性和分子系统发育，是鉴定黄杆菌属物种最准确的方法。我们从官方收藏中获得了各种分离株；这些菌株之前已由第三方使用各种鉴定方法进行了表征。我们使用先前针对 gyrB 和 gyrA 基因发表的引物通过 PCR 基因分型分析了分离株，这两个基因分别被认为是黄杆菌属和嗜冷黄杆菌的特异性基因。基因组分析后，近一半的分离株重新评估了其身份：其中约四分之一被重新分配到其他属，两个分离株是新的黄杆菌种。回想起来，表型方法的准确性最低。虽然 gyrB 基因分型在本研究中包含的分离株中是准确的，但生物信息学分析表明，只有 70%的黄杆菌属物种可以通过这种方法进行适当鉴定。我们建议使用全基因组分类学来进行准确的黄杆菌属鉴定，并鼓励细菌收藏对通过表型鉴定的分离株进行重新鉴定。
