Institut Pasteur, Genotyping of Pathogens and Public Health (PF8), 28 rue du Dr Roux, F-75724 Paris Cedex, France.
Res Microbiol. 2010 Mar;161(2):82-90. doi: 10.1016/j.resmic.2009.12.006. Epub 2010 Jan 11.
The genus Bifidobacterium comprises several species that are important contributors to the gut microbiome, with some strains having beneficial health effects. Understanding the evolutionary emergence of advantageous biological properties requires knowledge of the genetic diversity and clonal structure of species. We sequenced seven housekeeping genes in 119 Bifidobacterium strains of Bifidobacterium animalis, Bifidobacterium bifidum, Bifidobacterium breve and Bifidobacterium longum. Phylogenetic analysis of concatenated sequences delineated sequence clusters that correspond to previously named taxa, and suggested that B. longum subsp. infantis is a nascent lineage emerging from within B. longum subsp. longum. Clear traces of recombination among distant bifidobacterial species indicate leaky species borders and warn against the practice of single gene-based identification. Multilocus sequence typing achieved precise strain genotyping, with discrimination indices above 99% in B. bifidum, B. breve and B. longum, providing a powerful tool for strain traceability, colonization dynamics and ecological studies. Frequent homologous recombination accelerates clonal diversification and may facilitate the transfer of biological properties among bifidobacterial strains.
双歧杆菌属包含几个对肠道微生物群有重要贡献的物种，其中一些菌株具有有益的健康影响。了解有利生物特性的进化出现需要了解物种的遗传多样性和克隆结构。我们对 119 株双歧杆菌动物双歧杆菌、双歧杆菌双歧杆菌、双歧杆菌短双歧杆菌和长双歧杆菌的 7 个管家基因进行了测序。串联序列的系统发育分析划定了与先前命名的分类群相对应的序列簇，并表明长双歧杆菌亚种婴儿双歧杆菌是从长双歧杆菌亚种长双歧杆菌中出现的新生谱系。在远缘双歧杆菌种之间存在明显的重组痕迹表明种间边界存在渗漏，并警告不要基于单个基因进行识别。多位点序列分型实现了精确的菌株基因分型，在双歧杆菌双歧杆菌、双歧杆菌短双歧杆菌和长双歧杆菌中的区分指数均高于 99%，为菌株溯源、定植动态和生态研究提供了强大工具。频繁的同源重组加速了克隆多样化，可能有助于双歧杆菌菌株之间生物特性的转移。
