Wuyts Sander, Wittouck Stijn, De Boeck Ilke, Allonsius Camille N, Pasolli Edoardo, Segata Nicola, Lebeer Sarah
Research Group Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium.
Centre for Integrative Biology, University of Trento, Trento, Italy.
mSystems. 2017 Aug 22;2(4). doi: 10.1128/mSystems.00061-17. eCollection 2017 Jul-Aug.
Although the genotypic and phenotypic properties of the group have been studied extensively, the taxonomic structure has been the subject of debate for a long time. Here, we performed a large-scale comparative analysis by using 183 publicly available genomes supplemented with a strain isolated from the human upper respiratory tract. On the basis of this analysis, we identified inconsistencies in the taxonomy and reclassified all of the genomes according to their most closely related type strains. This led to the identification of a catalase-encoding gene in all 10 strains, making it the first described catalase-positive species in the genus. Moreover, we found that 6 of 10 genomes contained a SecA2/SecY2 gene cluster with two putative glycosylated surface adhesin proteins. Altogether, our results highlight current inconsistencies in the taxonomy of the group and reveal new clade-associated functional features. The closely related species of the group are extensively studied because of their applications in food fermentations and as probiotics. Our results show that many strains in this group are incorrectly classified and that reclassifying them to their most closely related species type strain improves the functional predictive power of their taxonomy. In addition, our findings may spark increased interest in the species. We find that after reclassification, only 10 genomes remain classified as . These strains show some interesting properties. First, they all appear to be catalase positive. This suggests that they have increased oxidative stress resistance. Second, we isolated an strain from the human upper respiratory tract and discovered that it and multiple other strains harbor one or even two large, glycosylated putative surface adhesins. This might inspire further exploration of this species as a potential probiotic organism.
尽管对该菌群的基因型和表型特性已进行了广泛研究，但分类结构长期以来一直是争论的焦点。在此，我们通过使用183个公开可用的基因组，并补充了一株从人类上呼吸道分离的菌株，进行了大规模比较分析。基于此分析，我们发现了分类学上的不一致之处，并根据它们与最密切相关的模式菌株对所有基因组进行了重新分类。这导致在所有10株该菌群菌株中鉴定出一个过氧化氢酶编码基因，使其成为该属中首个被描述的过氧化氢酶阳性物种。此外，我们发现10个该菌群基因组中有6个包含一个SecA2/SecY2基因簇以及两个假定的糖基化表面粘附素蛋白。总之，我们的结果突出了该菌群分类学中当前的不一致之处，并揭示了与新分支相关的功能特征。该菌群的密切相关物种因其在食品发酵和作为益生菌方面的应用而被广泛研究。我们的结果表明，该菌群中的许多菌株分类错误，将它们重新分类为与其最密切相关的物种模式菌株可提高其分类学的功能预测能力。此外，我们的发现可能会引发对该物种的更多关注。我们发现重新分类后，只有10个基因组仍被归类为该菌群。这些菌株表现出一些有趣的特性。首先，它们似乎都呈过氧化氢酶阳性。这表明它们具有更强的氧化应激抗性。其次，我们从人类上呼吸道分离出一株该菌群菌株，并发现它和其他多个该菌群菌株含有一种甚至两种大型糖基化假定表面粘附素。这可能会激发对该物种作为潜在益生菌生物体的进一步探索。
