Large-Scale Phylogenomics of the Group Highlights Taxonomic Inconsistencies and Reveals Novel Clade-Associated Features.

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.