Colonized Niche, Evolution and Function Signatures of Bifidobacterium pseudolongum within Bifidobacterial Genus

Background: Although genomic features of various bifidobacterial species have received much attention in the past decade, information on Bifidobacterium pseudolongum was limited. In this study, we retrieved 887 publicly available genomes of bifidobacterial species, and tried to elucidate phylogenetic and potential functional roles of B. pseudolongum within the Bifidobacterium genus. Results: The results indicated that B. pseudolongum formed a population structure with multiple monophyletic clades, and had established associations with different types of mammals. The abundance of B. pseudolongum was inversely correlated with that of the harmful gut bacterial taxa. We also found that B. pseudolongum showed a strictly host-adapted lifestyle with a relatively smaller genome size, and higher intra-species genetic diversity in comparison with the other tested bifidobacterial species. For functional aspects, B. pseudolongum showed paucity of specific metabolic functions, and enrichment of specific enzymes degrading complex plant carbohydrates and host glycans. In addition, B. pseudolongum possessed a unique signature of probiotic effector molecules compared with the other tested bifidobacterial species. The investigation on intra-species evolution of B. pseudolongum indicated a clear evolution trajectory in which considerable clade-specific genes, and variation on genomic diversity by clade were observed. Conclusions: These findings provide valuable information for explaining the host adaptability of B. pseudolongum, its evolutionary role, as well as its potential probiotic effects.