Genome-scale insights into the metabolic landscape and evolutionary development of Bifidobacterium bifidum

Abstract

Background: Bifidobacterium bifidum (B. bifidum) is an infant gut symbiont specialized in degrading host-derived glycans. Despite its relevance in early life, the species’ genomic diversity has not yet been comprehensively surveyed, and current reference collections capture only a fraction of the global B. bifidum pangenome. Methods: In this study, we reconstructed the first comprehensive pangenome of B. bifidum using 1,351 high-quality genomes, including metagenome-assembled genomes. This dataset was used for in silico comparative genomics analyses to identify species-specific genetic and functional features. In vitro transcriptomics analyses were further performed to validate and functionally characterize selected species-specific traits. Results: Comparative genomic analysis with other human-associated bifidobacteria species identified 667 B. bifidum-specific clusters of orthologous genes mostly involved in carbohydrate utilization, osmotic regulation, and host interaction. Notably, B. bifidum displays the most extensive enzymatic repertoire for host-glycan degradation, dedicating 43% of its conserved glycoside hydrolases to these substrates. We identified significant gain-of-function events, including two unique phosphotransferase systems (PTS) for disaccharide uptake. Transcriptomic profiling corroborated the functional relevance of these PTS clusters, which were significantly up-regulated during growth on human milk oligosaccharides, mucin, and N-acetylglucosamine. While the species exhibits high genomic stability, a localized divergence (average nucleotide identitiy, ANI < 98.5%) was identified in rural, non-Westernized populations, reflecting niche-specific adaptations. Conclusion: The identified genomic framework highlighted a distinct evolutionary path of B. bifidum, placing this taxon as a metabolic cornerstone in the neonatal gut via extensive metabolic specialization toward glycan hosts.