{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T03:28:29Z","timestamp":1786505309967,"version":"build-2736575974"},"reference-count":108,"publisher":"OAE Publishing Inc.","issue":"3","content-domain":{"domain":["oaepublish.com"],"crossmark-restriction":false},"short-container-title":["Microbiome Res Rep."],"abstract":"<jats:p>Background: Bifidobacterium bifidum (B. bifidum) is an infant gut symbiont specialized in degrading host-derived glycans. Despite its relevance in early life, the species\u2019 genomic diversity has not yet been comprehensively surveyed, and current reference collections capture only a fraction of the global B. bifidum pangenome.<\/jats:p>\n                  <jats:p>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.<\/jats:p>\n                  <jats:p>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 &lt; 98.5%) was identified in rural, non-Westernized populations, reflecting niche-specific adaptations.<\/jats:p>\n                  <jats:p>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.<\/jats:p>","DOI":"10.20517\/mrr.2026.19","type":"journal-article","created":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T02:52:33Z","timestamp":1786503153000},"update-policy":"https:\/\/doi.org\/10.20517\/oae.crossmark.policy","source":"Crossref","is-referenced-by-count":0,"title":["Genome-scale insights into the metabolic landscape and evolutionary development of Bifidobacterium 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