{
  "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.",
  "abstract_shown": true,
  "affiliations": [
    "Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma 43124, Italy.",
    "Department of Medicine and Surgery, University of Parma, Parma 43124, Italy.",
    "Microbiome Research Hub, University of Parma, Parma 43124, Italy."
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 10,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Emanuele Selleri"
    },
    {
      "affs": [
        0
      ],
      "name": "Giulia Longhi"
    },
    {
      "affs": [
        0
      ],
      "name": "Chiara Tarracchini"
    },
    {
      "affs": [
        0
      ],
      "name": "Erica de Carolis"
    },
    {
      "affs": [
        0
      ],
      "name": "Silvia Petraro"
    },
    {
      "affs": [
        1,
        2
      ],
      "name": "Leonardo Mancabelli"
    },
    {
      "affs": [
        0,
        2
      ],
      "name": "Christian Milani"
    },
    {
      "affs": [
        0,
        2
      ],
      "name": "Francesca Turroni"
    },
    {
      "affs": [
        0,
        2
      ],
      "name": "Marco Ventura"
    },
    {
      "affs": [
        0,
        2
      ],
      "name": "Gabriele Andrea Lugli"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/48rssqx4fw2ac.bib",
  "cited_by": 0,
  "doi": "10.20517/mrr.2026.19",
  "fulltext_url": "https://europepmc.org/articles/PMC13678547",
  "id": "48rssqx4fw2ac",
  "issns": [
    "2771-5965"
  ],
  "landing_url": "https://europepmc.org/article/MED/42899037",
  "language": "eng",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1312|Gut microbiota and health"
    ]
  ],
  "openalex": "W7202229813",
  "pdf_url": "https://europepmc.org/articles/PMC13678547?pdf=render",
  "pmcid": "PMC13678547",
  "pmid": "42899037",
  "published": "2026-08-12",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/48rssqx4fw2ac.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:19:41Z",
      "native_id": "MED:42899037",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42899037"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Gut microbiota and health",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Genome-scale insights into the metabolic landscape and evolutionary development of Bifidobacterium bifidum.",
  "title_text": "Genome-scale insights into the metabolic landscape and evolutionary development of Bifidobacterium bifidum.",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:19:41Z",
  "url": "https://research.draconitic.com/paper/48rssqx4fw2ac",
  "venue": "Microbiome research reports",
  "versions": []
}