Genome-scale insights into the metabolic landscape and evolutionary development of Bifidobacterium bifidum.
- 1Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma 43124, Italy.
- 2Department of Medicine and Surgery, University of Parma, Parma 43124, Italy.
- 3Microbiome Research Hub, University of Parma, Parma 43124, Italy.
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.
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BibTeX
@article{selleri2026genomescale,
title = {{Genome-scale insights into the metabolic landscape and evolutionary development of Bifidobacterium bifidum.}},
author = {Emanuele Selleri and Giulia Longhi and Chiara Tarracchini and Erica de Carolis and Silvia Petraro and Leonardo Mancabelli and Christian Milani and Francesca Turroni and Marco Ventura and Gabriele Andrea Lugli},
journal = {Microbiome research reports},
year = {2026},
month = aug,
doi = {10.20517/mrr.2026.19},
url = {https://europepmc.org/article/MED/42899037},
note = {CC BY},
}
RIS
TY - JOUR
TI - Genome-scale insights into the metabolic landscape and evolutionary development of Bifidobacterium bifidum.
AU - Emanuele Selleri
AU - Giulia Longhi
AU - Chiara Tarracchini
AU - Erica de Carolis
AU - Silvia Petraro
AU - Leonardo Mancabelli
AU - Christian Milani
AU - Francesca Turroni
AU - Marco Ventura
AU - Gabriele Andrea Lugli
PY - 2026
DA - 2026/08/12
JO - Microbiome research reports
DO - 10.20517/mrr.2026.19
UR - https://europepmc.org/article/MED/42899037
AB - 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.
SN - 2771-5965
ER -