title: Insights from genomes of representatives of the human gut commensal Bifidobacterium bifidum.
abstract: Bifidobacteria are bacterial gut commensals of mammals, birds and social insects that are perceived to influence the metabolism/physiology of their host. In this context, members of the Bifidobacterium bifidum species are believed to significantly contribute to the overall microbiota of the human gut at infant stage. However, the molecular reasons for their adaptation to this environment are poorly understood. In this study, we analysed the pan-genome of B. bifidum species by decoding genomes of 15 B. bifidum strains, which highlighted the existence of a conserved gene uniquely present in this bifidobacterial taxon, underscoring a nutrient acquisition strategy that targets host-derived glycans, such as those present in mucin. Growth experiments and corresponding transcriptomic analyses confirmed the in silico data and supported these intriguing and unique host glycan-specific saccharolytic features. The ubiquity of the genetic features of B. bifidum for the breakdown of host glycans was confirmed by interrogating metagenomic datasets, thereby supporting the notion that metabolic access to host-derived glycans is a potent evolutionary force that has shaped B. bifidum genomes and consequently the ecology of the infant intestinal microbiota.
authors.affiliation: Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy.
authors.forename: Sabrina
authors.initials: S
authors.lastname: Duranti
authors.affiliation: Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy.
authors.forename: Christian
authors.initials: C
authors.lastname: Milani
authors.affiliation: Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy.
authors.forename: Gabriele Andrea
authors.initials: GA
authors.lastname: Lugli
authors.affiliation: Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland.
authors.forename: Francesca
authors.initials: F
authors.lastname: Turroni
authors.affiliation: Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy.
authors.forename: Leonardo
authors.initials: L
authors.lastname: Mancabelli
authors.affiliation: Departamento de Microbiologia y Bioquimica de Productos Lacteos, Consejo Superior de Investigaciones Científicas, CSIC, Villaviciosa, Asturias, Spain.
authors.forename: Borja
authors.initials: B
authors.lastname: Sanchez
authors.affiliation: Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy.
authors.forename: Chiara
authors.initials: C
authors.lastname: Ferrario
authors.affiliation: Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy.
authors.forename: Alice
authors.initials: A
authors.lastname: Viappiani
authors.affiliation: Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy.
authors.forename: Marta
authors.initials: M
authors.lastname: Mangifesta
authors.affiliation: Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy.
authors.forename: Walter
authors.initials: W
authors.lastname: Mancino
authors.affiliation: Departamento de Microbiologia y Bioquimica de Productos Lacteos, Consejo Superior de Investigaciones Científicas, CSIC, Villaviciosa, Asturias, Spain.
authors.forename: Miguel
authors.initials: M
authors.lastname: Gueimonde
authors.affiliation: Departamento de Microbiologia y Bioquimica de Productos Lacteos, Consejo Superior de Investigaciones Científicas, CSIC, Villaviciosa, Asturias, Spain.
authors.forename: Abelardo
authors.initials: A
authors.lastname: Margolles
authors.affiliation: Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland.
authors.forename: Douwe
authors.initials: D
authors.lastname: van Sinderen
authors.affiliation: Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: Ventura
mesh_terms: D000818:Animals; D001644:Bifidobacterium / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism*; D005075:Biological Evolution; D000069196:Gastrointestinal Microbiome; D041981:Gastrointestinal Tract / Q000382:microbiology*; D016680:Genome, Bacterial; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D008969:Molecular Sequence Data; D009077:Mucins / Q000378:metabolism; D011134:Polysaccharides / Q000378:metabolism*
chemical_list: D009077:Mucins; D011134:Polysaccharides