title: Prophages of the genus Bifidobacterium as modulating agents of the infant gut microbiota.
abstract: Phage predation is one of the key forces that shape genetic diversity in bacterial genomes. Phages are also believed to act as modulators of the microbiota composition and, consequently, as agents that drive bacterial speciation in complex bacterial communities. Very little is known about the occurrence and genetic variability of (pro)phages within the Bifidobacterium genus, a dominant bacterial group of the human infant microbiota. Here, we performed cataloguing of the predicted prophage sequences from the genomes of all currently recognized bifidobacterial type strains. We analysed their genetic diversity and deduced their evolutionary development, thereby highlighting an intriguing origin. Furthermore, we assessed infant gut microbiomes for the presence of (pro)phage sequences and found compelling evidence that these viral elements influence the composition of bifidobacterial communities in the infant gut microbiota.
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: 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: Francesca
authors.initials: F
authors.lastname: Turroni
authors.affiliation: Département de Biochimie, Microbiologie et Bio-Informatique and PROTEO, Faculté des Sciences et de Génie, Félix d'Hérelle Reference Center for Bacterial Viruses and GREB, Faculté de Médecine Dentaire, Université Laval, Québec City, Québec, Canada.
authors.forename: Denise
authors.initials: D
authors.lastname: Tremblay
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: Leonardo
authors.initials: L
authors.lastname: Mancabelli
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: Broad Institute of MIT and Harvard, Cambridge, MA, USA.
authors.forename: Doyle V
authors.initials: DV
authors.lastname: Ward
authors.affiliation: Department of Medical-Veterinary Science, University of Parma, Parma, Italy.
authors.forename: Maria Cristina
authors.initials: MC
authors.lastname: Ossiprandi
authors.affiliation: Département de Biochimie, Microbiologie et Bio-Informatique and PROTEO, Faculté des Sciences et de Génie, Félix d'Hérelle Reference Center for Bacterial Viruses and GREB, Faculté de Médecine Dentaire, Université Laval, Québec City, Québec, Canada.
authors.forename: Sylvain
authors.initials: S
authors.lastname: Moineau
authors.affiliation: APC Microbiome Institute and School of Microbiology, 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: D001644:Bifidobacterium / Q000145:classification / Q000235:genetics / Q000302:isolation & purification / Q000821:virology*; D005075:Biological Evolution; D005260:Female; D000069196:Gastrointestinal Microbiome; D041981:Gastrointestinal Tract / Q000382:microbiology; D014644:Genetic Variation; D006801:Humans; D007223:Infant; D008297:Male; D010802:Phylogeny; D039002:Prophages / Q000145:classification / Q000235:genetics / Q000302:isolation & purification* / Q000502:physiology