title: Comparative genomics of the Bifidobacterium breve taxon.
abstract: BACKGROUND
  Bifidobacteria are commonly found as part of the microbiota of the gastrointestinal tract (GIT) of a broad range of hosts, where their presence is positively correlated with the host's health status. In this study, we assessed the genomes of thirteen representatives of Bifidobacterium breve, which is not only a frequently encountered component of the (adult and infant) human gut microbiota, but can also be isolated from human milk and vagina.
  
  
  RESULTS
  In silico analysis of genome sequences from thirteen B. breve strains isolated from different environments (infant and adult faeces, human milk, human vagina) shows that the genetic variability of this species principally consists of hypothetical genes and mobile elements, but, interestingly, also genes correlated with the adaptation to host environment and gut colonization. These latter genes specify the biosynthetic machinery for sortase-dependent pili and exopolysaccharide production, as well as genes that provide protection against invasion of foreign DNA (i.e. CRISPR loci and restriction/modification systems), and genes that encode enzymes responsible for carbohydrate fermentation. Gene-trait matching analysis showed clear correlations between known metabolic capabilities and characterized genes, and it also allowed the identification of a gene cluster involved in the utilization of the alcohol-sugar sorbitol.
  
  
  CONCLUSIONS
  Genome analysis of thirteen representatives of the B. breve species revealed that the deduced pan-genome exhibits an essentially close trend. For this reason our analyses suggest that this number of B. breve representatives is sufficient to fully describe the pan-genome of this species. Comparative genomics also facilitated the genetic explanation for differential carbon source utilization phenotypes previously observed in different strains of B. breve.
authors.forename: Francesca
authors.initials: F
authors.lastname: Bottacini
authors.forename: Mary
authors.initials: M
authors.lastname: O'Connell Motherway
authors.forename: Justin
authors.initials: J
authors.lastname: Kuczynski
authors.forename: Kerry Joan
authors.initials: KJ
authors.lastname: O'Connell
authors.forename: Fausta
authors.initials: F
authors.lastname: Serafini
authors.forename: Sabrina
authors.initials: S
authors.lastname: Duranti
authors.forename: Christian
authors.initials: C
authors.lastname: Milani
authors.forename: Francesca
authors.initials: F
authors.lastname: Turroni
authors.forename: Gabriele Andrea
authors.initials: GA
authors.lastname: Lugli
authors.forename: Aldert
authors.initials: A
authors.lastname: Zomer
authors.forename: Daria
authors.initials: D
authors.lastname: Zhurina
authors.forename: Christian
authors.initials: C
authors.lastname: Riedel
authors.affiliation: Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Western Road, Cork, Ireland. marco.ventura@unipr.it.
authors.forename: Marco
authors.initials: M
authors.lastname: Ventura
authors.forename: Douwe
authors.initials: D
authors.lastname: van Sinderen
mesh_terms: D001644:Bifidobacterium / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D050260:Carbohydrate Metabolism; D016000:Cluster Analysis; D019295:Computational Biology; D004251:DNA Transposable Elements; D023061:Gene Order; D056726:Genetic Association Studies; D014644:Genetic Variation; D016680:Genome, Bacterial; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D055442:Metabolome; D055432:Metabolomics; D008969:Molecular Sequence Data; D005810:Multigene Family; D010802:Phylogeny
chemical_list: D004251:DNA Transposable Elements