Comparative genomics of the genus Bifidobacterium.
Whole-genome sequencing efforts have revolutionized the study of bifidobacterial genetics and physiology. Unfortunately, the sequence of a single genome does not provide information on bifidobacterial genetic diversity and on how genetic variability supports improved adaptation of these bacteria to the environment of the human gastrointestinal tract (GIT). Analysis of nine genomes from bifidobacterial species showed that such genomes display an open pan-genome structure. Mathematical extrapolation of the data indicates that the genome reservoir available to the bifidobacterial pan-genome consists of more than 5000 genes, many of which are uncharacterized, but which are probably important to provide adaptive abilities pertinent to the human GIT. We also define a core bifidobacterial gene set which will undoubtedly provide a new baseline from which one can examine the evolution of bifidobacteria. Phylogenetic investigation performed on a total of 506 orthologues that are common to nine complete bifidobacterial genomes allowed the construction of a Bifidobacterium supertree which is largely concordant with the phylogenetic tree obtained using 16S rRNA genes. Moreover, this supertree provided a more robust phylogenetic resolution than the 16S rRNA gene-based analysis. This comparative study of the genus Bifidobacterium thus presents a foundation for future functional analyses of this important group of GIT bacteria.
Bottacini
Francesca
F
Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Western Road, Cork, Ireland.|Laboratory of Probiogenomics, Department of Genetics, Biology of Microorganisms, Anthropology and Evolution, University of Parma, Italy.
Medini
Duccio
D
Novartis Vaccines and Diagnostics, Siena, Italy.
Pavesi
Angelo
A
Laboratory of Probiogenomics, Department of Genetics, Biology of Microorganisms, Anthropology and Evolution, University of Parma, Italy.
Turroni
Francesca
F
Laboratory of Probiogenomics, Department of Genetics, Biology of Microorganisms, Anthropology and Evolution, University of Parma, Italy.
Foroni
Elena
E
Laboratory of Probiogenomics, Department of Genetics, Biology of Microorganisms, Anthropology and Evolution, University of Parma, Italy.
Riley
David
D
Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, USA.
Giubellini
Vanessa
V
Laboratory of Probiogenomics, Department of Genetics, Biology of Microorganisms, Anthropology and Evolution, University of Parma, Italy.
Tettelin
Hervé
H
Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, USA.
van Sinderen
Douwe
D
Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Western Road, Cork, Ireland.
Ventura
Marco
M
Laboratory of Probiogenomics, Department of Genetics, Biology of Microorganisms, Anthropology and Evolution, University of Parma, Italy.
D001644:Bifidobacterium / Q000235:genetics*; D055028:Comparative Genomic Hybridization; D004269:DNA, Bacterial / Q000235:genetics; D041981:Gastrointestinal Tract / Q000382:microbiology; D016680:Genome, Bacterial; D023281:Genomics; D006801:Humans; D015999:Multivariate Analysis; D010802:Phylogeny; D020543:Proteome; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
D004269:DNA, Bacterial; D020543:Proteome; D012336:RNA, Ribosomal, 16S