Comparative genomics of the genus Bifidobacterium
| Autor: | Vanessa Giubellini, Francesca Bottacini, David R. Riley, Marco Ventura, Douwe van Sinderen, Elena Foroni, Duccio Medini, Angelo Pavesi, Francesca Turroni, Hervé Tettelin |
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| Rok vydání: | 2010 |
| Předmět: |
DNA
Bacterial Proteome Genomics Computational biology Biology Microbiology Genome DNA sequencing Phylogenetics RNA Ribosomal 16S Humans Phylogeny Bifidobacterium Genetics Comparative genomics Comparative Genomic Hybridization Phylogenetic tree Sequence Analysis DNA biology.organism_classification Supertree Gastrointestinal Tract Multivariate Analysis Sequence Alignment Genome Bacterial |
| Zdroj: | Microbiology. 156:3243-3254 |
| ISSN: | 1465-2080 1350-0872 |
| Popis: | 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 aBifidobacteriumsupertree 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 genusBifidobacteriumthus presents a foundation for future functional analyses of this important group of GIT bacteria. |
| Databáze: | OpenAIRE |
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