The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract

作者：Mark A. Schell, Maria Karmirantzou, ‎Berend Snel, David Vilanova, Bernard W. Berger, Gabriella Pessi, Marie-Camille Zwahlen, Frank Desiere, Peer Bork, Michèle Delley, Raymond David Pridmore, Fabrizio Arigoni · 发表于：Proceedings of the National Academy of Sciences · 年份：2002 · DOI：10.1073/pnas.212527599 · 被引用次数：953 · 研究领域：Probiotics and Fermented Foods、Enzyme Production and Characterization、Genomics and Phylogenetic Studies

Bifidobacteria are Gram-positive prokaryotes that naturally colonize the human gastrointestinal tract (GIT) and vagina. Although not numerically dominant in the complex intestinal microflora, they are considered as key commensals that promote a healthy GIT. We determined the 2.26-Mb genome sequence of an infant-derived strain of Bifidobacterium longum, and identified 1,730 possible coding sequences organized in a 60%-GC circular chromosome. Bioinformatic analysis revealed several physiological traits that could partially explain the successful adaptation of this bacteria to the colon. An unexpectedly large number of the predicted proteins appeared to be specialized for catabolism of a variety of oligosaccharides, some possibly released by rare or novel glycosyl hydrolases acting on "nondigestible" plant polymers or host-derived glycoproteins and glycoconjugates. This ability to scavenge from a large variety of nutrients likely contributes to the competitiveness and persistence of bifidobacteria in the colon. Many genes for oligosaccharide metabolism were found in self-regulated modules that appear to have arisen in part from gene duplication or horizontal acquisition. Complete pathways for all amino acids, nucleotides, and some key vitamins were identified; however, routes for Asp and Cys were atypical. More importantly, genome analysis provided insights into the reciprocal interactions of bifidobacteria with their hosts. We identified polypeptides that showed homology to mos...