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Microbiology
The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract
¶
*Nestlé Research Center, Vers-Chez-les-Blanc, Lausanne 1000,
Switzerland; Department of Microbiology, University of
Georgia, Athens, GA 30602; and European Molecular Biology
Laboratory, Meyerhoffstrasse 1, 69117 Heidelberg, Germany
Communicated by Dieter Söll, Yale University, New Haven, CT and approved August 30, 2002 (received for review July 3, 2002)
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 most major proteins needed for production of glycoprotein-binding fimbriae, structures that could possibly be important for adhesion and persistence in the GIT. We also found a eukaryotic-type serine protease inhibitor (serpin) possibly involved in the reported immunomodulatory activity of bifidobacteria.
Abbreviations: GIT, gastrointestinal tract; E, expect value; IS, insertion sequence
Present address: Serono Pharmaceutical Research
Institute, Ch. des Aulx 14, 1204 Geneva, Switzerland. ¶ Present address: Computational Genomics, Nijmegen Center for Molecular Life Sciences, Center for Molecular and Biomolecular Informatics, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands.
|| Present address: Center for Microbial Pathogenesis, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT 06030-3710.
** To whom correspondence should be addressed. E-mail: fabrizio.arigoni{at}rdls.nestle.com.
Data deposition: The sequences reported in this paper have been deposited in the GenBank database (accession nos. AF540971 and AE014295).
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