A collection of research articles explores developments in interfacial transport and mixing, with wide-ranging practical applications.
New Research In
Physical Sciences
Featured Portals
Articles by Topic
Biological Sciences
Featured Portals
Articles by Topic
-
Communicated by Dieter Söll, Yale University, New Haven, CT (received for review July 3, 2002)
Abstract
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.
Footnotes
-
↵‡ 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. and ).
Abbreviations
-
GIT, gastrointestinal tract
-
E, expect value
-
IS, insertion sequence
- Received July 3, 2002.
- Accepted August 30, 2002.
- Copyright © 2002, The National Academy of Sciences
- Mark A. Schell*†,
- Maria Karmirantzou*‡,
- Berend Snel§¶,
- David Vilanova*,
- Bernard Berger*,
- Gabriella Pessi*∥,
- Marie-Camille Zwahlen*,
- Frank Desiere*,
- Peer Bork§,
- Michele Delley*,
- R. David Pridmore*, and
- Fabrizio Arigoni***
- *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 (received for review July 3, 2002)
Abstract
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.
Footnotes
-
↵‡ 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. and ).
Abbreviations
-
GIT, gastrointestinal tract
-
E, expect value
-
IS, insertion sequence
- Received July 3, 2002.
- Accepted August 30, 2002.
- Copyright © 2002, The National Academy of Sciences
The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract
Sign up for Article Alerts
Jump to section
You May Also be Interested in
Quantum computers capture headlines, but a quieter revolution in the world of sensors may be just as profound.
Image credit: Ola J. Joensen (Niels Bohr Institute, Copenhagen, Denmark).
Opinion: To advance sustainable stewardship, we must document not only biodiversity but geodiversity
Key abiotic features and processes should be incorporated into policy documents.
Image credit: Shutterstock/1968.
Researchers report a marine ammonite from the Cretaceous Period preserved in Burmese amber from Myanmar, and the rare specimen in amber warrants exploration of the possibly exceptional circumstances of its fossilization.
Image courtesy of Bo Wang.
Exposure to low humidity makes mice infected with influenza more susceptible to severe disease by impairing airway tissue repair and innate antiviral defense, suggesting that controlling humidity may help curb influenza during winter.
Image courtesy of Pixabay/qimono.