The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract
By M. Schell, M. Karmirantzou, Berend Snel, David Vilanova, B. Berger, Gabriella Pessi, M. Zwahlen, Frank Desiere, Peer Bork, M. Delley and 2 more. Proceedings of the National Academy of Sciences of the United States of America, 2002
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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.
Subfields: Biotechnology, Food Science, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/409697882b023096cae22cd66cbc31aeeb93ad10
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Citations in the corpus
- Dietary modulation of the human colonic microbiota: updating the concept of prebiotics (2004, background): “In this context, several genes specific for oligosaccharide metabolism have been identified in bifidobacteria to help explain the selective action of prebiotics that is clearly an integral part of the overall prebiotic effect (Schell et al. 2002).”
- Carbohydrate metabolism in Bifidobacteria (2011, background): “The gene content of a bifidobacterial genome seems to reflect its adaptation to the human GIT environment, as is evident from the presence of genes that encode a variety of carbohydrate-modifying enzymes, such as glycosyl hydrolases, sugar ABC transporters, and PEP-PTS (PEP— phosphoenolpyruvate; PTS”
- Bifidobacteria and Butyrate-Producing Colon Bacteria: Importance and Strategies for Their Stimulation in the Human Gut (2016, background): “The only gene (i.e., BL1543) that was first annotated as a β-endoxylanase in B. longum NCC2705 (Schell et al., 2002) has shown to be an extracellular membraneassociated α-arabinofuranosidase (Lagaert et al., 2010, 2014; Rivière et al., 2014).”
- Bifidobacteria and Their Role as Members of the Human Gut Microbiota (2016, background): “Fifteen out of the 20 patients remained in remission throughout the trial, suggesting that administration of this bacterial cocktail is beneficial in maintaining remission from ulcerative colitis (Venturi et al., 1999; Gionchetti et al., 2000).”
- Ecological Role of Lactobacilli in the Gastrointestinal Tract: Implications for Fundamental and Biomedical Research (2008, neutral): “vironmentally regulated expression systems (83, 110).”
- Xylanases, xylanase families and extremophilic xylanases. (2005, background): “[135] Schell,M.”
- Understanding the effects of diet on bacterial metabolism in the large intestine (2007, background): “Both Bifidobacterium longum (Schell et al. 2002) and Bacteroides thetaiotaomicron (Xu et al. 2003) dedicate at least 8% of their genomes to carbohydrate transport and metabolism functions.”