The abundance and variety of carbohydrate-active enzymes in the human gut microbiota
Tóm tắt
Từ khóa
Tài liệu tham khảo
Hooper, L. V., Littman, D. R. & Macpherson, A. J. Interactions between the microbiota and the immune system. Science 336, 1268–1273 (2012).
Wang, Z. et al. Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease. Nature 472, 57–63 (2011).
Karlsson, F. H. et al. Symptomatic atherosclerosis is associated with an altered gut metagenome. Nature Commun. 3, 1245 (2012).
Henao-Mejia, J. et al. Inflammasome-mediated dysbiosis regulates progression of NAFLD and obesity. Nature 482, 179–185 (2012).
Turnbaugh, P. J. et al. A core gut microbiome in obese and lean twins. Nature 457, 480–484 (2009). Metagenomic and 16S rRNA sequencing suggest the existence of a functional core microbiome and that obesity is associated with reduced bacterial diversity and altered metabolic pathways.
Qin, J. et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 490, 55–60 (2012). This huge metagenomic sequencing effort on the gut microbiota of 124 individuals has revealed a set of 3.3 million non-redundant genes. If 1.5–2% of these genes encode GHs and PLs (our model mini-microbiome has 1.75%), this would amount to some 50,000–60,000 GHs and PLs.
Ley, R. E. et al. Obesity alters gut microbial ecology. Proc. Natl Acad. Sci. USA 102, 11070–11075 (2005).
Paliy, O., Kenche, H., Abernathy, F. & Michail, S. High-throughput quantitative analysis of the human intestinal microbiota with a phylogenetic microarray. Appl. Environ. Microbiol. 75, 3572–3579 (2009).
Eckburg, P. B. et al. Diversity of the human intestinal microbial flora. Science 308, 1635–1638 (2005).
Lagier, J. C., Million, M., Hugon, P., Armougom, F. & Raoult, D. Human gut microbiota: repertoire and variations. Front. Cell. Infect. Microbiol. 2, 136 (2012).
Yatsunenko, T. et al. Human gut microbiome viewed across age and geography. Nature 486, 222–227 (2012).
Qin, J. et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59–65 (2010).
Abubucker, S. et al. Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput. Biol. 8, e1002358 (2012).
Grabitske, H. A. & Slavin, J. L. Low-digestible carbohydrates in practice. J. Am. Diet. Assoc. 108, 1677–1681 (2008).
Topping, D. L. & Clifton, P. M. Short-chain fatty acids and human colonic function: roles of resistant starch and nonstarch polysaccharides. Physiol. Rev. 81, 1031–1064 (2001).
Lattimer, J. M. & Haub, M. D. Effects of dietary fiber and its components on metabolic health. Nutrients 2, 1266–1289 (2010).
Martens, E. C. et al. Recognition and degradation of plant cell wall polysaccharides by two human gut symbionts. PLoS Biol. 9, e1001221 (2011). This study shows that two species of gut bacteria, B. thetaiotaomicron and Bacteroides ovatus , are capable of utilizing nearly all the major plant and host complex glycans, including type II rhamnogalacturonan.
Cantarel, B. L., Lombard, V. & Henrissat, B. Complex carbohydrate utilization by the healthy human microbiome. PLoS ONE 7, e28742 (2012). This analysis of 520 metagenomic samples from five major body sites shows that even when the microbial community composition varies, the CAZyme profiles are very similar within a body site, suggesting that the observed functional profile and microbiota have adapted to the local carbohydrate composition.
Bernalier-Donadille, A. [Fermentative metabolism by the human gut microbiota]. Gastroenterol. Clin. Biol. 34 (Suppl. 1), S16–S22 (2010) (in French).
McNeil, N. I. The contribution of the large intestine to energy supplies in man. Am. J. Clin. Nutr. 39, 338–342 (1984).
Hijova, E. & Chmelarova, A. Short chain fatty acids and colonic health. Bratisl. Lek. Listy 108, 354–358 (2007).
Floch, M. H. & Hong-Curtiss, J. Probiotics and functional foods in gastrointestinal disorders. Curr. Treat. Opt. Gastroenterol. 5, 311–321 (2002).
Hamer, H. M. et al. Review article: the role of butyrate on colonic function. Aliment. Pharmacol. Ther. 27, 104–119 (2008).
Henrissat, B. A classification of glycosyl hydrolases based on amino acid sequence similarities. Biochem. J. 280, 309–316 (1991).
Koropatkin, N. M., Cameron, E. A. & Martens, E. C. How glycan metabolism shapes the human gut microbiota. Nature Rev. Microbiol. 10, 323–335 (2012).
Lombard, V. et al. A hierarchical classification of polysaccharide lyases for glycogenomics. Biochem. J. 432, 437–444 (2010).
Gloster, T. M., Turkenburg, J. P., Potts, J. R., Henrissat, B. & Davies, G. J. Divergence of catalytic mechanism within a glycosidase family provides insight into evolution of carbohydrate metabolism by human gut flora. Chem. Biol. 15, 1058–1067 (2008).
Davies, G. & Henrissat, B. Structures and mechanisms of glycosyl hydrolases. Structure 3, 853–859 (1995).
Henrissat, B. & Bairoch, A. Updating the sequence-based classification of glycosyl hydrolases. Biochem. J. 316, 695–696 (1996).
Henrissat, B. & Bairoch, A. New families in the classification of glycosyl hydrolases based on amino acid sequence similarities. Biochem. J. 293, 781–788 (1993).
Henrissat, B. & Davies, G. Structural and sequence-based classification of glycoside hydrolases. Curr. Opin. Struct. Biol. 7, 637–644 (1997).
Cantarel, B. L. et al. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res. 37, D233–D238 (2009).
Lairson, L. L., Henrissat, B., Davies, G. J. & Withers, S. G. Glycosyltransferases: structures, functions, and mechanisms. Annu. Rev. Biochem. 77, 521–555 (2008).
Bjursell, M. K., Martens, E. C. & Gordon, J. I. Functional genomic and metabolic studies of the adaptations of a prominent adult human gut symbiont, Bacteroides thetaiotaomicron, to the suckling period. J. Biol. Chem. 281, 36269–36279 (2006).
Mirande, C. et al. Dietary fibre degradation and fermentation by two xylanolytic bacteria Bacteroides xylanisolvens XB1A and Roseburia intestinalis XB6B4 from the human intestine. J. Appl. Microbiol. 109, 451–460 (2010).
Flint, H. J., Bayer, E. A., Rincon, M. T., Lamed, R. & White, B. A. Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis. Nature Rev. Microbiol. 6, 121–131 (2008).
Robert, C., Del'Homme, C. & Bernalier-Donadille, A. Interspecies H2 transfer in cellulose degradation between fibrolytic bacteria and H2-utilizing microorganisms from the human colon. FEMS Microbiol. Lett. 205, 209–214 (2001).
Sonnenburg, J. L. et al. Glycan foraging in vivo by an intestine-adapted bacterial symbiont. Science 307, 1955–1959 (2005).
Markowitz, V. M. et al. The integrated microbial genomes system: an expanding comparative analysis resource. Nucleic Acids Res. 38, D382–D390 (2010).
Markowitz, V. M. et al. IMG: the Integrated Microbial Genomes database and comparative analysis system. Nucleic Acids Res. 40, D115–D122 (2012).
The Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature 486, 207–214 (2012).
Kuriki, T. & Imanaka, T. The concept of the α-amylase family: structural similarity and common catalytic mechanism. J. Biosci. Bioeng. 87, 557–565 (1999).
Stam, M. R., Danchin, E. G., Rancurel, C., Coutinho, P. M. & Henrissat, B. Dividing the large glycoside hydrolase family 13 into subfamilies: towards improved functional annotations of α-amylase-related proteins. Protein Eng. Des. Sel. 19, 555–562 (2006).
Leitch, E. C., Walker, A. W., Duncan, S. H., Holtrop, G. & Flint, H. J. Selective colonization of insoluble substrates by human faecal bacteria. Environ. Microbiol. 9, 667–679 (2007).
Vollmer, W., Joris, B., Charlier, P. & Foster, S. Bacterial peptidoglycan (murein) hydrolases. FEMS Microbiol. Rev. 32, 259–286 (2008).
Hehemann, J. H. et al. Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature 464, 908–912 (2010).
Kitahara, M., Sakamoto, M., Ike, M., Sakata, S. & Benno, Y. Bacteroides plebeius sp. nov. and Bacteroides coprocola sp. nov., isolated from human faeces. Int. J. Syst. Evol. Microbiol. 55, 2143–2147 (2005).
Hehemann, J. H., Kelly, A. G., Pudlo, N. A., Martens, E. C. & Boraston, A. B. Bacteria of the human gut microbiome catabolize red seaweed glycans with carbohydrate-active enzyme updates from extrinsic microbes. Proc. Natl Acad. Sci. USA 109, 19786–19791 (2012).
Zoetendal, E. G., Plugge, C. M., Akkermans, A. D. & de Vos, W. M. Victivallis vadensis gen. nov., sp. nov., a sugar-fermenting anaerobe from human faeces. Int. J. Syst. Evol. Microbiol. 53, 211–215 (2003).