Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes
2010
Tasse, Lena | Bercovici, Juliette | Pizzut-Serin, Sandra | Robe, Patrick | Tap, Julien | Klopp, Christophe | Cantarel, Brandi L. | Coutinho, Pedro, M | Henrissat, Bernard | Leclerc, Marion | Dore, Joel | Monsan, Pierre | Remaud Simeon, Magali | Potocki-Veronese, Gabrielle | Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP) ; Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse) ; Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS) | LibraGenSA | Unité de recherche d'Écologie et Physiologie du Système Digestif (UEPSD) ; Institut National de la Recherche Agronomique (INRA) | Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA) ; Institut National de la Recherche Agronomique (INRA) | Architecture et fonction des macromolécules biologiques (AFMB) ; Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS) | Region Midi-Pyrenees, France; European Regional Development Fund; Institut National de la Recherche Agronomique, France (the French National Institute for Agricultural Research); ANR-Agence Nationale de la Recherche-The French National Research Agency [ANR-06-PNRA-024]; French National Institute for Agricultural Research
The human gut microbiome is a complex ecosystem composed mainly of uncultured bacteria. It plays an essential role in the catabolism of dietary fibers, the part of plant material in our diet that is not metabolized in the upper digestive tract, because the human genome does not encode adequate carbohydrate active enzymes (CAZymes). We describe a multi-step functionally based approach to guide the in-depth pyrosequencing of specific regions of the human gut metagenome encoding the CAZymes involved in dietary fiber breakdown. High-throughput functional screens were first applied to a library covering 5.4 X 10(9) bp of metagenomic DNA, allowing the isolation of 310 clones showing beta-glucanase, hemicellulase, galactanase, amylase, or pectinase activities. Based on the results of refined secondary screens, sequencing efforts were reduced to 0.84 Mb of nonredundant metagenomic DNA, corresponding to 26 clones that were particularly efficient for the degradation of raw plant polysaccharides. Seventy-three CAZymes from 35 different families were discovered. This corresponds to a fivefold target-gene enrichment compared to random sequencing of the human gut metagenome. Thirty-three of these CAZy encoding genes are highly homologous to prevalent genes found in the gut microbiome of at least 20 individuals for whose metagenomic data are available. Moreover, 18 multigenic clusters encoding complementary enzyme activities for plant cell wall degradation were also identified. Gene taxonomic assignment is consistent with horizontal gene transfer events in dominant gut species and provides new insights into the human gut functional trophic chain. [Supplemental material is available online at http://www.genome.org. The sequence data from this study have been submitted to GenBank (http://www.ncbi.nlm.nih.gov/Genbank/) under accession nos. GU942928-GU942942 and GU942944-GU942954.]
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