The DOI matches its Crossref record; 8 of the 8 references it cites were found in a registry or an index.
Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes
Open accessAbstract
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 × 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.
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A human gut microbial gene catalogue established by metagenomic sequencing
MetaHIT Consortium, Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., et al. (2010) · Nature · doi:10.1038/nature08821 · Cited by 11,624
Self-citationCAP3: A DNA Sequence Assembly Program
Huang, X., & Madan, A. (1999) · Genome Research · doi:10.1101/gr.9.9.868 · Cited by 5,261
Evolution of mammals and their gut microbes
Ley, R. E., Hamady, M., Lozupone, C., Turnbaugh, P. J., Ramey, R. R., Bircher, J. S., Schlegel, M. L., Tucker, T. A., Schrenzel, M. D., Knight, R., et al. (2008) · Science · doi:10.1126/science.1155725 · Cited by 3,747
Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach
Manichanh, C., Rigottier-Gois, L., Bonnaud, E., Gloux, K., Pelletier, E., Frangeul, L., Nalin, R., Jarrin, C., Chardon, P., Marteau, P., et al. (2006) · Gut · doi:10.1136/gut.2005.073817 · Cited by 2,277
Self-citationGlycan foraging in vivo by an intestine-adapted bacterial symbiont
Sonnenburg, J. L., Xu, J., Leip, D. D., Chen, C.-H., Westover, B. P., Weatherford, J., Buhler, J. D., & Gordon, J. I. (2005) · Science · doi:10.1126/science.1109051 · Cited by 1,184
Towards the human intestinal microbiota phylogenetic core
Tap, J., Mondot, S., Levenez, F., Pelletier, E., Caron, C., Furet, J., Ugarte, E., Muñoz‐Tamayo, R., Paslier, D. L. E., Nalin, R., et al. (2009) · Environmental Microbiology · doi:10.1111/j.1462-2920.2009.01982.x · Cited by 927
Self-citationComparative metagenomics revealed commonly enriched gene sets in human gut microbiomes
Kurokawa, K., Itoh, T., Kuwahara, T., Oshima, K., Toh, H., Toyoda, A., Takami, H., Morita, H., Sharma, V. K., Srivastava, T. P., et al. (2007) · DNA Research · doi:10.1093/dnares/dsm018 · Cited by 869
The convergence of carbohydrate active gene repertoires in human gut microbes
Lozupone, C. A., Hamady, M., Cantarel, B. L., Coutinho, P. M., Henrissat, B., Gordon, J. I., & Knight, R. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0807339105 · Cited by 139
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Gut microbiota functions: metabolism of nutrients and other food components
Rowland, I., Gibson, G., Heinken, A., Scott, K., Swann, J., Thiele, I., & Tuohy, K. (2018) · European Journal of Nutrition · doi:10.1007/s00394-017-1445-8 · Cited by 2,878
“[114] using in-depth pyrosequencing, discovered 73 CAZymes from 35 different families and also identified 18 multigenic clusters encoding complementary enzyme activities for fibre degradation.”
Microbial degradation of complex carbohydrates in the gut
Flint, H. J., Scott, K. P., Duncan, S. H., Louis, P., & Forano, E. (2012) · Gut Microbes · doi:10.4161/gmic.19897 · Cited by 2,331
Chemical transformation of xenobiotics by the human gut microbiota
Koppel, N., Maini Rekdal, V., & Balskus, E. P. (2017) · Science · doi:10.1126/science.aag2770 · Cited by 1,080
Diet-microbiota interactions and personalized nutrition
Kolodziejczyk, A. A., Zheng, D., & Elinav, E. (2019) · Nature Reviews Microbiology · doi:10.1038/s41579-019-0256-8 · Cited by 879
Intestinal microbiota in human health and disease: the impact of probiotics
Gerritsen, J., Smidt, H., Rijkers, G. T., & de Vos, W. M. (2011) · Genes & Nutrition · doi:10.1007/s12263-011-0229-7 · Cited by 724
Metadata
- Authors
- Tasse, L., Bercovici, J., Pizzut-Serin, S., Robe, P., Tap, J., Klopp, C., Cantarel, B. L., Coutinho, P. M., Henrissat, B., Leclerc, M., Doré, J., Monsan, P., Remaud-Simeon, M., & Potocki-Veronese, G.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2010-09-14
- Volume
- 20
- Issue
- 11
- Pages
- 1605-1612
- ISSN
- 1088-9051 (ISSN-L)
- OpenAlex
- W2147847105
- Cited by
- 273
- References
- 8
- Type
- posted content
- Language
- en
- Open access
- bronze
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- Tasse, L., Bercovici, J., Pizzut-Serin, S., Robe, P., Tap, J., Klopp, C., Cantarel, B. L., Coutinho, P. M., Henrissat, B., Leclerc, M., Doré, J., Monsan, P., Remaud-Simeon, M., & Potocki-Veronese, G. (2010). Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes. Genome Research. https://doi.org/10.1101/gr.108332.110
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