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The convergence of carbohydrate active gene repertoires in human gut microbes
Open accessAbstract
The extreme variation in gene content among phylogenetically related microorganisms suggests that gene acquisition, expansion, and loss are important evolutionary forces for adaptation to new environments. Accordingly, phylogenetically disparate organisms that share a habitat may converge in gene content as they adapt to confront shared challenges. This response should be especially pronounced for functional genes that are important for survival in a particular habitat. We illustrate this principle by showing that the repertoires of two different types of carbohydrate-active enzymes, glycoside hydrolases and glycosyltransferases, have converged in bacteria and archaea that live in the human gut and that this convergence is largely due to horizontal gene transfer rather than gene family expansion. We also identify gut microbes that may have more similar dietary niches in the human gut than would be expected based on phylogeny. The techniques used to obtain these results should be broadly applicable to understanding the functional genes and evolutionary processes important for adaptation in many environments and useful for interpreting the large number of reference microbial genome sequences being generated for the International Human Microbiome Project.
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Metadata
- Authors
- Lozupone, C. A., Hamady, M., Cantarel, B. L., Coutinho, P. M., Henrissat, B., Gordon, J. I., & Knight, R.
- Affiliations
- University of Colorado Boulder (US)
- Centre National de la Recherche Scientifique (FR)
- Washington University in St. Louis (US)
- ORCID
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2008-09-30
- Volume
- 105
- Issue
- 39
- Pages
- 15076-15081
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC2546442
- OpenAlex
- W2075770792
- Cited by
- 139
- References
- 35
- Citations by year
- 2026: 2 · 2025: 1 · 2024: 8 · 2023: 3 · 2022: 4 · 2021: 5 · 2020: 7 · 2019: 8 · 2018: 7 · 2017: 7 · 2016: 4 · 2015: 9 · 2014: 9 · 2013: 11 · 2012: 17
- FWCI
- 5.07
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Science Foundation (0812861)
- Crohn's and Colitis Foundation of America
- Crohn's and Colitis Foundation
- National Institutes of Health
- National Institute of General Medical Sciences (T32GM065103, T32GM008759, T32GM142607)
- National Institute of Diabetes and Digestive and Kidney Diseases (R37DK030292, DK-30292, P01DK078669, DK78669, DK 70977, R01DK070977, R01DK030292)
- Office of International Science and Engineering
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Keywords
- carbohydrate-active enzymes, glycoside hydrolases, glycosyltransferases, horizontal gene transfer, gene family expansion, human gut microbiome, gut microbiota, gut archaea, dietary niche, microbial adaptation
- MeSH terms
- Archaea, Bacteria, Carbohydrates, Genes, Bacterial, Multigene Family, Glycoside Hydrolases, Humans, Intestines, Phylogeny, Genetic Variation, Cluster Analysis, Glycosyltransferases, Genes, Archaeal, Gene Transfer, Horizontal
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