Cited by 139Gut microbiota and healthGenomics and Phylogenetic StudiesMicrobial Community Ecology and Physiology

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The convergence of carbohydrate active gene repertoires in human gut microbes

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Lozupone, Catherine A., Hamady, Micah, Cantarel, Brandi L., Coutinho, Pedro M., Henrissat, Bernard, Gordon, Jeffrey I., Knight, Rob·2008·Proceedings of the National Academy of Sciences

DOI 10.1073/pnas.0807339105PMC PMC2546442

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Abstract

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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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: Lozupone, Catherine A.
Cantarel, Brandi L.
Coutinho, Pedro M.
Henrissat, Bernard
Gordon, Jeffrey I.
Knight, Rob
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
DOI: 10.1073/pnas.0807339105
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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The convergence of carbohydrate active gene repertoires in human gut microbes

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