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

The convergence of carbohydrate active gene repertoires in human gut microbes

Open access
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

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.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1073/pnas.0807339105

Cites

35 of 35 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Fermentation of dietary fibre is one of the dominant microbial metabolic activities in the colon.

    “the fermentation of dietary fibre represents one of the dominant microbial metabolic activities in the colon”

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Research works printed but not linked: 1

  1. [28]Stanier RY. Studies on non-fruiting myxobacteria I Cytophaga Johnsonae, N Sp, a chitin-decomposing myxobacterium. J Bacteriol. 1947;53:297–315. [PMC free article] [PubMed] [Google Scholar]

Cited by

Sorted by citations

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)
Venue
Proceedings of the National Academy of Sciences
Published
2008-09-30
Volume
105
Issue
39
Pages
15076-15081
ISSN
  • 0027-8424 (ISSN-L)
  • 1091-6490
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
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

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review