Cited by 1,048Gut microbiota and healthGenetic Associations and EpidemiologyOral microbiology and periodontitis research

Genetic determinants of the gut microbiome in UK twins

Open access
Goodrich, Julia K., Davenport, Emily R., Beaumont, Michelle, Jackson, Matthew A., Knight, Rob, Ober, Carole, Spector, Tim D., Bell, Jordana T. +2 more·2016·Cell Host & Microbe

Abstract

Studies in mice and humans have revealed intriguing associations between host genetics and the microbiome. Here we report a 16S rRNA-based analysis of the gut microbiome in 1,126 twin pairs, a subset of which was previously reported. Tripling the sample narrowed the confidence intervals around heritability estimates and uncovered additional heritable taxa, some of which are validated in other studies. Repeat sampling of subjects showed heritable taxa to be temporally stable. A candidate gene approach uncovered associations between heritable taxa and genes related to diet, metabolism, and olfaction. We replicate an association between Bifidobacterium and the lactase (LCT) gene locus and identify an association between the host gene ALDH1L1 and the bacteria SHA-98, suggesting a link between formate production and blood pressure. Additional genes detected are involved in barrier defense and self/non-self recognition. Our results indicate that diet-sensing, metabolism, and immune defense are important drivers of human-microbiome co-evolution.

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Crossref · 10.1016/j.chom.2016.04.017

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  • Twin studies and GWAS show that host genetics can influence the microbiome composition, and microbes can exert effects on the host genome, although the environment has an important role.

    “Twin studies and GWAS show that host genetics can influence the microbiome composition, and microbes can exert effects on the host genome, although the environment has an important role [121,122].”

    From Polycystic Ovary Syndrome: An Evolutionary Adaptation to Lifestyle and the Environment (2022) · cites this paper as [121]

    The Introduction reports that twin studies found a small host-genetic effect while environmental factors were paramount in shaping the microbiome. The Discussion and Experimental Procedures describe associations between host genes and microbial taxa, including GWAS analyses. Our copy does not show that microbes exert effects on the host genome; its discussion of gene–microbe interactions does not establish that direction of effect. (LLM, conf=0.86)

    Experimental — accuracy not yet measured
  • Host genetics influence the gut microbiome, as shown by twin studies demonstrating shared community structures between related individuals and temporally stable heritable taxa.

    “Host genetic influence15,16,1718, 19,20 on the gut microbiome is apparent from studies of monozygotic and dizygotic twin pairs that demonstrate shared community structures between related individuals21 and temporally stable heritable taxa17.”
  • Christensenella spp. is associated with lean body mass and variants in genes such as ALDH1L1 and GNA12.

    “For example, Christensenella spp. is associated with lean body mass and variants in genes such as ALDH1L1 and GNA12.65,66”
  • Genetics only perform a limited role in shaping the gut microbiota with an average level of 8.8% according to a 2016 data analysis of 1126 twins.

    “Genetics only perform a limited role in shaping the gut microbiota with an average level of 8.8% according to a 2016 data analysis of 1126 twins [7].”
  • Host-genetic influences on gut microbiome composition are likely to play a role in influencing the rate and extent of microbial xenobiotic metabolism.

    “host-genetic influences on gut microbiome composition (Goodrich et al., 2016;Rothschild et al., 2018) are also likely to play a role in influencing the rate and extent of microbial xenobiotic metabolism.”

    From Gut reactions: Breaking down xenobiotic–microbiome interactions (2019) · cites this paper as Goodrich et al., 2016

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Authors
Goodrich, J. K., Davenport, E. R., Beaumont, M., Jackson, M. A., Knight, R., Ober, C., Spector, T. D., Bell, J. T., Clark, A. G., & Ley, R. E.
Affiliations
  • Cornell University (US)
  • King's College London (GB)
  • University of California San Diego (US)
  • University of Chicago (US)
Corresponding author
Ley, Ruth E.
Venue
Cell Host & Microbe
Publisher
Elsevier BV
Published
2016-05
Volume
19
Issue
5
Pages
731-743
ISSN
1931-3128 (ISSN-L)
OpenAlex
W2360231252
Cited by
1,048
References
92
Citations by year
2026: 56 · 2025: 82 · 2024: 86 · 2023: 109 · 2022: 124 · 2021: 139 · 2020: 158 · 2019: 115 · 2018: 86 · 2017: 64 · 2016: 28 · 2015: 1
FWCI
50.74
Type
journal article
Language
en
Open access
Locations
  • Cell Host & Microbe (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
  • eScholarship (California Digital Library) (submittedVersion)
  • Research Portal (King's College London) (submittedVersion, cc-by-nc-nd)
  • Max Planck Institute for Plasma Physics (submittedVersion)
Funders
  • National Science Foundation
  • Wellcome Trust
  • National Institute for Health and Care Research (NF-SI-0507-10228, NF-SI-0514-10027)
  • King's College London
  • National Institutes of Health (1dp2od007444-01)
  • Medical Research Council (MR/N030125/1, MR/N01183X/1)
  • National Institute of Diabetes and Digestive and Kidney Diseases (F32DK109595, R01DK093595, P30DK020541)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
  • Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
Keywords
gut microbiota, host genetics, heritability, twins, Bifidobacterium, lactase gene, LCT gene, ALDH1L1, formate production, blood pressure, metabolism, olfaction, immune defense, self/non-self recognition, temporal stability
MeSH terms
Gastrointestinal Microbiome, Base Sequence, Female, United Kingdom, Humans, Male, Twins, Genetic Variation, Microbial Consortia

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