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The Relationship Between the Human Genome and Microbiome Comes into View
Open accessAbstract
The body's microbiome, composed of microbial cells that number in the trillions, is involved in human health and disease in ways that are just starting to emerge. The microbiome is assembled at birth, develops with its host, and is greatly influenced by environmental factors such as diet and other exposures. Recently, a role for human genetic variation has emerged as also influential in accounting for interpersonal differences in microbiomes. Thus, human genes may influence health directly or by promoting a beneficial microbiome. Studies of the heritability of gut microbiotas reveal a subset of microbes whose abundances are partly genetically determined by the host. However, the use of genome-wide association studies (GWASs) to identify human genetic variants associated with microbiome phenotypes has proven challenging. Studies to date are small by GWAS standards, and cross-study comparisons are hampered by differences in analytical approaches. Nevertheless, associations between microbes or microbial genes and human genes have emerged that are consistent between human populations. Most notably, higher levels of beneficial gut bacteria called Bifidobacteria are associated with the human lactase nonpersister genotype, which typically confers lactose intolerance, in several different human populations. It is time for the microbiome to be incorporated into studies that quantify interactions among genotype, environment, and the microbiome in order to predict human disease susceptibility.
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“Differences in microbiome diversity have been shown to be partially attributed by genotype and sex [79–83].”
From Gut microbiota changes in children with autism spectrum disorder: a systematic review (2020) · cites this paper as [80]
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Metadata
- Authors
- Goodrich, J. K., Davenport, E. R., Clark, A. G., & Ley, R. E.
- Affiliations
- Cornell University (US)
- Venue
- Annual Review of Genetics
- Publisher
- Annual Reviews
- Published
- 2017-11-27
- Volume
- 51
- Issue
- 1
- Pages
- 413-433
- ISSN
- 0066-4197 (ISSN-L)
- 1545-2948
- PMC
- PMC5744868
- OpenAlex
- W2611069262
- Cited by
- 311
- References
- 74
- Citations by year
- 2026: 9 · 2025: 22 · 2024: 35 · 2023: 30 · 2022: 37 · 2021: 52 · 2020: 62 · 2019: 43 · 2018: 20 · 2017: 1
- FWCI
- 3.25
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Locations
- Annual Review of Genetics (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Max Planck Digital Library (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Funders
- Max-Planck-Gesellschaft
- National Institutes of Health
- National Institute of Diabetes and Digestive and Kidney Diseases (F32DK109595, R01DK093595)
- 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
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Nutrition, Genetics, and Disease
- Keywords
- human microbiome, gut microbiota, host genetics, genetic variation, genome-wide association study, Bifidobacterium, lactase non-persistence, lactose intolerance, disease susceptibility
- MeSH terms
- Gastrointestinal Microbiome, Human Genetics, Amyotrophic Lateral Sclerosis, Bifidobacterium, Diet, Genotype, Humans, Lactose Intolerance, Obesity, Phenotype, Schizophrenia, Genetic Variation, Genome, Human, Quantitative Trait, Heritable, Gastrointestinal Tract, Genome-Wide Association Study
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 ›
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