Cited by 351Gut microbiota and healthGenomics and Phylogenetic StudiesOral microbiology and periodontitis research

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Structural variation in the gut microbiome associates with host health

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Zeevi, David, Korem, Tal, Godneva, Anastasia, Bar, Noam, Kurilshikov, Alexander, Lotan-Pompan, Maya, Weinberger, Adina, Fu, Jingyuan, Wijmenga, Cisca, Zhernakova, Alexandra, Segal, Eran·2019·Nature

DOI 10.1038/s41586-019-1065-y

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Abstract

Differences in the presence of even a few genes between otherwise identical bacterial strains may result in critical phenotypic differences. Here we systematically identify microbial genomic structural variants (SVs) and find them to be prevalent in the human gut microbiome across phyla and to replicate in different cohorts. SVs are enriched for CRISPR-associated and antibiotic-producing functions and depleted from housekeeping genes, suggesting that they have a role in microbial adaptation. We find multiple associations between SVs and host disease risk factors, many of which replicate in an independent cohort. Exploring genes that are clustered in the same SV, we uncover several possible mechanistic links between the microbiome and its host, including a region in Anaerostipes hadrus that encodes a composite inositol catabolism-butyrate biosynthesis pathway, the presence of which is associated with lower host metabolic disease risk. Overall, our results uncover a nascent layer of variability in the microbiome that is associated with microbial adaptation and host health.

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Authors: Zeevi, D., Korem, T., Godneva, A., Bar, N., Kurilshikov, A., Lotan-Pompan, M., Weinberger, A., Fu, J., Wijmenga, C., Zhernakova, A., & Segal, E.
Affiliations: Weizmann Institute of Science (IL)
Columbia University Irving Medical Center (US)
University Medical Center Groningen (NL)
Corresponding author: Zeevi, David
Segal, Eran
ORCID: Zeevi, David
Korem, Tal
Godneva, Anastasia
Kurilshikov, Alexander
Weinberger, Adina
Fu, Jingyuan
Wijmenga, Cisca
Zhernakova, Alexandra
Segal, Eran
Venue: Nature
Publisher: Springer Science and Business Media LLC
Published: 2019-03-27
Volume: 568
Issue: 7750
Pages: 43-48
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/s41586-019-1065-y
OpenAlex: W2924485771
Cited by: 351
References: 53
Citations by year: 2026: 33 · 2025: 40 · 2024: 58 · 2023: 46 · 2022: 55 · 2021: 51 · 2020: 45 · 2019: 23
FWCI: 14.39
Type: journal article
Language: en
Open access: green
hdl.handle.net
Licence: other-oa
www.springer.com/tdm (tdm)
Locations: Nature (publishedVersion)
PubMed (publishedVersion)
RePEc: Research Papers in Economics (submittedVersion)
University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion, other-oa)
Funders: James S. McDonnell Foundation
Nederlandse Organisatie voor Wetenschappelijk Onderzoek (864.13.013, 016.Vidi.178.056)
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
Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
Keywords: gut microbiota, structural variants, bacterial genomes, antibiotic production, Anaerostipes hadrus, metabolic disorders, host-microbe interactions, bacterial adaptation
MeSH terms: Gastrointestinal Microbiome, Host Microbial Interactions, Adaptation, Physiological, Bacteria, Butyrates, Disease Susceptibility, Eubacterium, Feces, Genes, Bacterial, Health, Humans, Inositol, Risk Factors, Genetic Variation, Cohort Studies, Ecosystem, Microbial Viability, Metagenomics

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