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Zahavi L, Lavon A, Reicher L, Shoer S, Godneva A, Leviatan S, Rein M, Weissbrod O, Weinberger A, Segal E. Bacterial SNPs in the human gut microbiome associate with host BMI. Nat Med 2023; 29:2785-2792. [PMID: 37919437 PMCID: PMC10999242 DOI: 10.1038/s41591-023-02599-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 09/19/2023] [Indexed: 11/04/2023]
Abstract
Genome-wide association studies (GWASs) have provided numerous associations between human single-nucleotide polymorphisms (SNPs) and health traits. Likewise, metagenome-wide association studies (MWASs) between bacterial SNPs and human traits can suggest mechanistic links, but very few such studies have been done thus far. In this study, we devised an MWAS framework to detect SNPs and associate them with host phenotypes systematically. We recruited and obtained gut metagenomic samples from a cohort of 7,190 healthy individuals and discovered 1,358 statistically significant associations between a bacterial SNP and host body mass index (BMI), from which we distilled 40 independent associations. Most of these associations were unexplained by diet, medications or physical exercise, and 17 replicated in a geographically independent cohort. We uncovered BMI-associated SNPs in 27 bacterial species, and 12 of them showed no association by standard relative abundance analysis. We revealed a BMI association of an SNP in a potentially inflammatory pathway of Bilophila wadsworthia as well as of a group of SNPs in a region coding for energy metabolism functions in a Faecalibacterium prausnitzii genome. Our results demonstrate the importance of considering nucleotide-level diversity in microbiome studies and pave the way toward improved understanding of interpersonal microbiome differences and their potential health implications.
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Affiliation(s)
- Liron Zahavi
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Amit Lavon
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Lee Reicher
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- Lis Maternity and Women's Hospital, Tel Aviv Sourasky Medical Center, Tel Aviv University (affiliated with Sackler Faculty of Medicine), Tel Aviv, Israel
| | - Saar Shoer
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Anastasia Godneva
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sigal Leviatan
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Michal Rein
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Adina Weinberger
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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Shoer S, Shilo S, Godneva A, Ben-Yacov O, Rein M, Wolf BC, Lotan-Pompan M, Bar N, Weiss EI, Houri-Haddad Y, Pilpel Y, Weinberger A, Segal E. Impact of dietary interventions on pre-diabetic oral and gut microbiome, metabolites and cytokines. Nat Commun 2023; 14:5384. [PMID: 37666816 PMCID: PMC10477304 DOI: 10.1038/s41467-023-41042-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 08/17/2023] [Indexed: 09/06/2023] Open
Abstract
Diabetes and associated comorbidities are a global health threat on the rise. We conducted a six-month dietary intervention in pre-diabetic individuals (NCT03222791), to mitigate the hyperglycemia and enhance metabolic health. The current work explores early diabetes markers in the 200 individuals who completed the trial. We find 166 of 2,803 measured features, including oral and gut microbial species and pathways, serum metabolites and cytokines, show significant change in response to a personalized postprandial glucose-targeting diet or the standard of care Mediterranean diet. These changes include established markers of hyperglycemia as well as novel features that can now be investigated as potential therapeutic targets. Our results indicate the microbiome mediates the effect of diet on glycemic, metabolic and immune measurements, with gut microbiome compositional change explaining 12.25% of serum metabolites variance. Although the gut microbiome displays greater compositional changes compared to the oral microbiome, the oral microbiome demonstrates more changes at the genetic level, with trends dependent on environmental richness and species prevalence in the population. In conclusion, our study shows dietary interventions can affect the microbiome, cardiometabolic profile and immune response of the host, and that these factors are well associated with each other, and can be harnessed for new therapeutic modalities.
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Affiliation(s)
- Saar Shoer
- Department of Computer Science and Applied Mathematics, The Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Smadar Shilo
- Department of Computer Science and Applied Mathematics, The Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, Israel
- The Jesse Z and Sara Lea Shafer Institute for Endocrinology and Diabetes, National Center for Childhood Diabetes, Schneider Children's Medical Center, Petah Tikva, Israel
| | - Anastasia Godneva
- Department of Computer Science and Applied Mathematics, The Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Orly Ben-Yacov
- Department of Computer Science and Applied Mathematics, The Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Michal Rein
- Department of Computer Science and Applied Mathematics, The Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Bat Chen Wolf
- Department of Computer Science and Applied Mathematics, The Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Maya Lotan-Pompan
- Department of Computer Science and Applied Mathematics, The Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Noam Bar
- Department of Computer Science and Applied Mathematics, The Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Ervin I Weiss
- Goldschleger School of Dental Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Prosthodontics, The Hebrew University-Hadassah School of Dental Medicine, Jerusalem, Israel
| | - Yael Houri-Haddad
- Department of Prosthodontics, The Hebrew University-Hadassah School of Dental Medicine, Jerusalem, Israel
| | - Yitzhak Pilpel
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | - Adina Weinberger
- Department of Computer Science and Applied Mathematics, The Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, The Weizmann Institute of Science, Rehovot, Israel.
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, Israel.
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