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Beaumont M, Goodrich JK, Jackson MA, Yet I, Davenport ER, Vieira-Silva S, Debelius J, Pallister T, Mangino M, Raes J, Knight R, Clark AG, Ley RE, Spector TD, Bell JT. Heritable components of the human fecal microbiome are associated with visceral fat. Genome Biol 2016; 17:189. [PMID: 27666579 PMCID: PMC5036307 DOI: 10.1186/s13059-016-1052-7] [Citation(s) in RCA: 150] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 08/31/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Variation in the human fecal microbiota has previously been associated with body mass index (BMI). Although obesity is a global health burden, the accumulation of abdominal visceral fat is the specific cardio-metabolic disease risk factor. Here, we explore links between the fecal microbiota and abdominal adiposity using body composition as measured by dual-energy X-ray absorptiometry in a large sample of twins from the TwinsUK cohort, comparing fecal 16S rRNA diversity profiles with six adiposity measures. RESULTS We profile six adiposity measures in 3666 twins and estimate their heritability, finding novel evidence for strong genetic effects underlying visceral fat and android/gynoid ratio. We confirm the association of lower diversity of the fecal microbiome with obesity and adiposity measures, and then compare the association between fecal microbial composition and the adiposity phenotypes in a discovery subsample of twins. We identify associations between the relative abundances of fecal microbial operational taxonomic units (OTUs) and abdominal adiposity measures. Most of these results involve visceral fat associations, with the strongest associations between visceral fat and Oscillospira members. Using BMI as a surrogate phenotype, we pursue replication in independent samples from three population-based cohorts including American Gut, Flemish Gut Flora Project and the extended TwinsUK cohort. Meta-analyses across the replication samples indicate that 8 OTUs replicate at a stringent threshold across all cohorts, while 49 OTUs achieve nominal significance in at least one replication sample. Heritability analysis of the adiposity-associated microbial OTUs prompted us to assess host genetic-microbe interactions at obesity-associated human candidate loci. We observe significant associations of adiposity-OTU abundances with host genetic variants in the FHIT, TDRG1 and ELAVL4 genes, suggesting a potential role for host genes to mediate the link between the fecal microbiome and obesity. CONCLUSIONS Our results provide novel insights into the role of the fecal microbiota in cardio-metabolic disease with clear potential for prevention and novel therapies.
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Affiliation(s)
- Michelle Beaumont
- Department of Twin Research & Genetic Epidemiology, King's College London, St Thomas' Hospital, 3rd Floor, South Wing, Block D, London, SE1 7EH, UK
| | - Julia K Goodrich
- Department of Microbiology, Cornell University, Ithaca, NY, 14853, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Matthew A Jackson
- Department of Twin Research & Genetic Epidemiology, King's College London, St Thomas' Hospital, 3rd Floor, South Wing, Block D, London, SE1 7EH, UK
| | - Idil Yet
- Department of Twin Research & Genetic Epidemiology, King's College London, St Thomas' Hospital, 3rd Floor, South Wing, Block D, London, SE1 7EH, UK
| | - Emily R Davenport
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Sara Vieira-Silva
- Department of Microbiology and Immunology, KU Leuven - University of Leuven, Leuven, Belgium
- VIB lab for Bioinformatics and (eco-)systems biology, Leuven, Belgium
| | - Justine Debelius
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, 80309, USA
- Present address: Departments of Pediatrics and Computer Science and Engineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Tess Pallister
- Department of Twin Research & Genetic Epidemiology, King's College London, St Thomas' Hospital, 3rd Floor, South Wing, Block D, London, SE1 7EH, UK
| | - Massimo Mangino
- Department of Twin Research & Genetic Epidemiology, King's College London, St Thomas' Hospital, 3rd Floor, South Wing, Block D, London, SE1 7EH, UK
| | - Jeroen Raes
- Department of Microbiology and Immunology, KU Leuven - University of Leuven, Leuven, Belgium
- VIB lab for Bioinformatics and (eco-)systems biology, Leuven, Belgium
| | - Rob Knight
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, 80309, USA
- Biofrontiers Institute, University of Colorado, Boulder, CO, 80309, USA
- Howard Hughes Medical Institute, Boulder, CO, 80309, USA
- Present address: Departments of Pediatrics and Computer Science and Engineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Andrew G Clark
- Department of Microbiology, Cornell University, Ithaca, NY, 14853, USA
| | - Ruth E Ley
- Department of Microbiology, Cornell University, Ithaca, NY, 14853, USA
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Tim D Spector
- Department of Twin Research & Genetic Epidemiology, King's College London, St Thomas' Hospital, 3rd Floor, South Wing, Block D, London, SE1 7EH, UK.
| | - Jordana T Bell
- Department of Twin Research & Genetic Epidemiology, King's College London, St Thomas' Hospital, 3rd Floor, South Wing, Block D, London, SE1 7EH, UK.
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