Genetic Determinants of the Gut Microbiome in UK Twins

• Published in: Cell host & microbe Vol. 19; no. 5; pp. 731 - 743
• Main Authors: Goodrich, Julia K., Davenport, Emily R., Beaumont, Michelle, Jackson, Matthew A., Knight, Rob, Ober, Carole, Spector, Tim D., Bell, Jordana T., Clark, Andrew G., Ley, Ruth E.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 11.05.2016
• Subjects: Base Sequence; Female; Gastrointestinal Microbiome - genetics; Genetic Variation; Humans; Male; Microbial Consortia - genetics; Twins; United Kingdom
• ISSN: 1931-3128; 1934-6069
• DOI: 10.1016/j.chom.2016.04.017

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. [Display omitted] •16S rRNA-based analysis of the gut microbiome in 1,126 twin pairs•Heritable bacterial taxa are temporally stable•Bifidobacterium associates with lactase gene variants; formate production links to blood pressure•Gene-microbe links involve genes related to diet, metabolism, olfaction, and defense Does host genotype shape the microbiome? Goodrich et al. present a gut microbiome analysis of 1,126 twin pairs, which extends the association between host genetics and select bacterial taxa. Lactase nonpersistence was linked to higher levels of Bifidobacteria. Other gene/microbe links relate to diet and barrier defense.