Twin study suggests gut microbial taxa abundance is partly regulated by host genotype

Your genes may influence your gut microbiota composition v

A recent study, led by Prof. Ruth Ley from the Department of Molecular Biology and Genetics at Cornell University in Ithaca (USA), has found that some human genes related to diet sensing, metabolism, and immunity may have a role in regulating the abundance of certain gut microbial taxa.

 Through a 16S ribosomal ribonucleic acid (rRNA)-based analysis of the gut microbiome in a cohort of 1,126 twin pairs (both identical –monozygotic– and fraternal –dizygotic– twins who were raised together) from the TwinsUK Study, the researchers demonstrated that some human genes related to diet, metabolism, taste and immune defence are involved in the regulation of the gut microbiome. The researchers used the genome-wide association (GWA) approach to look for connections between genetic variations in different twin pairs and certain bacterial types that were present and stable in the study subjects.

Relative abundance of the genus Bifidobacterium was related to lactase (LCT) gene variants: those who do not maintain a high lactase level throughout adulthood (called lactase nonpersistent) and thus likely have difficulty digesting lactose harboured higher levels of Bifidobacterium. Researchers also found links between specific gut bacteria and host genes involved in immunity, inflammation, fat sensing on the tongue, absorption of long-chain fatty acids in the gut, and formate production and consumption (the latter correlated with blood pressure). On the whole, these data show that host genes may influence phenotype through modulating microbiome components.

The taxon with the highest heritability — that is, the largest proportion of variance in a host trait explained by genetic rather than environmental effects — was Christensenellaceae, which forms co-occurrence consortium with other heritable taxa such as Methanobrevibacter smithii. When 530 individuals with samples collected at a second time, spaced out 946 days, were examined, it was found that heritable bacterial taxa were among the most stable taxa in the TwinsUK Dataset. This means heritable bacterial taxa are temporally stable.

According to Prof. Ley, “there have been identified more than a dozen microbes with known links to health that are heritable…, and although they are environmentally acquired, the genome also plays a part by determining which microorganisms are more dominant than others”.

In conclusion, these results highlight that there is genetic control of certain gut microbial taxa and gene-microbe associations involving genes related to diet, metabolism, taste and immunity.




Goodrich JK, Davenport ER, Beaumont M, et al. Genetic determinants of the gut microbiome in UK twins. Cell Host Microbe. 2016; 19(5):731-43.

Andreu Prados
Andreu Prados
Andreu Prados holds a Bachelor of Science Degree in Pharmacy & Human Nutrition and Dietetics. Science writer specialised in gut microbiota and probiotics, working also as lecturer and consultant in nutrition and healthcare. Follow Andreu on Twitter @andreuprados