Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort

Youwen Qin; Aki S. Havulinna; Yang Liu; Pekka Jousilahti; Scott C. Ritchie; Alex Tokolyi; Jon G. Sanders; Liisa Valsta; Marta Brożyńska; Qiyun Zhu; Anupriya Tripathi; Yoshiki Vázquez-Baeza; Rohit Loomba; Susan Cheng; Mohit Jain; Teemu Niiranen; Leo Lahti; Rob Knight; Veikko Salomaa; Michael Inouye; Guillaume Méric

doi:10.1038/s41588-021-00991-z

Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort

Youwen Qin, Aki S. Havulinna, Yang Liu, Pekka Jousilahti, Scott C. Ritchie, Alex Tokolyi, Jon G. Sanders, Liisa Valsta, Marta Brożyńska, Qiyun Zhu, Anupriya Tripathi, Yoshiki Vázquez-Baeza, Rohit Loomba, Susan Cheng, Mohit Jain, Teemu Niiranen, Leo Lahti, Rob Knight, Veikko Salomaa, Michael InouyeGuillaume Méric

Life Sciences, School of (SOLS)

Research output: Contribution to journal › Article › peer-review

136 Scopus citations

Abstract

Human genetic variation affects the gut microbiota through a complex combination of environmental and host factors. Here we characterize genetic variations associated with microbial abundances in a single large-scale population-based cohort of 5,959 genotyped individuals with matched gut microbial metagenomes, and dietary and health records (prevalent and follow-up). We identified 567 independent SNP–taxon associations. Variants at the LCT locus associated with Bifidobacterium and other taxa, but they differed according to dairy intake. Furthermore, levels of Faecalicatena lactaris associated with ABO, and suggested preferential utilization of secreted blood antigens as energy source in the gut. Enterococcus faecalis levels associated with variants in the MED13L locus, which has been linked to colorectal cancer. Mendelian randomization analysis indicated a potential causal effect of Morganella on major depressive disorder, consistent with observational incident disease analysis. Overall, we identify and characterize the intricate nature of host–microbiota interactions and their association with disease.

Original language	English (US)
Pages (from-to)	134-142
Number of pages	9
Journal	Nature Genetics
Volume	54
Issue number	2
DOIs	https://doi.org/10.1038/s41588-021-00991-z
State	Published - Feb 2022

ASJC Scopus subject areas

Genetics

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Qin, Y., Havulinna, A. S., Liu, Y., Jousilahti, P., Ritchie, S. C., Tokolyi, A., Sanders, J. G., Valsta, L., Brożyńska, M., Zhu, Q., Tripathi, A., Vázquez-Baeza, Y., Loomba, R., Cheng, S., Jain, M., Niiranen, T., Lahti, L., Knight, R., Salomaa, V., ... Méric, G. (2022). Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort. Nature Genetics, 54(2), 134-142. https://doi.org/10.1038/s41588-021-00991-z

Qin, Y, Havulinna, AS, Liu, Y, Jousilahti, P, Ritchie, SC, Tokolyi, A, Sanders, JG, Valsta, L, Brożyńska, M, Zhu, Q, Tripathi, A, Vázquez-Baeza, Y, Loomba, R, Cheng, S, Jain, M, Niiranen, T, Lahti, L, Knight, R, Salomaa, V, Inouye, M & Méric, G 2022, 'Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort', Nature Genetics, vol. 54, no. 2, pp. 134-142. https://doi.org/10.1038/s41588-021-00991-z

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abstract = "Human genetic variation affects the gut microbiota through a complex combination of environmental and host factors. Here we characterize genetic variations associated with microbial abundances in a single large-scale population-based cohort of 5,959 genotyped individuals with matched gut microbial metagenomes, and dietary and health records (prevalent and follow-up). We identified 567 independent SNP–taxon associations. Variants at the LCT locus associated with Bifidobacterium and other taxa, but they differed according to dairy intake. Furthermore, levels of Faecalicatena lactaris associated with ABO, and suggested preferential utilization of secreted blood antigens as energy source in the gut. Enterococcus faecalis levels associated with variants in the MED13L locus, which has been linked to colorectal cancer. Mendelian randomization analysis indicated a potential causal effect of Morganella on major depressive disorder, consistent with observational incident disease analysis. Overall, we identify and characterize the intricate nature of host–microbiota interactions and their association with disease.",

author = "Youwen Qin and Havulinna, {Aki S.} and Yang Liu and Pekka Jousilahti and Ritchie, {Scott C.} and Alex Tokolyi and Sanders, {Jon G.} and Liisa Valsta and Marta Bro{\.z}y{\'n}ska and Qiyun Zhu and Anupriya Tripathi and Yoshiki V{\'a}zquez-Baeza and Rohit Loomba and Susan Cheng and Mohit Jain and Teemu Niiranen and Leo Lahti and Rob Knight and Veikko Salomaa and Michael Inouye and Guillaume M{\'e}ric",

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AU - Jousilahti, Pekka

AU - Ritchie, Scott C.

AU - Tokolyi, Alex

AU - Sanders, Jon G.

AU - Valsta, Liisa

AU - Brożyńska, Marta

AU - Zhu, Qiyun

AU - Tripathi, Anupriya

AU - Vázquez-Baeza, Yoshiki

AU - Loomba, Rohit

AU - Cheng, Susan

AU - Jain, Mohit

AU - Niiranen, Teemu

AU - Lahti, Leo

AU - Knight, Rob

AU - Salomaa, Veikko

AU - Inouye, Michael

AU - Méric, Guillaume

PY - 2022/2

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Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort

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