A comprehensive assessment of demographic, environmental, and host genetic associations with gut microbiome diversity in healthy individuals

Scepanovic et al. Microbiome (2019) 7:130 https://doi.org/10.1186/s40168-019-0747-x RESEARCH Open Access A comprehensive assessment of demographic, environmental, and host genetic associations with gut microbiome diversity in healthy individuals Petar Scepanovic1,2, Flavia Hodel1,2, Stanislas Mondot3, Valentin Partula4,5, Allyson Byrd6, Christian Hammer6,7, Cécile Alanio8, Jacob Bergstedt9, Etienne Patin10,11, Mathilde Touvier4, Olivier Lantz12,13, Matthew L. Albert6, Darragh Duffy14, Lluis Quintana-Murci10,11, Jacques Fellay1,2,15* and The Milieu Intérieur Consortium Abstract Background: The gut microbiome is an important determinant of human health. Its composition has been shown to be influenced by multiple environmental factors and likely by host genetic variation. In the framework of the Milieu Intérieur Consortium, a total of 1000 healthy individuals of western European ancestry, with a 1:1 sex ratio and evenly stratified across five decades of life (age 20–69), were recruited. We generated 16S ribosomal RNA profiles from stool samples for 858 participants. We investigated genetic and non-genetic factors that contribute to individual differences in fecal microbiome composition. Results: Among 110 demographic, clinical, and environmental factors, 11 were identified as significantly correlated with α-diversity, ß-diversity, or abundance of specific microbial communities in multivariable models. Age and blood alanine aminotransferase levels showed the strongest associations with microbiome diversity. In total, all non-genetic factors explained 16.4% of the variance. We then searched for associations between > 5 million single nucleotide polymorphisms and the same indicators of fecal microbiome diversity, including the significant non-genetic factors as covariates. No genome-wide significant associations were identified after correction for multiple testing. A small fraction of previously reported associations between human genetic variants and specific taxa could be replicated in our cohort, while no replication was observed for any of the diversity metrics. Conclusion: In a well-characterized cohort of healthy individuals, we identified several non-genetic variables associated with fecal microbiome diversity. In contrast, host genetics only had a negligible influence. Demographic and environmental factors are thus the main contributors to fecal microbiome composition in healthy individuals. Trial registration: ClinicalTrials.gov identifier NCT01699893 Keywords: Microbiome, Gut, Human, Genomics, 16S rRNA gene sequencing, GWAS, Healthy, Demographics, Environment * Correspondence: 1 School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland 2 Swiss Institute of Bioinformatics, Lausanne, Switzerland Full list of author information is available at the end of the article © The Author(s). 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Scepanovic et al. Microbiome (2019) 7:130 Background A wide diversity of microbial species colonizes the human body, providing considerable benefits to the host through a range of different functions [1]. Notably, these microbes generate metabolites that can act as energy sources for cell metabolism, promote the development and the functionality of the immune system, and prevent colonization by pathogenic microorganisms [2]. The human intestine harbors a particularly diverse microbial ecosystem. Multiple 16S ribosomal RNA (rRNA) gene sequencing and metagenomic studies established that each individual gut microbiome harbors a unique combination of microbial life [3, 4]. An estimated 150 to 400 bacterial species reside in each person’s gut [5]. Typically, the human gut microbiome is dominated by five bacterial phyla: Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Verrucomicrobia [6, 7]. These contain almost all of the bacterial species found in the human gastrointestinal tract, which can also be classified in higher-level taxonomic groups such as genera, families, orders, and classes [8]. The relative proportions of microbial species vary extensively between individuals [9] and have been shown to be age-dependent [10]. The microbiome composition evolves rapidly during the first 3 years of life, followed by a more gradual maturation [11], and then is predicted to remain relatively stable throughout adult life [12]. A variety of environmental and clinical factors including diet, lifestyle, diseases, and medications can induce substantial shifts in the microbiome composition [13, 14]. Multiple studies have shown that diet and medications are the main forces influencing gut microbial diversity [15–22]. Yet, they only explain a small percentage of the microbiome variation observed in the human population. Host genetics has also been proposed as a contributor in determining the relative Page 2 of 15 abundance of specific gut microbes [23, 24]. Several studies have searched for associations between human genetic variation and gut microbiome diversity [20–22, 25–28], but only a few genetic loci have been replicated across these studies. As a consequence, most of the interindividual variability in gut microbiome composition remains unexplained. In this study, we leveraged the in-depth phenotypic and genotypic information available for the Milieu intérieur (MI) cohort—a population-based study of 1000 healthy individuals of western European ancestry, evenly stratified by sex (1:1) and age. We investigated the role of socio-demographic and environmental factors in inter-individual gut microbiome variation (Fig. 1). In particular, we were able to assess the impact of family status, income, occupational status and educational level, smoking habits, sleeping habits, psychological problems, and nutritional behavior. We also evaluated the influence of basic physiological parameters (such as body mass index), family and personal medical history (including vaccination history), and multiple laboratory results (comprising mostly blood biochemical measurements). Finally, we investigated the potential impact of human genetic variation using a genome-wide association study (GWAS) framework, including as covariates, the non-genetic factors that were found to be correlated with various measures of gut microbiome diversity. Results Gut microbiome diversity in healthy donors To characterize the bacterial diversity of the gut flora of the 1000 healthy donors, we performed 16S (...truncated)