Heritable components of the human fecal microbiome are associated with visceral fat

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.

Keywords: Fecal microbiome; Genetic association; Heritability; Obesity; Twins; Visceral fat.

Fig. 1

Distribution and heritability of adiposity phenotypes. a Scatterplot matrix showing the distribution and correlation between six adiposity measures in 3666 twins. The distribution of each phenotype (prior to normalisation) is shown along the diagonal. The lower panel shows scatterplots for each pair of adiposity phenotypes, and the upper panel denotes the coefficients of determination. b Heritability of six adiposity measures in the TwinsUK cohort, as well as visceral fat measures in three independent cohorts: Framingham [39], Quebec [41] and Heritage [40]. The total variance of each adiposity phenotype is decomposed into variance components attributed to additive genetics (A) or narrow-sense heritability (h ²), common environment (C) and unique environment (E)

Fig. 2

Alpha diversity of the fecal microbiome in individuals with high and low fat content. For each phenotype, individuals who were more than 1.5 standard deviations from the mean of the phenotype were assigned to high and low phenotype groups respectively. Alpha diversity measures (using Shannon diversity) were compared between the high and low phenotype groups (Wilcoxon test * = 0.05 ** = 0.001 *** = 0.0001)

Fig. 3

Associations between fecal microbiome 16S OTUs and visceral fat in the TwinsUK and replication datasets. a The inner circle denotes the phylogenetic tree of OTUs, produced using iTOL [93] based on Greengenes May 2013 tree filtered for the OTUs in the sample. Tree leaves are coloured according to the direction of association with visceral fat, where blue indicates a negative association, while red indicates a positive association. The outer circle denotes the significance of each OTU-visceral fat association, where P values are plotted as –log₁₀ (P value), and the red line shows the Bonferroni significance threshold. The figure highlights the most-associated OTU in the sample (OTU 372146), as well as the two closed-reference OTUs that were significantly associated with host genetic variants in genes FHIT (OTU 181702) and ELAVL4 (194733). It also highlights the heritable Christensenellaceae OTU 176318. The figure also denotes the tree branches containing members of Clostridiales, Bacteroides and Christensenellaceae to accompany results and discussion in the main text. b Forest plot of beta coefficients with confidence intervals of eight OTUs that replicated robustly in a meta-analysis of three independent cohorts (TUK-R, AG and FGFP)

Fig. 4

Microbial functional analysis in obesity. a Microbial PICRUSt-predicted KEGG functions relevant to metabolism in the twin dataset, and their association with the six adiposity measures. The heatmap denotes the direction of association between each microbial PICRUSt-predicted KEGG function and adiposity measures, where blue indicates a negative association, while red indicates a positive association. Bonferroni-significant associations are highlighted (*). b Five KO genes that are differentially abundant between high and low visceral fat individuals in glyoxylate and dicarboxylate metabolism, as tested by a two-sided Welch’s t test. FDR-adjusted P values are reported at the right of the image, and stars indicate Bonferroni-significant associations. Figure was produced using STAMP [45]

Fig. 5

Peak genetic associations between obesity human genetic variants and adiposity-associated OTUs in the twin fecal microbiome. a Association between OTU 181702 and FHIT SNP rs74331972. The boxplot indicates change in OTU 181702 abundance with genotype at SNP rs74331972. The LocusZoom plot denotes the strength of association of OTU 181702 with SNP rs74331972, as well as the SNPs in the surrounding region. b Association between open reference OTU 25576 and TDRG1 SNP rs1433723. The boxplot indicates change in open reference OTU 25576 abundance with genotype at SNP rs1433723. The LocusZoom plot denotes the strength of association of open reference OTU 25576 with SNP rs1433723, as well as the SNPs in the surrounding region. c Association between OTU 194733 and ELAVL4 SNP rs2480677. The boxplot indicates change in OTU 194733 abundance with genotype at SNP rs2480677. The LocusZoom plot denotes the strength of association of OTU 194733 with SNP rs2480677, as well as the SNPs in the surrounding region. SNPs in all LocusZoom plots are coloured according to their strength of linkage disequilibrium with the peak SNP plotted