Systems genetics uncovers associations among host amylase locus, gut microbiome, and metabolic traits in mice

Abstract

Background: Population studies have revealed associations between host genetic and gut microbiome in humans and mice. However, the molecular bases for how host genetic variation impacts the gut microbial community and bacterial metabolic niches remain largely unknown.

Results: We leveraged 90 inbred hyperlipidemic mouse strains from the hybrid mouse diversity panel (HMDP), previously studied for a variety of cardio-metabolic traits. Metagenomic analysis of cecal DNA followed by genome-wide association analysis identified genomic loci that were associated with microbial enterotypes in the gut. Among these, we detected a genetic locus surrounding multiple amylase genes that were associated with abundances of Firmicutes (Lachnospiraceae family) and Bacteroidetes (Muribaculaceae family) taxa encoding distinct starch and sugar degrading capabilities. The genetic variants at the amylase gene locus were associated with distinct gut microbial communities (enterotypes) with different predicted metabolic capacities for carbohydrate degradation. Mendelian randomization analysis revealed host phenotypes, including liver fibrosis and plasma HDL-cholesterol levels, that were associated with gut microbiome enterotypes.

Conclusions: This work reveals novel relationships among host genetic variation, gut microbial enterotypes, and host metabolic traits and supports the notion that variation of host amylase may represent a key determinant of gut microbiome in mice. Video Abstract.

Keywords: Genetic association study; Gut microbiome; Hybrid mouse diversity panel; Metagenomics; Systems genetics.

Fig. 1

Gut microbial enterotypes and bacterial co-abundance groups. A Clustering identified three microbial enterotypes in the Ath-HMDP mouse cohort. B Relative abundances of Firmicutes, Bacteroidetes, and Verrucomicrobia in the three enterotypes. C Correlation network of bacterial species (average relative abundance > 0.1% and present in at least 20% of samples) using CCREPE with a checkerboard score, indicating the co-occurrence or co-exclusion between species. Nodes represent the species and lines represent the similarity score. Solid lines represent co-occurrence bacterial species and dashed lines represent co-exclusion bacterial species. Significance was calculated by unpaired two-tailed Wilcoxon signed-rank test and is designated as follows: **p value < 0.01; ***p value < 0.001; ****p value < 0.0001. ET-B, Bacteroidetes enterotype; ET-F, Firmicutes enterotype; ET-V, Verrucomicrobia enterotype

Fig. 2

Host genomic loci are associated with gut microbial enterotypes. A PCA plot of microbial functions with the assignment of gut microbial enterotypes for each mouse. B SNP associations for microbial functions’ PC1 on chromosome 3. Protein coding genes are displayed for Chr3: 112–116 Mbp region. C Genomic locus at Chr3: 113–114 Mbp is associated with microbial functions’ PC1. The lead SNP is an intergenic SNP rs31001780. Dashed lines represent significance thresholds determined by permutation tests (P < 4 × 10⁻⁶). D Mice with alleles AA or GG at SNP rs31001780 are visualized in PCoA of microbial species beta-diversity (left) and PCA of microbial functions (right). E Relative abundance of Firmicutes, Bacteroidetes, and Verrucomicrobia from mice with AA or GG at SNP rs31001780. F Number of mice that have AA or GG at SNP rs31001780 in each of three enterotypes. Statistical difference between groups was tested by unpaired two-tailed Wilcoxon signed-rank test

Fig. 3

Muribaculaceae and gut bacterial alpha-amylase genes are more abundant in mouse strains with low-amylase gene copy numbers. A Phylogenetic relationship among the six mouse strains tested, C57BL/6 J (B6), A/J (A/J), 129S1/SvImJ (129), NOD/ShiLtJ (NOD), NZO/HLtJ (NZO), and CAST/EiJ (CAST). B Amylase gene (Amy1 and Amy2) copy number in the six mouse strains. C Relative abundance of Muribaculaceae family across the six mouse strains fed a high carbohydrate diet and its correlation with host amylase gene copy number. D Relative abundance of gut bacterial alpha-amylase gene (K07405) across the six mouse strains and its correlation with host amylase gene copy number. Statistical difference among groups was tested by unpaired two-tailed Wilcoxon signed-rank test

Fig. 4

Host metabolic phenotypes are associated with gut microbial enterotypes. A Spearman’s correlation between bacteria species from Firmicutes CAG and Bacteroidetes CAG with host metabolic phenotypes. B Bidirectional MR analysis between host metabolic traits and gut microbial functions’ PC1, which is the representative microbial features that distinguish Firmicutes and Bacteroidetes enterotypes. MR beta effect sizes using gut microbial functions’ PC1 as exposure and host metabolic traits as an outcome. C MR beta effect sizes using host metabolic traits as exposure and gut microbial functions’ PC1 as outcome