Linking the gut microbiome to host DNA methylation by a discovery and replication epigenome-wide association study

Both gene methylation and the gut microbiome are partially determined by host genetics and partially by environment. We investigated the relations between gene methylation in blood and the abundance of common gut bacteria profiled by 16s rRNA gene sequencing in two population-based Dutch cohorts: LifeLines-Deep (LLD, n = 616, discovery) and the Netherlands Twin Register (NTR, n = 296, replication). In LLD, we also explored microbiome composition using data generated by shotgun metagenomic sequencing (n = 683). We then investigated if genetic and environmental factors can explain the methylation-microbiota associations in a set of 78 associated CpG-taxa pairs from the EWAS meta-analysis. In both cohorts, blood and stool samples were collected within 2 weeks of each other. Methylation was profiled in blood samples using the Illumina 450K array. Methylation and microbiome analysis pipelines were harmonized across cohorts. Epigenome-wide association study (EWAS) of microbial features were analysed using linear regression with adjustment for technical covariates. Discovery and replication analysis using 16s data identified two independent CpGs associated with the genus Eggerthella: cg16586104 (Pmeta-analysis = 3.21 x 10-11) and cg12234533 (Pmeta-analysis = 4.29 x 10-10). While we did not find human genetic variants that could explain the associated CpG-taxa/pathway pairs, we show that microbiome can mediate the effect of environmental factors on epigenetics. In this first association study linking epigenome to microbiome, we found and replicated the associations of two CpGs to the abundance of genus Eggerthella and identified microbiome as a mediator of the exposome.