The interplay between gut microbiome and host epigenome under cyanobacterial stress in Daphnia

We here aim to study the interplay between the gut microbiome and epigenome in response to cyanobacterial stress using the water flea Daphnia magna in combination with the cyanobacterium Microcystis aeruginosa. From previous research, we know that the gut microbiome and the epigenome are involved in the stress response of Daphnia sp. to Microcystis. Yet, so far, the lack of a combined integrative approach made it impossible to establish causal links between the different levels of regulation. This project will use an integrative and innovative approach to unravel the contributions of both the epigenome and gut microbiome and their interaction. Via gut transplants of susceptible and tolerant genotypes, in combination with a whole genome (bisulfite sequencing of Daphnia) and microbiome approach (metagenetics and metagenomics), we aim to unravel whether the microbiome structures the epigenome and vice versa and how this affects the phenoytpic outcome of stress responses up to life history responses and the metabolite level. More in particular, we hypothesize that changes in the composition and gene functions of the gut microbiome drive changes in DNA methylation patterns and gene expression levels, leading to  changes in the expression and alternative splicing of digestive proteins (proteases, e.g. trypsins and chymotrypsins) ultimately resulting in increased tolerance to Microcystis stress.