Defining the Daphnia magna microbiota
What species are present in the Daphnia magna microbiota? Daphnia is a potentially interesting system for studying the microbiota for a few reasons. Their microbiota seems relatively simple, allowing for high coverage of the genomes present within. Most of the confounding factors for microbiome research can be tightly controlled within this system as well, which really lets us focus on the functions contained within the microbiota in a given environment.
Plus they totally look like mini aliens.
Though 16S sequencing can be used to find the general community composition of the microbiota of any organism, getting species-level identification is quite difficult. This is especially true for organisms that have not undergone extensive sequencing efforts. I’m using shotgun sequencing and long-read sequencing to resolve the species present in the Daphnia microbiota. I’m also using this data to find unique functions for each species (or metagenome-assembled genome), finding genes involved in potential interactions between the host and its microbes and between microbial species within the microbiota.