As interest in environmental genomics emerges, the roles of microbiota in the ecology and evolution of an increasing number of non-model organisms are being investigated, revealing a high diversity in the types of effects observed (Fraune and Bosch, 2010; Engel et al., 2012; Koch and Schmid-Hempel, 2011; Brucker and Bordenstein, 2013). Here we present the first experiments addressing the role of microbiota in a crustacean model, Daphnia.