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Background  Regulatory circuits of infection in the emerging experimental model system, water flea  Daphnia  and their microparasites, remain largely unknown. Here we provide the first molecular insights into the response of  Daphnia galeata  to its highly virulent and common parasite  Caullerya mesnili , an ichthyosporean that infects the gut epithelium. We generated a transcriptomic dataset using RNAseq from  parasite-exposed  (vs.  control )  Daphnia , at two time points (4 and 48 h) after parasite exposure.    Results  We found a down-regulation of metabolism and immunity-related genes, at 48 h (but not 4 h) after parasite exposure. These genes are involved in lipid metabolism and fatty acid biosynthesis, as well as microbe recognition (e.g. c-type lectins) and pathogen attack (e.g. gut chitin).    Conclusions  General metabolic suppression implies host energy shift from reproduction to survival, which is in agreement with the known drastic reduction in  Daphnia  fecundity after  Caullerya  infection. The down-regulation of gut chitin indicates a possible interaction between the peritrophic matrix and the evading host immune system. Our study provides the first description of host transcriptional responses in this very promising host-parasite experimental system.    Electronic supplementary material  The online version of this article (10.1186/s12864-018-5312-7) contains supplementary material, which is available to authorized users.

Daphnia galeata responds to the exposure to an ichthyosporean gut parasite by down-regulation of immunity and lipid metabolism