Host outnumbered: microbiomes and a fungal parasite interact to shape host genotype-dependent survival

Microbiomes are key determinants of host health, yet empirical evidence demonstrating their influence on host-parasite interactions is limited. We conducted a proof-of-principle experiment using the water flea Daphnia magna and its virulent yeast parasite Australozyma monospora (formerly Metschnikowia bicuspidata) to test if microbiome composition alters infection outcomes. Axenic hosts were inoculated with a control microbiome (homogenates of laboratory-cultured Daphnia reared in natural freshwater) or a single bacterial strain (Rhizobium sp.), and exposed to the parasite. Host survival differed markedly between microbiome treatments and depended on parasite exposure. Prior to parasite exposure, hosts of one genotype exhibited high juvenile mortality when inoculated with the control microbiome (79%), compared to Rhizobium (19%) (the other genotype: 48% vs. 50%). Parasite exposure reduced survival, but the extent varied with microbiome composition: survival of hosts with a control microbiome (averaged across genotypes) declined from 66% to 0%; survival of those inoculated with Rhizobium sp. declined from 35% to 10%. In contrast, microbiome composition did not influence parasite infectivity or transmission. Our results indicate that microbiome effects on host survival are genotype- and contextdependent, differing between parasite-free and parasite-exposed conditions. Microbiome composition may therefore impact host-parasite dynamics primarily by influencing host viability rather than parasite performance.