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bioRxiv · 10.64898/2026.01.31.703031

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

Rajarajan, A.·Coone, M.·Wolinska, J.·Spaak, P.·Decaestecker, E.
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Abstract

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 para-site Australozyma monospora (formerly Metschnikowia bicuspidata) to test if micro-biome 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, micro-biome composition did not influence parasite infectivity or net reproduction. Our results indicate that microbiome effects on host survival are genotype- and life-stage-dependent, differ between parasite-free and parasite-exposed conditions and may impact host-parasite dynamics primarily by influencing host viability rather than para-site performance.

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Rajarajan, A., Coone, M., Wolinska, J., Spaak, P., Decaestecker, E.. 2026-02-03. Host outnumbered: microbiomes and a fungal parasite interact to shape host genotype-dependent survival. https://doi.org/10.64898/2026.01.31.703031

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