Drivers of Microbiome Composition Among Helminth Parasites Sharing the Same Insectivorous Bat Host

Parasitic metazoans are increasingly recognised to form close associations with microbial taxa. Under the holobiont concept, these associations are an eco-evolutionary unit under joint selection. However, for most parasitic helminth species and particularly those associated with wildlife, these interactions and their effect on parasite evolution remain unknown. Investigating the factors determining the composition of helminth microbiomes is the first step towards a better understanding of helminth holobionts. Using the insectivorous bat Peropteryx kappleri and its parasitic helminths as a model system, we characterised the microbiome of 41 helminth individuals of four trematode and one nematode species in various bat intestinal and biliary microhabitats, along with bat tissues and luminal fluids. Our results based on 16S rRNA metabarcoding revealed that the microbiome composition of the different helminth species is partly influenced by their microhabitat (bat tissue), but ultimately each helminth species exhibits a distinctive microbial signature. Microbiome composition among the four trematode species showed no phylogenetic signal (no correlation with genetic similarity). Compared to the bat host, each helminth species exhibited enriched microbial taxa with putative symbiotic potential, some of which are commonly found in arthropods (potential intermediate hosts of helminths) and may be conserved throughout the parasite's life cycle. We propose that helminth microbiomes are determined by ecologically relevant factors and provide a basis for future functional research with implications for parasite establishment, development, and transmission.