Parasite-associated microbiomes: An unseen microenvironment

Parasites harbor diverse microbial ecosystems that include not only bacteria but also archaea, fungi, viruses and microbial eukaryotes. These parasite-associated microbiomes, long overlooked, are now recognized as important determinants of parasite development, fitness, virulence and interactions with hosts across medical, veterinary, agricultural and ecological systems. However, current understanding of parasite-associated microbiomes remains fragmented, with most studies focusing on a narrow set of human parasites, relying heavily on bacterial surveys and rarely capturing the full multi-kingdom diversity of microbial partners. Important challenges include expanding research to encompass neglected parasite groups and their non-bacterial associates, establishing causal links between microbiome members and parasite phenotypes, and overcoming the technical barriers posed by low-biomass, host-contaminated and/or experimentally intractable systems. Progress will also depend on developing robust reference genomes and analytical tools that can resolve multi-kingdom communities and integrate parasite and symbiont biology. This chapter synthesizes current knowledge across helminths, protozoa, ectoparasites and plant-infecting parasites. We consider how microbiome manipulation may contribute to parasite control while recognizing the evolutionary and ecological complexities involved in altering host-parasite-microbiome interactions. Embracing an explicitly multi-kingdom, holobiont-focused perspective promises to illuminate fundamental aspects of parasitism. Such knowledge may contribute to new avenues for mitigating the impact of parasitic diseases on human and animal health, food security and ecosystems.