An Evolutionarily Conserved Laterally Acquired Toolkit Enables Microbiota Targeting by <i>Trichomonas</i>

Trichomonas species are a diverse group of microbial eukaryotes (also commonly referred to as protists) that are obligate extracellular symbionts associated with or attributed to various inflammatory diseases. They colonize mucosal surfaces across a wide range of hosts, all of which harbor a resident microbiota. Their evolutionary history likely involved multiple host transfers, including zoonotic events from columbiform birds to mammals. Using comparative transcriptomics, this study examines Trichomonas gallinae co-cultured with Escherichia coli, identifying a molecular toolkit that Trichomonas species may use to interact with bacterial members of the microbiota. Integrating transcriptomic data with comparative genomics and phylogenetics revealed a conserved repertoire of protein-coding genes likely acquired through multiple lateral gene transfers (LGTs) in a columbiform-infecting ancestor. These LGT-derived genes encode muramidases, glucosaminidases, and antimicrobial peptides-enzymes and effectors capable of targeting bacterial cell walls, potentially affecting the bacterial-microbiota composition across both avian and mammalian hosts. This molecular toolkit suggests that Trichomonas species can actively compete with and exploit their surrounding microbiota for nutrients, potentially contributing to dysbiosis associated with Trichomonas infections. Their ability to target bacterial populations at mucosal surfaces provides insight into how Trichomonas species may have adapted to diverse hosts and how they could influence inflammatory mucosal diseases in birds and mammals.