We're colonized with a complex mix of bacteria, fungi, protozoans, helminths and viruses, yet the majority of microbiome studies worldwide only include bacteria. What influence do non-bacterial microbes have in the gut microbiome? How do these microbes affect bacterial communities? How to they interact with our immune system? We're applying ecological theory concepts to explore the relationships between microbial eukaryotes and prokaryotes, using bioinformatic and mouse model strategies.