Professor Gary Wu expands on our knowledge of the gut microbiome by examining the non-microbial members of the gut community, including viruses and fungi. He begins by illustrating the influence of long-term dietary patterns on the gut microbiota. For example, the European diet versus the rural African diet results in a distinct microbial fingerprint, creating gradients in Bacteroides and Prevotella enterotypes. This concept can be extended to disease: for instance, choline is metabolized differently by different gut microbes, affecting the levels of metabolite trimethylamine N-oxide, thereby modulating the risk of atherosclerotic coronary vascular disease. But what about the other players residing in the gut? Wu explores the fascinating world of fungi and viruses. Fungal profiling studies divide humans into two classes with respect to their fungal signatures, and there is early evidence to suggest that these can also regulate immune response, as in Crohn’s disease. Viruses (bacteriophages) exert a profound influence on the composition of gut bacteria, but there are also novel classes of viruses whose roles are still a mystery. Future studies are needed to identify and establish the role of non-bacterial gut microbes in health and disease.