A clash of kings: Tools to study cross-kingdom interactions in the human gut microbiota

A large amount of microbial cells is found in the human gastrointestinal tract. The gut microbiota consists of microbes from different kingdoms: bacteria, viruses and fungi. Studies on the gut viruses and fungi show that they can be important in human health and therefore tools to research them are needed. In this thesis, in vitro gut fermentation models were used for research on viruses and fungi in the human gut. The survival of bacteriophages in the stomach and the small intestine, and in the colon was investigated with the use of the TIM systems. These studies show the importance of survival studies in the design of successful phage therapy. The gut fungal community, and interactions with the bacterial community were also investigated in an in vitro model of the colon (TIM-2). Fungal-bacterial interactions were furthermore studied in a large number of fecal samples. These experiments gave more insights in the gut fungal community.