Metaproteomics of Gut Fungi in Gnotobiotic Mice

Intestinal fungi are a fundamental component of the gut microbiome and play important roles in mammalian host biology. At the same time, the contribution of gut fungi to host health and disease remains understudied due to their low abundance. In that respect, gnotobiotic animals with defined microbial populations of reduced complexity represent a well-suited model system that highlights the effects of low abundant gut fungi on host physiology and other members of the microbial community. In this chapter, a label-free quantitative metaproteomic approach for the characterization of simplified microbial communities in gnotobiotic mice is presented. The model allows for exploring various research questions on the role of gut fungi in disease pathogenesis, microbial ecosystem maturation, or host-microbiome crosstalk.