The significance of the gastrointestinal microbiota composition towards the balance between human health or disease has been demonstrated in numerous studies over the last decades. Most research focused on bacteria as the most numerous components of the intestinal microbiota. More recently, however, fungal colonization has been shown to have a specific and profound impact on development and function of the immune system.

As functional studies in humans are often not possible due to ethical and practical constraints, laboratory mice are commonly used to investigate the impact of the microbiota and fungal colonization on the host. However, laboratory mice are usually maintained in a highly standardized environment with strict hygiene regimens. Compared to wild mice, they exhibit less immune activation and lower microbial diversity due to the lack of environmental exposure to a wider range of microbes, including fungi.

In order to identify fungi that can colonize the gut of wild rodents, and to determine the possible impact of host-specific factors and the environment, we analyse over 300 gut samples from different mouse species captured in different habitats in Thuringia. Overall abundance of fungal DNA is determined by qPCR; ITS-sequencing will be used for phylogenetic analysis. This provides not only additional information on the microbiome of wild rodents, but might also identify fungi that colonize a range of host species in different environments, or as specialists are associated with specific host species or habitats.