Jacob Bak Holm:
The gut microbiota in host metabolism and pathogen challenges

Date: 14-08-2015    Supervisor: Karsten Kristiansen & Lise Madsen

The human microbiota consists of a complex community of microbial cells that live on and inside each person in a close relationship with their host. The majority of the microbial cells are harboured by the gastro intestinal tract where 10-100 trillion bacteria reside. The microbiota is a dynamic community where both composition and function can be affected by changes in the local environment. With the microbiota containing ~150 times more genes than the human host, the microbiota provides a large modifiable “secondary genome” (metagenome). Within the last decade, changes in the gut microbiota composition has indeed been established as a factor contributing to the health of the host. Therefore, being able to understand, control and modify the gut microbiota is a promising way of improving health.

The following thesis is based on four different projects investigating the murine gut microbiota in relation to pathogen challenges and host metabolism.

Paper I: Parasitic worms (helminth) including Trichuris (whipworms) have evolved to live, sideby- side with the gut microbiota, inside the gastrointestinal tract of its mammalian host. With ~500 million Trichuris trichiura infected people worldwide, knowledge about the consequences of such pathogenic infections are valuable. We investigated which effects Trichuris muris infection has on the gut microbiota composition and immune response in mice. Chronic infection with T. muris resulted in major changes in the gut microbiota composition in parallel with induction of a Th1 dominated immune response. In particular, the relative abundance of Lactobacillaceae was increased from <5% to 15% within 35 days. Furthermore, alpha diversity decreased and beta diversity increased as a consequence of the infection.

Paper II: The immune system is essential for maintaining a healthy gut homeostasis. Intestinal mucosal dendritic cells (DCs) sample and internalise antigens from luminal pathogens and activate T cell-mediated immune responses. The expression of transcriptions factors in the DCs is important for their ability to regulate the immune response. We investigated the role of transcription factor interferon regulatory factor 8 (IRF8)-dependent intestinal DCs on the regulation of intestinal T cell homeostasis, the gut microbiota and the susceptibility to T. muris infections. Mice lacking IRF8- dependent intestinal DCs were unable to mount a proper Th1 immune response to T. muris infections. Furthermore, the lack of IRF8-dependent DCs made the mice resistant to T. muris infections, illustrating that the ability to mount a Th1 immune response was a determining factor for susceptibility or resistance to the infection. Despite lacking IRF8-dependent DCs and major T cell subsets no differences in the gut microbiota composition were observed in the steady state.

Paper III: Recently low levels of paracetamol were ubiquitously observed in the urine of both Danish and German individuals, despite no record of recent paracetamol use. Based on this, we investigated whether the environmental pollutant aniline, via metabolic conversion, could be a potential source of paracetamol exposure. We confirmed that treating mice orally with aniline resulted in significant levels of paracetamol in the urine. It has been indicated that certain bacteria are able to convert aniline to paracetamol. However, our data suggested a microbiota-independent conversion by the host tissue where the liver, at least in part, is responsible for the conversion. As paracetamol has been associated with reproductive disorders and showed anti-androgenic effects we tested the hypothesis that intrauterine exposure to aniline or paracetamol would impair the reproductive development of the male offspring. Interestingly, intrauterine exposure to both aniline and paracetamol resulted in shortening of the anogenital distance, a sensitive marker of fetal androgen levels, which in humans are associated with reproductive malformations and later life reproductive disorders.

Paper IV: High-protein diets protect against diet-induced obesity. However, it remains to be established how different protein sources consumed at standard dietary levels affect metabolism. We investigated how a mixture of lean seafood or lean meat in a Western background diet modulated body weight development, metabolism and gut microbiota composition. Feeding mice a diet containing lean seafood resulted in reduced energy consumption, fat mass, plasma cholesterol and respiratory exchange ratio (RER) compared to mice fed the diet containing lean meat. The lower energy consumption of the seafood fed mice and no difference in diet preference test suggests an effect on satiety by the diets. Furthermore, differences in the relative abundance within the orders Bacteroidales and Clostridiales were observed between the gut microbiota of the seafoodand meat-fed mice.