Conditions for Faecalibacterium prausnitzii colonization, survival and host-microbe interactions in the human host

Human beings sustain a balanced equilibrium with many microorganisms that live inside and outside their body, collectively referred to as the microbiome. The gut microbiome has special implications for human health, since it trains and strengthens the immune system. Moreover, it provides protection and nutrition for the host. Conversely, a disbalance in the gut microbiome may lead to inflammation, oxidative stress and increased permeability of the gut epithelial barrier.
The PhD research described in this thesis revolves around one of the key bacterial species that promote human health, namely Faecalibacterium prausnitzii. This strict anaerobe is a major producer of butyrate, which is an important nutrient for gut epithelial cells. To obtain a better understanding of how gut bacteria interact with the human host, the so-called HoxBan system was employed, which allowed studies on the effects of F. prausnitzii, or even complex bacterial mixtures from total human stool samples, on co-cultured gut epithelial cells. This allowed for the first time an in vitro visualization of the host-microbe cross-talk in the human gut. In addition, survival mechanisms of F. prausnitzii were investigated with the aim to understand how the growth of this strictly anaerobic bacterium can be promoted in disease scenarios, like inflammatory bowel disease, where the abundance of this and other butyrate-producers is decreased. Altogether, the obtained insights may be used to design smart probiotics, or even ‘pharmacobiotics’ based on the bioactive molecules produced by the human gut microbiota bacteria and to test their efficacy in vitro.