Scientific research in the last decades has revolutionized our insight in how microorganisms colonizing the human body correlate with and even impact our health and how intricate the microbe-microbe and the host-microbe interactions are. Subtle imbalances in our microbial populations can cause disease and studies have shown correlations between gut microbiota composition and obesity, inflammatory bowel diseases, diabetes, cancer, acute appendicitis, colon cancer, … Research into identification of biomarkers for gut health and ways to modulate the microbiota composition and activity to improve health, has put A. muciniphila in the spotlight. Its abundance is decreased in patients suffering from IBD,
obesity, diabetes and autism, but it occurs in high abundance and with high prevalence in healthy people. As a mucin degrader, A. muciniphila colonizes an interesting but not-fully
described niche, being host-glycan degradation. These mucin glycans make up the protective mucus layer that separates the epithelial cells from the gut lumen. Besides acting
as a barrier, the mucus layer, and specifically the mucin glycans, also serve as a substrate for growth for colonic bacteria, an aspect that has gained more attention recently. Previously, it was thought that mucin degradation was detrimental for gut health but it is now clear that it
is part of a normal turnover process. Given the diversity and complexity of host glycan structures, strategies for degradation to free sugars rely on the action of a panel of enzymes, produced by only 1% of the microbial community. The release of oligosaccharides and fermentation products during mucin degradation can be used by other bacteria, thereby expanding the host glycan degradation niche. The ability of these microorganisms to profit; both directly and indirectly, from endogenous glycans can facilitate their close location to the host epithelium, where they may exert a disproportionate effect on human health. Plenty of research concerning A. muciniphila has been done, but more information is required concerning its behaviour in the complex microbial ecosystem in the colon, the potential role of mucins to influence A. muciniphila behaviour and the impact of its probiotic administration on the microbial ecosystem and the host, which was the focus of this PhD research. In vitro
technology used in this research, such as the simulator or the human intestinal ecosystem (SHIME®) and the transwell co-culture cell model, allowed for mechanistic research that
aimed at unravelling the ecology of mucin degraders and helped to overcome some confounding elements of in vivo studies, such as variations in mucin production by the host.
The first part of this PhD research focused on the role of A. muciniphila in host glycan degradation and the importance of this niche for the microbial ecosystem. Chapter 2 studied
the colonization behaviour of A. muciniphila under variable conditions and revealed that A. muciniphila preferentially colonized the distal colon and that this preference was due to
pH, which is more neutral compared to the proximal colon. Mucin deprivation decreased A. muciniphila abundances and subsequent mucin supplementation caused a specific
increase of A. muciniphila, far exceeding the response of other bacteria present. To study the biological reproducibility of these findings, the effect of pH and the presence or absence of a host-glycan degradation niche was investigated in colon compartments separately inoculated with the microbiota from eight donors in Chapter 3. pH specificity and nutrient sensitivity of A. muciniphila was confirmed in these different microbial communities. Mucin supplementation resulted in more similar microbial communities for the eight donors,
indicating host glycans to constitute an important ecological niche shaping the microbiota composition. The effect of colonic pH had a less profound impact on the microbiome with
donor origin explaining most of the variability.
To asses microbial cross-feeding and competition interactions of A. muciniphila more in detail, Chapter 4 investigated different primary degraders for host or dietary glycan degradation and their effect on butyrate production. These interactions are difficult to study in a complex bacterial community and so a synthetic microbial community was used, with A. muciniphila and B. thetaiotaomicron as the primary glycan degraders. Joint presence of both primary degraders did not lead to a competitive exclusion in the presence of mucin;
A. muciniphila was not even overgrown by B. thetaiotaomicron when additional dietary glycans were available. Shifts in pH and primary degrader abundance was selective for
butyrate producers while the butyrate producing functionality was maintained.
The second part of this PhD research focused on the modulation of the microbial community by administration of A. muciniphila and the presence/absence of a host-glycan
degradation niche, and its impact gut barrier function and immune response. Addition of both mucin and A. muciniphila to microbial gut communities from different donors (Chapter 5)
might lead to A. muciniphila dominating the mucin degradation niche, while sole mucin addition led to involvement of several species, including A. muciniphila, Ruminococcus,
Clostridium cluster XIVa, and Lachnospiraceae. Supernatant samples were taken from the microbial communities shaped by these treatments, to study their effect on the intestinal
epithelium and the underlying immune cells in Chapter 6. The supernatant of the treatment with both mucin and A. muciniphila induced the most beneficial response, with the mucin responsible for increased trans-epithelial resistance (TEER) and reduced TNF-α and IL-6 production, and A. muciniphila responsible for decreased epithelial permeability
Overall, this research, using the complex microbial communities from several donors, showed the nutrient specificity of A. muciniphila and its sensitivity to changes in the colon environment, and provided valuable information about the prebiotic-like action of host derived glycans. However, the inter-individual differences impacting our results need further