Microbial ecology and bile acid conversion within the pig intestine in colon carcinogenesis

Wylensek, David Franz; Pabst, Oliver (Thesis advisor); Clavel, Thomas (Thesis advisor)

Aachen : RWTH Aachen University (2022, 2023)
Dissertation / PhD Thesis

Dissertation, RWTH Aachen University, 2022


Despite increasing efforts to improve our understanding of the complex bacterial communities within intestinal microbiomes, a large fraction of species, their metabolites and functions, which have the potential to influence host health, are still largely unknown. One example is the association between a Westernized diet and the occurrence of colorectal cancer (CRC), which is linked to shifts in the intestinal microbiota and microbial metabolites such as secondary bile acids (sec. BAs). However, the relevance and causality of these observations remain unproven. Therefore, the aim of my thesis was to investigate the causal role of sec. BAs produced by the gut microbiota in colon carcinogenesis. To do so, in chapter I, I provided experimental proof of the detrimental role of a Western diet enriched in red meat and lard in the APC1311/+ porcine model of early state CRC. This diet increased the number and size of polyps in the colon and induced shifts in faecal microbiota profiles as well as increased sec. BA levels, primarily deoxycholic acid (DCA) and 12-ketolithocholic acid (12-KLCA). However, to prove the causality of sec. BAs in CRC, gnotobiotic animals in combination with bacterial isolates are necessary to perform mechanistic studies. Therefore, in chapter II, I focused on the isolation and characterization of bacterial species from the pig intestine with special focus on bile salt conversion. In total, 117 strains were isolated and made publicly available, representing 110 species across 40 families and 9 phyla to establish the first comprehensive bacterial collection from the pig intestine (www.dsmz.de/pibac). Fifty isolates showed bile salt hydrolase activity, the initial step in bile salt conversion. Moreover, the species Clostridium scindens was able to produce the sec. BA DCA by 7α-dehydroxylation. Besides these findings, 34.5% of the isolated species represented novel taxa, which were all taxonomically described. This contributed to extend our understanding of microbial functions in the pig gut, for instance via the identification of a previous unknown fucosyltransferase from the novel species Clostridium porci or via the description of biosynthetic gene clusters encoding potentially novel sactipeptide-like small proteins. In chapter III, based on this unique collection of isolates, I created two synthetic bacterial communities (SYNs) with and without the ability to produce sec. BAs. These SYNs were used in proof-of-concept studies in gnotobiotic mice and pigs, whereby the majority of SYN strains engrafted in the intestine. In addition to that, faecal samples from piglets colonized by C. scindens were characterized by DCA production. In summary, this PhD thesis represents a solid foundation of work towards experimental proof of the detrimental role of Western diets in CRC.