Beamish, Emma and Rigby, Rachael and Fielden, Peter (2017) Investigating dysbiosis as a cause and predictor of intestinal pathology. PhD thesis, Lancaster University.
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Abstract
Intestinal dysbiosis involves a shift in microbial composition and abundance within the gut and compelling evidence has highlighted the pivotal role dysbiosis plays in the onset and pathogenesis of numerous diseases, including inflammatory bowel disease (IBD), allergies and even mental health disorders. The intestinal microbiota is largely defined by host diet; a recent mouse model of total parenteral nutrition (TPN) showed that a dysbiotic shift in microbial dominance occurs following enteral nutrient depravation. Furthermore, metabolomics studies have identified that IBD patients can be discriminated from healthy based on their urinary metabolite profiles, but whether such profiles are accountable to intestinal dysbiosis remains uncertain. The research presented herein employed two human models; a novel TPN model in loop ileostomy patients, and patients with IBD, to assess microbial shifts and associated physiological consequences as well as determine whether urinary metabolite profiles are reflective of the intestinal microbiota. Using 16S rDNA-qPCR and -DGGE methods we revealed extensive variations in the microbiota of functional and defunctioned ileum following enteral nutrient deprivation, with a significant relative decrease in the Firmicutes phylum and concomitant increases in γ-Proteobacteria. Immunohistochemical techniques exposed a distinct physiological environment associated with a dysbiotic microbiota. Such environment was defined by reduced epithelial cell proliferation and mucosal atrophy that is likely due to altered host-microbiota interactions at the epithelial surface. We also observed post-operative complications that were potentially dysbiosis-mediated in almost 50% of the study cohort. Urinary NMR and Illumina 16S next-generation sequencing multi-omics statistical analyses identified correlations between dietary-associated urinary metabolites, particularly epicatechin, and distinct enterotype-like microbiota profiles. Application of this principle to prediction of IBD, as an example of a dysbiosis-associated disease, proved to be difficult due to limited sample numbers confounding interpatient variability. This research furthers the utilisation of intestinal microbiota as a therapeutic target, possibly via novel prebiotic administration to the defunctioned ileum with the potential to restore microbiota function prior to reanastomosis and reduce post-operative complications. Furthermore, it also provides promise for inexpensive, non-invasive detection of dysbiosis as a risk-factor of associated diseases. Further research, employing greater numbers of participants, is required to fully evaluate the potential predictive value of dysbiosis.