title: The human gut microbiota, dietary fibre and production of short chain fatty acids in inflammatory bowel disease
Creators: name: McGowan, Mhairi
Publisher: name: University of Glasgow
Year: 2017
Subjects: subject: Inflammatory bowel disease, Crohn's Disease, Ulcerative Colitis, fibre, gastroenterology, microbiota.

description: Research must be implemented to further our current understanding of the pathogenesis of Inflammatory Bowel Diseases (IBD) in order to improve the clinical treatment of these idiopathic conditions. Current evidence suggests that the aetiology of both Crohn’s Disease (CD) and Ulcerative Colitis (UC) is multifactorial and with advancements in microbiological techniques, there has been much interest in the role of the gut microbiota in these diseases. The indigenous gut community play many vital roles within the colon, one of which is the fermentation of dietary fibre which produces various metabolites, including the health-promoting organic anions, short chain fatty acids (SCFA). SCFA, particularly butyrate, provide up to 70% of colonocyte energy and play a vital role in gut immunoregulation. Some studies have reported improvements in clinical IBD symptoms in response to dietary fibre supplementation however others do not support a therapeutic effect. The medicinal properties of a fibre-free diet used to successfully treat paediatric CD suggests that fibre may not be as important as we think for colonic health and on the contrary may aggravate inflammation in active disease, and this may be mediated by either the profile of resident bacteria, and/or their functional capacity. Indeed, there is some evidence to suggest that the bacteria of IBD patients have a reduced capacity to utilise dietary fibre and efficiently produce SCFA, which may either initiate or perpetuate colonic inflammation. The studies within this thesis aimed to investigate the interaction between dietary fibre and the human gut microbiota of IBD patients. The first study aimed to quantify the in vitro production of SCFA by the human gut microbiota of adult UC and CD patients in remission in response to the anaerobic fermentation of various fibres, and compare these values to those of matched healthy controls Another aspect of this study was to investigate SCFA production by the gut bacteria of newly diagnosed, treatment-naïve paediatric CD patients, comparing it to that of matched CD patients on concomitant medication and to healthy controls. The second study within this thesis aimed to characterise the baseline bacterial profile of a subset of adult UC patients, CD patients and healthy controls, and to assess differences in the bacterial response to various fibrous stimuli between groups. Patients of this study were recruited in gasteroenterology clinics in Glasgow Royal Infirmary and at the Royal Hospital for Sick Children Yorkhill. Healthy controls were matched to patients in terms of age, gender and body mass index. All participants were asked to donate a single stool sample which was used in the well-established batch culture fermentation model employed by this study. A further short methodological study was conducted with the objection of quantifying the production of in vitro SCFA in association with substrate availability, to gain insight into potential of product inhibition with increasing fibre. The results of the first study implied that IBD patients, particularly UC patients, displayed an overall tendency of reduced in vitro total SCFA and butyrate production compared to matched healthy controls. In particular, butyrate production was significantly less in UC patients compared to healthy controls when fermented with hi-maize, a known butyrogenic fibre (median (IQR) HC; 58.87 (17.69) vs. UC; 44.92 (21.49) p=0.02). Both CD and UC patients displayed a significantly lower concentration of total SCFA compared to healthy controls (median (IQR) HC; 51.76 (22.02) vs. CD; 41.12 (23.28) vs. UC; 41.94 (14.72) p=0.02). The proportional contribution of butyrate to total SCFA following fermentation with mixed fibre was also signficiantly higher for healthy controls compared to UC patients (median (IQR) HC; 10.76 (8.26) vs. CD; 8.75 (4.74) p=0.049) but not CD patients. In no cases were there any significant differences between the SCFA concentration or relative contribution in CD or UC patients ( p&gt;0.05). There was a clear tendancy for total SCFA, acetate, propionate and butyrate concentrations to be highest in healthy children for most substrates; however these differences did not reach statistical significance (p&gt;0.05). The exceptions to this was total SCFA and acetate concentration in response to fermentation of hi-maize, which was significantly higher in healthy controls compared to newly diagnosed patients (total SCFA; mean ± SEM, healthy controls; 57.99 ± 5.11 vs newly diagnosed; 38.89 ± 3.23, p=0.01, acetate; mean ± SEM, healthy controls; 32.93 ± 2.93 vs newly diagnosed; 21.41 ± 2.48, p=0.02) but not those who were on medication. Although not significant, there was a clear trend for total SCFA concentration to be the highest in healthy children, lower in patients who had already been on treatment, and lowest in newly diagnosed patients for all substrates. The second study of this project reported that the baseline microbial diveristy of CD patients was lower than that of healthy controls, however there was not sufficient power to conduct statistical analysis. Fermentation with all fermentable fibres signficantly reduced microbial diversity in healthy participants (p&lt;0.05), however showed little statistically relevant changes CD patients and none in UC patients. Baseline community structure of UC patients was statistically different to that of healthy controls. However the structure of all participants groups responded similarly to fermentation with all fibres, and these changes were not dependant on participant type (interaction = 1.00). In terms of the relative abundance of bacterial phyla, there was evidence of an increased abundance of in unidentified species and those within the Proteobacteria phylum in CD patients at baseline, although increased power is necessary to assert statistical significance on this observation. The results of these studies shed some further light on the interaction between dietary fibre and the gut bacteria of IBD patients, implying that there is a reduced ability to efficiently utilise dietary fibre to produce important SCFA in vitro in the disease state. As the prime SCFA involved in colonic health, the tendency for reduced butyrate production in the disease state is potentially fundamental to disease pathogenesis as this acid has important immunoregulation properties within the colon. The obvious trend of reduced total and individual SCFA production in newly diagnosed, treatment naïve paediatric CD patients compared to both healthy controls and CD children on medication suggests that the severity of disease activity is associated with SCFA production. This study implies that in a reduced in vitro production is an underlying issue despite the management of inflammation and clinical symptoms. This study, particularly the paediatric cohort, would benefit greatly from increased power to statistically ascertain the trends observed. The reduced microbial diversity of CD patients observed in the baseline samples of this study are in coherence with multiple other studies in this area. Microbial diversity is important in gut immune function, the regulation of pathogenic bacteria, and the breakdown of vital nutrients and thus this reduction is extremely likely to play a role in IBD. Nonetheless, the in vitro fermentation of a solitary dietary fibre is likely to benefit specific bacteria and thus a reduction in diversity during such experiments, as shown in the healthy controls in this study, would be expected. However, neither CD nor UC patients reduced diversity to the same extent as healthy controls, implying that the baseline bacteria of patients could not optimally utilise the fibres provided. This may indicate a reduced functional capacity of the innate bacteria, or indeed a difference in baseline microbial profile. Indeed, the increase in unidentified bacteria and those within the Proteobacteria phylum in CD are in line with other studies. Nonetheless, the community structure of both patients and healthy controls responded in the same way to fermentation despite differences at baseline, indicated that to some extent, dietary fibre can modulate the gut community of IBD patients to be more like that of a healthy GIT. In conclusion, this thesis ascertains previous beliefs that there is an abnormal gut bacterial response to dietary fibre in IBD. It is likely that the subdued response in IBD exacerbates inflammation, but whether it is the initial cause of disease is unlikely. The implications of this study highlight that the intake of dietary fibre in remission is important in order to overcome innate inabilities to utilise these compounds to the same extent as healthy controls, and regain colonic homeostasis.