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Inflammatory Bowel Diseases (IBD) result from the nexus of a genetic predisposition, dysregulated immunologic insult against commensal microflora, and an environmental trigger. The intestinal epithelium is a single cell layer that separates a highly active mucosal immune system from a large antigenic load in the intestinal lumen. Innate immune recognition combined with a highly regulated adaptive immune response maintains this tolerance. The intestinal epithelium in collusion with antigen presenting cells primarily modulates this activity. In this thesis, we show that, in response to DNA isolated from bacteria, innate toll like receptor 9 (TLR9) activation in intestinal epithelial cells modulates both arms of the immune system, to regulate intestinal homeostasis, and through this mechanism, Bifidobacteria breve DNA exerts its anti-inflammatory function. / Experimental Medicine

Thesis (M.Sc.)--Memorial University of Newfoundland, 2004. / Bibliography: leaves 126-133.

Inflammatory bowel disease (IBD) is a growing disorder with unknown etiology. However, increasing evidence strongly highlights the role of gut microbiota with possible involvement of microbial plasmidome in the inflammatory process. Although the composition of the gut microbiota has been extensively studied, important functional groups such as butyrate producers remain poorly characterized, particularly in pediatric IBD. Furthermore, evaluation of the gut plasmidome in healthy and IBD children is missing. In this study, we used molecular techniques involving quantitative PCR (qPCR) and next-generation sequencing of functional and 16S rRNA genes to analyze the level and composition of butyrate-producing microbes in mucosal washes collected from the right colon of healthy children and Crohn's disease (CD) patients during diagnostic colonoscopy. Also, we isolated and characterized the gut plasmidome from the right colon mucosal washes collected from pediatric non-IBD control, ulcerative colitis (UC), and CD subjects. Although no difference was observed in the total amount of butyrate producers that utilize the butyrate kinase (BUK) pathway for butyrate synthesis, butyrate producers that use the butyryl CoA:acetate CoA-transferase (BCoAT) pathway were decreased in CD patients with inflamed colon as compared to controls. This functional gene approach shows that pediatric CD is characterized by generalized decreased abundance of Eubacterium rectale and increased abundance of Faecalibacterium prausnitzii in patients with inflamed colon. Also, phylogenetic analysis highlighted 15 Operational Taxonomic Units (OTUs) as potential novel butyrate producers, five of which were decreased in CD patients. Using 16S rRNA sequencing approach validated the functional gene results and showed decreased abundance of Coprococcus in CD patients with inflamed colon. Furthermore, non-IBD plasmidome has higher level of genes involved in butyrate synthesis and regulation of different cellular processes and stress response. On the other hand, IBD plasmidome is enriched with antibiotic resistance genes and phage elements, and pediatric CD plasmidome in particular has higher abundance of the adenosine-5'-phosphosulfate reductase gene. Altogether, our study represents the first comprehensive description of gut butyrate producers and plasmidome of pediatric subjects that emphasize a characteristic dysbiosis of butyrate producers in pediatric CD and a potential link between the gut plasmidome and IBD pathogenesis.

In recent years, the association between inflammatory bowel diseases (IBDs) and gut microbiota has been extensively studied in adults using post-treatment cohorts of patients. However, microbial composition and functional interplay between host genetics and microorganisms in newly diagnosed early IBD onset remain poorly defined. Using colonoscopic mucosal washes to collect mucosal-luminal microbiota from different intestinal locations, we studied the gut microbiome in a large number of children with either Crohn’s disease (CD) or ulcerative colitis (UC). Although no significant difference in the diversity was evident between the gut microbiota of IBD-affected and control children, the microbiome of IBD subjects is characterized by an increased abundance of potent hydrogen sulfide (H2S) producers and decreased abundance of beneficial butyrate producers. Microbiota and proteomic profiling revealed that the abundance of Atopobium parvulum, a potent H2S producer, was associated with increased CD severity and a concurrent reduction in the expression of the host H2S detoxification pathway. Gnotobiotic and conventionalized colitis-susceptible interleukin-10-deficient (Il-10-/-) mice showed that A. parvulum induces severe colitis, a phenotype requiring the presence of the gut microbiota. In addition, administration of bismuth, an H2S scavenger, prevented A. parvulum-induced colitis in Il-10-/- mice. Our findings have identified A. parvulum as a major mediator of inflammation severity. We also reveal an imbalance between the H2S production and detoxification in the gastrointestinal tract of pediatric IBD patients. Altogether, our findings provide new avenues for diagnostics as well as therapies to treat IBD.

BACKGROUND: Inflammatory Bowel Disease (IBD) is a collective term that refers to chronic inflammatory diseases involving the gastrointestinal (GI) tract. The most common forms of IBD include Crohn’s Disease (CD) and ulcerative colitis (UC). GOALS: The goal of this study is to compare baseline and one-year follow-up measures of anxiety, depression, and quality of life in children with newly diagnosed IBD. A secondary goal of this study is to determine if there are parallel changes in the psychologic parameters in the parents of these children over a similar one-year interval. METHODS: This prospective cohort study was conducted in the Center for Inflammatory Bowel Diseases at Boston Children’s Hospital (BCH). The parents and children with newly diagnosed IBD completed validated questionnaires about their disease at baseline (within six months of their diagnosis) and then again 12-18 months later. RESULTS: Baseline data were collected from 75 patients with IBD, and 15 of these patient/parent dyads have completed follow-up questionnaires. The incidence of anxiety and depression trended downwards after the first year, and overall quality of life trended upwards, indicating an improvement in a global state of adjustment. Measures of anxiety and depression, as well as the reported frequency and difficulty of adverse events, all decreased in parental responses after the first year. CONCLUSION: While a larger sample size is necessary to better assess changes in psychometrics over time, existing data suggests that parents manifest the most significant change in anxiety and depression over the course of the first year from diagnosis. Children appear to be less anxious and depressed at baseline. Further enrollment and data collection will permit a more definitive assessment of the relationship between patient and parent coping strategies. Ideally, the results of this ongoing study will determine if impaired parental coping lowers a patient’s quality of life, contributes to higher childhood anxiety and depression scores, and results in higher healthcare utilization.

The intestinal microbiome contributes in immune system function. It contains a large number of microorganisms that interact with each other and thus affect the host. Currently, attention is being directed towards investigating the influence of the intestinal microbiome on hosts, but also on foreign substances. Foreign substances may influence its composition and subsequent microbial metabolism. Crohn's disease patients have been found to have lower bacterial representation of beneficial bacteria. Therefore it is appropriate to examine the intestinal microbiome of these patients and so understand in greater detail the influence of bacteria on the course of the disease progression and on the medication used. The RP-HPLC method were analysed the faecal samples collected (B, C, D), which were incubated at 0, 3 and 6 hours. The incubation took place the addition of myricetin in the McDougall buffer and BHI medium. The analysis was found that myricetin degradation takes place in faecal samples during incubation, regardless of the medium used. In the faecal sample B, degradation of myricetin occurs faster in the BHI medium than in the McDougall's buffer. In faecal samples C and D, degradation is similar in both media. From these results, it is impossible to judge which medium is more suitable for...

Background and aims: Chronic intestinal failure (CIF) has been long-recognized, however the underlying etiology and risk factors have not been historically well-studied. We aim to study the underlying etiologies of CIF and predictive factors for long-term parenteral support (PS). Methods: We retrospectively identified patients with newly diagnosed CIF who received PS to maintain nutrition at the Cleveland Clinic between 2000 and 2017. Long-term PS was defined as a duration of more than 3 months. Univariable and multivariable logistic regression analyses were performed to identify the predictors of the need for long-term PS. Results: We identified 350 patients with CIF, 150 (43%) and 200 (57%) were diagnosed before and after 2010, respectively. The most common etiology was Crohn's disease (CD) in both cohorts (34.7% versus 30.5%, p = 0.41). Graft-versus-host-disease (GVHD) was a less frequent cause of CIF after 2010 (12.7% versus 2.5%, p = 0.0002). The type of PS was mostly total parenteral nutrition before and after 2010, 95% and 96%, respectively (p = 0.55). On univariable analysis, absence of ileocecal valve (p < 0.0001), ischemic bowel disease (p = 0.009), and whole colon resection (p = 0.033) were associated with the need for long-term PS. On multivariable analysis, absence of ileocecal valve (OR 2.19, p = 0.011) and ischemic bowel disease (OR 3.04, p = 0.003) remained statistically significant predictors of long-term PS. Conclusion: In our cohort of patients with CIF, CD remains the leading etiology over the last 20 years, whereas GVHD is less common after 2010. The absence of ileocecal valve and ischemic bowel disease were reliable predictive factors for requiring long-term PS.

Background: Crohn's disease is a chronic inflammatory disease of the intestine in humans, with no known cause. Johne's disease is a chronic intestinal disease of ruminants caused by Mycobacterium avium suhspecies paratuberculosis (MAP), and has some features similar to Crohn's disease. Although MAP has been purported to play an etiologic role in Crohn's disease, this causal link is still under debate. Objective: The overall aim of this project is to analyze MAP strains from different hosts (cattle, sheep and humans) and regions in North Dakota by biochemical and epidemiological methods, in order to better understand the pathogenesis and epidemiology of MAP strains and the relationship between MAP and Crohn's disease. The specific aims of this research are the following: Aim 1. Investigate the epidemiological evidence for MAP as a cause of Crohn's disease. Aim 2. Conduct a comparative causality study to investigate whether MAP or other enteric pathogens cause Crohn's disease. Aim 3. Evaluate the occurrence of MAP infections in cattle in North Dakota, 1995-2005. Aim 4. Analyze MAP strains from symptomatic and asymptomatic cattle. Aim 5. Investigate the biochemical variations of rapid and slow growing MAP strains. Aim 6. Evaluate MAP strains from low shedders and high shedders. Methods: MAP isolates were analyzed by biochemical methods of gas chromatography, high performance liquid chromatography and mass spectrometry. In addition, extensive literature review was performed to (1) determine the epidemiologic causal link between MAP and Crohn' s disease and (2) determine whether MAP or other enteric pathogens cause Crohn's disease. Results: Results from our study indicated the availablity of epidemiologic evidence supporting the causal role of MAP in Crohn's disease. It was also demonstrated that MAP is the most implicated organism in the etiology of Crohn's disease when compared to other infectious agents. Investigation of the occurrence of MAP infection in North Dakota showed an increase in number of MAP cases reported, with seasonal trends. Biochemical typing of MAP strains from symptomatic and asymptomatic cattle indicated that the symptoms status of isolates was significantly associated with mass spectra patterns and shedder status (p < 0.05). However, the association between symptoms status and HPLC and GC patterns was not significant (p > 0.05). Investigation of biochemical variations of rapid and slow growing MAP strains showed associations between the biochemical variability of MAP strains and their growth rate and presence of symptoms in the source cattle. Evaluation of MAP strains of different shedding characteristics by univariate logistic regression revealed that the shedder status of isolates was significantly associated with growth rate of isolates, symptom status, and source regions, but not with mass spectra patterns of isolates. Conclusion: Overall, this study strengthens the theories of strain sharing, intraspecies and interspecies transmission, and supports an association between MAP and Crohn's disease. In addition, the understanding of the biochemical variation among MAP isolates will help in the future design of diagnostics, therapeutics and vaccines for Johne's and Crohn's diseases. / North Dakota State University. Department of Chemistry and Biochemistry

For many years there has been a suggested association between multiple sclerosis (MS) and inflammatory bowel disease (IBD). Aside from their common epidemiological and immunological similarities, there appears to be an association between the incidence of both diseases coexisting. We report a case of a 41-year-old man with chronic diarrhea and weakness, who was found to have concomitant MS and Crohn's Disease. Our report underscores the importance clinicians of maintaining a high degree of suspicion about the potential association of these conditions among these patient populations.