Inflammatory bowel disease (IBD), characterised by chronic intestinal inflammation, is hypothesised to arise from the interplay between susceptibility genes, the immune system, environmental factors, and gut microbiota. Akkermansia muciniphila is a symbiotic bacterium that accounts for 1-5% of the human fecal microbiota. This microbe has been hailed as a next-generation probiotic, principally with regards to its plethora of beneficial host interactions, including the ability to influence mucin secretion and strengthen the intestinal barrier. Though a clear-cut role and mechanism by which A. muciniphila influences inflammatory conditions is unknown, evidence indicates this microbe is depleted in IBD, suggesting it may have protective effects that are lost in these conditions. Here, we investigate the role and mechanism of A. muciniphila in intestinal inflammation and its influence on intestinal barrier function by utilizing barrier-disrupting models of colitis, including dextran sulphate sodium (DSS) and Trichuris muris. Though only minor benefits were derived from this microbe in germ-free mice, in specific pathogen-free (SPF) mice, administration of pasteurized A. muciniphila in a DSS recovery model ameliorated inflammation severity and promoted recovery compared to controls. When gavaged prior to DSS administration, both live and pasteurized A. muciniphila failed to diminish inflammatory markers indicating minimal preventative effects. T. muris-infected SPF mice treated with live A. muciniphila showed increased levels of Th2 and anti-inflammatory cytokines, decreased worm burden, and enhanced levels of the mucin, Muc5ac, compared with those receiving control broth or pasteurized bacteria. Further, both live and pasteurized A. muciniphila ameliorated the severity of inflammation in mucin 2 deficient (Muc2-/-) mouse model of spontaneous colitis, indicating that these protective effects are Muc2-independent. These observations provide us not only with an enhanced understanding of the role A. muciniphila plays in the pathogenesis of intestinal inflammatory conditions but also may fuel novel avenues of treatment for those with IBD. / Thesis / Master of Science (MSc) / Akkermansia muciniphila is a bacterium that accounts for 1-5% of the human fecal microbiota and has been shown to stimulate intestinal mucus production and strengthen the gut barrier. Though several studies have linked inflammatory bowel disease (IBD) with decreased levels of A. muciniphila, the precise role of this microbe in gut inflammation is unknown. In this research, we investigate the role of A. muciniphila in gut barrier function and inflammation. Across several experimental models, we find that supplementation with live, and in some cases, pasteurized A. muciniphila, can help curb established inflammation and promote a more anti-inflammatory gut environment. We also identify that these changes are independent of this bacteria’s ability to influence mucin 2, the main building block of intestinal mucus. This study has the potential to both enhance our understanding of microbial influence in intestinal inflammation and may also lead to the development of future treatments for IBD.

Interest in the gut bacterial community residing in the human intestine, otherwise known as the gut microbiota, has exploded in recent years. The gut microbiome has been linked to chronic diseases such as obesity, suggesting interventions that target the microbiome may be useful in treating obesity and its complications. Dietary pulses (e.g., common beans) are composed of nutrients and compounds that possess the potential to modulate the gut bacteria composition and function which can in turn improve appetite regulation and chronic inflammation in obesity. This review summarizes the current state of knowledge regarding the connection between the gut microbiome and obesity, appetite regulation, and systemic and adipose tissue inflammation. More specifically, it highlights the efficacy of interventions employing dietary common beans as a means to improve appetite regulation and inflammation in obesity in both rodent models and in humans. Collectively, results presented and discussed herein provide insight on the gaps in knowledge necessary for a comprehensive understanding of the potential of beans as a treatment for obesity while highlighting what further research is required to gain this understanding.

Cardiovascular disease (CVD) is a major cause of mortality and morbidity worldwide, often with heart failure as the terminal stage. Clinical studies have associated elevated levels of trimethylamine N-oxide (TMAO), a gut-derived metabolite, with adverse outcomes of CVD. As of today, TMAO's effects on cardiac structure and function are not well understood. In this study, both male and female TMAO-treated hearts showed functional deficits based on electrocardiography and echocardiography results. Immunohistochemistry results showed signs of hypertrophic cardiomyopathy in TMAO-treated male hearts while female TMAO-treated hearts showed signs of dilated cardiomyopathy. Neither TMAO group showed signs of fibrosis. Overproduction of reactive oxygen species was only observed in male TMAO-treated hearts. At the level of individual cardiomyocytes, significant delays in time to reach maximum contraction and dilation were only seen in TMAO-treated male hearts along with higher contractile force. Overall, TMAO-treated hearts show significant functional deficits with altered structure in a sex-specific way. Our study utilizes a variety of methods to comprehensively characterize features of TMAO-induced heart failure in both males and females which extends our current knowledge from human clinical associations. / Master of Science / Cardiovascular disease (CVD) is a major cause of mortality and morbidity worldwide, often with heart failure as the terminal stage. Clinical studies have associated elevated levels of trimethylamine N-oxide (TMAO), a compound derived from eggs, red meat and seafood, with adverse outcomes of CVD. As of today, TMAO's impact on the heart is not well understood. After supplementing mice with TMAO, we discovered deficiencies in heart function coupled with altered heart structure showing signs of hypertrophic cardiomyopathy in males and dilated cardiomyopathy in females. In-depth experiments suggest that TMAO-induced cell stress could be a potential underlying cause of previously mentioned changes but the specific mechanisms require further investigation. Overall, TMAO-treated hearts show significant functional deficits with altered structure in a sex-specific way. Our study utilizes a variety of methods to characterize features of TMAO-induced heart failure aiming to unravel relevant biological changes in both male and female mice which extends our knowledge from human clinical associations.

In the gastrointestinal (GI) tract, goblet cells are the major source of mucins, the main structural components of the mucus layer, which functions as the front line of innate defense. The GI tract contains trillions of commensal microbes, and these microbes can manipulate mucin production by activating different signalling cascades initiated by pattern recognition receptors (PRRs), including bacterial sensing Toll-like receptors (TLRs). In addition, sterile α motif pointed domain-containing ETS transcription factor (SPDEF) is a transcription factor that modulates goblet cell differentiation and positively regulates mucin production. During helminth infections, due to the co-existence of parasites and microbiota in close proximity of goblet cells in the gut, it is likely that helminth-microbiota interactions play an important role in mucin production. Indeed, goblet cell hyperplasia and increased mucin production are observed in many enteric helminth infections, including Trichuris muris, and these processes play key roles in host infection clearance. However, it should be noted that the role of microbiota within this axis is not yet understood. Here, we hypothesize T. muris-induced altered microbiota modulates goblet cell differentiation and mucin production via SPDEF-mediated transcriptional regulation and TLR2 signalling. C57BL/6 mice were gavaged with ~300 T. muris eggs. Mice were sacrificed 36 days post-infection. Microbiota from these T. muris-infected and non-infected mice were transferred into two groups of germ-free (GF) mice. Microbiota analysis revealed that treatments in both experiments (infection with T. muris and microbiota transfer from T. muris-infected mice into GF mice) significantly account for the among-sample variations in the composition of the gut microbiota between groups (p <= 0.001). In GF mice, transfer of T. muris-infected microbiota significantly increased goblet cell numbers and TLR2 expression as well as upregulated Muc2 expression compared to MSc Thesis –Yousefi Y; McMaster University – Medical Sciences v GF mice with non-infected microbiota. Antibiotic-treated (ABX-treated) TLR2 knockout (KO) mice after receiving microbiota from T. muris-infected mice showed significantly decreased expression of Muc2 and Muc5ac compared to ABX-treated wild-type (WT) mice receiving the same microbiota. To investigate whether SPDEF is a driving factor for Muc2 production in response to T. muris microbiota stimulation, we next transferred T. muris-infected microbiota into antibiotic-treated SPDEF KO and WT mice. We observed a slight, though not significant, the influence of SPDEF on the stimulation of mucin production by T. muris microbiota. These findings reveal important interactions among parasites, resident microbiota, and host in relation to goblet cell response in the gut. In addition, this study provides new information on TLR2-based innate signalling in the regulation of goblet cell biology and mucin productio / Thesis / Master of Science (MSc)

L’étude du microbiote digestif est un enjeu important de recherche en microbiologie. La première partie de cette thèse porte sur la recherche au sein du microbiote digestif de nouveaux antibactériens, qui apparait comme une des pistes clés dans la lutte contre la résistance aux antibiotiques. Les trois quarts des antibiotiques sont des produits naturels, ou dérivés, sécrétés par des microorganismes de l’environnement. Comme lui, le microbiote digestif représente un écosystème complexe où règne une grande compétition. Nous avons recherché des antagonismes de culture dans le microbiote digestif contre les bactéries les plus pathogènes pour l’homme. Nous avons trouvé une inhibition de S. aureus par P. avidum, de E. cloacae par B. fragilis, E. dispar, L. delbruckii, P. acidipropionici, S. equinus, S. gallolyticus, et enfin de E. aerogenes par B. vulgatus et E. dispar. Nous avons également trouvé des clusters de gène de métabolites secondaires dans le génome de ces bactéries. Ce travail préliminaire confirme que le microbiote digestif est une source potentielle de nouveau antibactériens. En dépit de l’explosion du nombre d’espèces isolées dans le microbiote digestif grâce à la culturomics, certaines restent fastidieuses à cultiver. Nous avons analysé par métagénomique et culturomics une selle avant et après incubation anaérobie en présence de 5% de rumen et 5% de sang de mouton. Ce travail montre une dynamique de croissance des bactéries très hétérogène. Le milieu d’enrichissement utilisé était efficace et permettait la culture d’un plus grand nombre d’espèces bactériennes. Ce travail apporte des éléments nouveaux permettant l’optimisation de cette étape de culturomics. / Gut microbiota is a major health concern for microbiologists. Its alterations were previously related to diseases. In the first step of this thesis, we have searched for new antimicrobials within the gut microbiota. Indeed, antibiotic resistance is a global health concern and research for new antibiotics is a cornerstone for fight against it, according to the WHO. Three quarter of all current antibiotics are natural products, or derived from them, synthesised by bacteria and fungi from soil. Gut microbiota is another complex ecosystem with strong competition. We have searched for antagonism in the gut microbiota species against most human pathogenic species. We found an inhibition of growth of S. aureus by P. avidum, of E.cloacae by B. fragilis, E. dispar, L. delbruckii, P. acidipropionici, S. equinus, S. gallolyticus,and an inhibition of E. aerogenes by B. vulgatus and E. dispar. We also found BGCs for all these species. This preliminary work confirm that gut microbiota is a potential source for new antibiotics. Despite the explosion of bacterial species isolated from gut, some fastidious species remains difficult to grow. We performed a metagenomic and culturomics analysis of a fresh stool sample before and after incubation into an anaerobic blood bottle supplemented with sheep blood and rumen fluid. This medium used in culturomics for enrichment was effective, allowing the isolation of higher number of species. This work show that the dynamic growth of bacteria is very variable. This work brings some precisions in the dynamic of bacterial growth that could improve the culturomics process.

Les infections digestives à Clostridium difficile nécessitent une première étape de colonisation de l’écosystème intestinal. Avant l’âge de deux ans, la colonisation par C. difficile est fréquente mais paradoxalement le plus souvent asymptomatique. Nous avons montré que plus d’un tiers des enfants de 0-3 ans, et plus de 70% de ceux de 7 à 9 mois (15% pour les souches toxinogènes), étaient porteurs sains de C. difficile à l’hôpital et dans la communauté. Deux périodes d’acquisition de C. difficile ont été identifiées : néonatale ou 3-6 mois. Les souches infantiles de C. difficile étaient identiques aux souches isolées chez l’adulte, faisant du jeune enfant un réservoir potentiel de souches infectieuses. Nous avons également montré par méthode moléculaire que des changements en espèces dominantes du microbiote étaient associés à la colonisation par C. difficile. Bifidobacterium longum caractérisait le microbiote des enfants non colonisés, et pourrait participer à la résistance à la colonisation par C. difficile. / Gastrointestinal infections with Clostridium difficile require a first step of colonization of the intestinal ecosystem. Under the age of two years, C. difficile colonization is frequent but paradoxically most often asymptomatic. We have shown that more than a third of children 0-3 years and more than 70% of those from 7 to 9 months (15% for toxigenic strains) were healthy carriers of C. difficile in the hospital and in the community. Two C. difficile-acquisition periods were identified: neonatal or 3-6 months. The C. difficile strains from infants were identical to strains isolated from adults, making infants a potential reservoir of infectious strains. We also showed by molecular method that changes in dominant species of the microbiota were associated with colonization by C. difficile. Bifidobacterium longum characterized the microbiota of children not colonized by C. difficile, and could be involved in the colonization resistance process.

A microbiota intestinal é um ecossistema complexo que desempenha um importante papel na gênese da obesidade. A ocorrência e participação dos Mollicutes na microbiota intestinal é praticamente desconhecida. Deste modo, o objetivo do presente estudo foi analisar a participação dos Mollicutes e dos Filos Firmicutes e Bacteroidetes na microbiota intestinal de mulheres obesas e eutróficas. A casuística foi de 20 mulheres obesas e 20 mulheres em eutrofia. Foram obtidas amostras de fezes, sangue e aplicado questionário semiestruturado sobre fatores relacionados com obesidade, microbiota intestinal e ambiente, além de Bioimpedância e questionário de frequência alimentar. Constatou-se uma associação positiva estatisticamente significante entre a presença de Mollicutes e mulheres obesas. Foi observada maior proporção de Firmicutes/Bacteroidetes na microbiota intestinal das mulheres obesas. Os resultados obtidos permitiram obter evidências importantes da participação dos micro-organismos da classe Mollicutes. As alterações da microbiota intestinal também contribuíram na definição de subconjuntos de indivíduos com diferentes perfis de risco metabólico e a da heterogeneidade associada a fenótipos humanos relacionados com a adiposidade. / The gut microbiota is a complex ecosystem that plays an important role in the pathogenesis of obesity. The occurrence and participation of Mollicutes in the gut microbiota is pratically unknown. The aim of this study was to analyze the participation of Mollicutes and Firmicutes and Bacteroidetes phylos in the gut microbiota of obese and normal weight women. For the study, it was collected samples of 20 women with obesity and 20 women of normal weight. It was collected stool samples, blood, semi-structured questionnaire on factors associated with obesity, gut microbiota and the environment, and anthropometric measurements using bioelectrical impedance and food frequency questionnaire. It was detected a statistically significant positive association between the presence of Mollicutes and obese women, and there was a higher proportion of Firmicutes/Bacteroidetes in the gut microbiota of obese women. The results provide important evidence about the participation of Mollicutes class in the gut microbiota of the population studied and interactions in intestinal microbiota can define subsets of individuals with different metabolic risk profiles and thus contribute to investigation of the heterogeneity associated phenotypes related to adiposity.

A microbiota intestinal é um ecossistema complexo que desempenha um importante papel na gênese da obesidade. A ocorrência e participação dos Mollicutes na microbiota intestinal é praticamente desconhecida. Deste modo, o objetivo do presente estudo foi analisar a participação dos Mollicutes e dos Filos Firmicutes e Bacteroidetes na microbiota intestinal de mulheres obesas e eutróficas. A casuística foi de 20 mulheres obesas e 20 mulheres em eutrofia. Foram obtidas amostras de fezes, sangue e aplicado questionário semiestruturado sobre fatores relacionados com obesidade, microbiota intestinal e ambiente, além de Bioimpedância e questionário de frequência alimentar. Constatou-se uma associação positiva estatisticamente significante entre a presença de Mollicutes e mulheres obesas. Foi observada maior proporção de Firmicutes/Bacteroidetes na microbiota intestinal das mulheres obesas. Os resultados obtidos permitiram obter evidências importantes da participação dos micro-organismos da classe Mollicutes. As alterações da microbiota intestinal também contribuíram na definição de subconjuntos de indivíduos com diferentes perfis de risco metabólico e a da heterogeneidade associada a fenótipos humanos relacionados com a adiposidade. / The gut microbiota is a complex ecosystem that plays an important role in the pathogenesis of obesity. The occurrence and participation of Mollicutes in the gut microbiota is pratically unknown. The aim of this study was to analyze the participation of Mollicutes and Firmicutes and Bacteroidetes phylos in the gut microbiota of obese and normal weight women. For the study, it was collected samples of 20 women with obesity and 20 women of normal weight. It was collected stool samples, blood, semi-structured questionnaire on factors associated with obesity, gut microbiota and the environment, and anthropometric measurements using bioelectrical impedance and food frequency questionnaire. It was detected a statistically significant positive association between the presence of Mollicutes and obese women, and there was a higher proportion of Firmicutes/Bacteroidetes in the gut microbiota of obese women. The results provide important evidence about the participation of Mollicutes class in the gut microbiota of the population studied and interactions in intestinal microbiota can define subsets of individuals with different metabolic risk profiles and thus contribute to investigation of the heterogeneity associated phenotypes related to adiposity.

Environmental contamination is a public health concern. In particular persistent organic pollutants like Polychlorinated Biphenyls (PCBs) have been associated with multiple chronic inflammatory diseases, including non-alcoholic fatty liver disease (NAFLD). NAFLD prevalence has steadily increased and is expected to continue to rise with an estimated 25% of the world’s population and 80-100 million people affected in the United States alone. Importantly, the liver is the primary site for endobiotic and xenobiotic metabolism, hence its proper function is critical for the body’s response to innate and extrinsic molecules. One way to combat the deleterious effects of PCB toxicity and fatty liver disease is by increasing consumption of beverages and foods that contain beneficial bioactive nutrients, like dietary polyphenols. However, the biological properties of these dietary compounds are subject to their bioavailability which is directly dependent on the activity of the liver. The first aim of this dissertation was to test the hypothesis that in the presence of a compromised liver, PCB-126 toxicity is altered. Indeed, hepatic and systemic PCB-126 toxicity was exacerbated in this severe liver injury mouse model with an observed increase in hepatic inflammation, systemic inflammation, and early markers of endothelial cell dysfunction. Interestingly, we also observed an increase in the novel gut-liver axis derived cardiovascular disease (CVD) marker trimethylamine-N-oxide (TMAO). Taken altogether, aim 1 proved that a compromised liver can alter PCB toxicity, with implications of the gut microbiota in disease pathology. In aim 2 we investigated whether GTE can protect against MCD-induced hepatic toxicity and development of NAFLD. Results indicated that MCD mice exhibited severe liver injury and gut dysbiosis and unexpectedly, GTE had no protective effects. Interestingly MCD mice displayed differential epigallocatechin-3-gallate (EGCG) metabolism at the hepatic and gut microbiota level, which may alter polyphenol bioavailability and therapeutic potential. Overall, the results provide insight into how a dysfunctional liver and gut dysbiosis can alter polyphenol metabolism, possibly reducing its therapeutic efficiency. In aim 3 we sought to determine potential protective effects of a prebiotic in this mouse model. MCD-fed mice were exposed to PCB-126 with or without inulin supplementation. Although findings from this study are preliminary, our evidence indicates that inulin restores body weight and body composition in this MCD+PCB mouse model and alters the expression of Cyp1a1 in PCB exposed mice, suggesting that inulin’s protective effects may be a result of its ability to interact with the AhR pathway. However further analysis will need to be done to examine the effects of inulin on hepatic, systemic, and gut microbiota endpoints. Overall the data contained in this dissertation suggests that in the presence of a compromised liver both pollutant toxicity and nutrient metabolism are altered, with implications of the gut-microbiota in disease risk. These findings suggest that individuals with end stage liver injury may be more susceptible to pollutant-induced toxicity and nutritional intervention may be unsuccessful at mitigating disease risk.

The human gut is host to a vast consortium of microorganisms, collectively referred to as the microbiota or microflora, which play important roles in health and disease. Current applications focus only on a single type of bacteria, which are not the most dominant numerically, and without detailed knowledge of the specific functions of these bacteria. A good indicator of the function of a bacterial species involves detailed analysis of its enzymes. Bacteroides thetaiotaomicron is one of the predominant bacterial species with a great representation of the carbohydrate processing enzymes, glycoside hydrolases in its proteome. This thesis reports the production and purification of one such enzyme, BT3299, suitable for kinetic and structural studies. The enzyme displayed a broad substrate specificity with a slight preference for 1-->3 and 1-->6 glycosidic linkages and longer chain saccharides. Future work will focus on structural analysis as an aid to the understanding of the enzyme function.