Autism spectrum disorder (ASD) is characterized by deficits in social communication and interaction as well as by repetitive patterns of behavior. It is thought to affect 1 in 68 children in the United States, yet researchers do not know what causes it and treatments are primarily focused on alleviating symptoms associated with ASD rather than treating any underlying cause. Various theories have been proposed over the years regarding what causes ASD in the hopes of finding effective treatment options. One of these theories, and the topic of this work, is that the intestinal bacteria play a role in the development of autism. The idea that gut bacteria may play a role in health and disease is one that has been gaining increased interest lately, and this has spread to the field of autism research. Reports of children with ASD suffering from gastrointestinal (GI) issues are widespread, and even the first reports of children with ASD mentioned that some of them experienced GI symptoms or had issues with feeding. While GI symptoms are uncomfortable for any child, they pose special circumstances for those with ASD because these children are likely unable to effectively communicate what they are experiencing. This thesis will first review the prevalence of GI issues in children with ASD as well as discuss studies that have examined if there is a difference between the gut bacteria of children with ASD compared to neurotypical children. As will be shown, many studies have in fact found a significant difference, but these differences vary across studies and a consensus has not been reached. Following this, the link between the gut bacteria and the brain, as well as how this relates to ASD will be discussed. Then, an overview of various treatment studies aimed at targeting the gut bacteria in animal models of ASD as well as in children with ASD will be analyzed. While this field of research is certainly exciting, there is still a lot of work to be done by researchers. For one, the wide range of methodologies used and populations studied introduces variables that could be skewing the results and contributing to the lack of agreement between researchers regarding what bacterial strains might be relevant to ASD. Additionally, just because there is a correlation between certain bacterial strains and ASD does not mean it can be assumed that this is causing the development of ASD in so many children. Nonetheless, the fact that some treatment studies have led to improvements in ASD-related behaviors when targeting the gut bacteria of children indicates that this field of research is worthy of attention and continued support.

Background: Recent research showing how dietary interventions substantially influence the potential presence of widespread and stable bacterial core phyla in the human colon has garnered a considerable amount of attention. Because the human gut can play a major role in host health, there is currently some interest in observing how diet influences human gut microbial composition and how changes in diet affect the potential for gut microbiota to transform mercury. This study aims to discover how different kinds of diet affect the nature and magnitude of microbial Hg transformations in the human gut environment. Methods: Fecal samples have been collected from 5 human male individuals at University of Ottawa and stored at -80ºC for further investigation. Using high throughput DNA amplicon sequencing targeting the 16s rRNA V4 region, we investigated the microbial community structure of the gut in 5 healthy male. Mercury biotransformations in the pooled fecal sample have been carried out using stable isotopes of mercury (198HgCl2 and Me199HgCl) and analysis was conducted by using inductively coupled plasma mass spectrometry (ICP-MS). Results and conclusions: We were not able to detect any significant Hg methylation or MeHg demethylation. We suspect this is due to Enterobacteria dominating the microbial community structure after 96h; Although Enterobacteria are part of the typical microbiota of a healthy individual, they do not possess genes required for Hg methylation. As such, our microbial data support our chemical analyses. We were not able to identify whether a change in diet affected Hg transformations in the human gut environment.

Cardiovascular disease (CVD) is the leading cause of death in the United States. Recently, the gut microbiota has been implicated in the pathophysiology and progression of CVD. Experimental evidence suggests that high fat feeding alters the functional composition of the gut microbiota (dysbiosis); leading to increased translocation of the pro-inflammatory, endotoxin, and increased production of the pro-atherogenic, trimethylamine-N-oxide (TMAO). Together, these changes are hypothesized to accelerate CVD progression. Conversely, administration of gut microbiota modulating agents, such as antibiotics and probiotics, attenuate high fat feeding induced CVD in rodent models. In humans, the capacity to produce TMAO following L-carnitine or phosphatidylcholine challenges is abolished after receiving broad spectrum antibiotics for a period of one week. However, whether gut modulation over a longer period of time decreases fasting serum endotoxin, fasting plasma TMAO, and CVD risk in response to high fat feeding has been unexplored in humans. To address these issues we conducted a randomized, placebo controlled, parallel group designed, controlled feeding study in healthy, non-obese males receiving the multi-strain probiotic, VSL #3 (or placebo), while a consuming a high fat diet for 4-weeks. First, we tested the hypothesis that VSL #3 would attenuate the rise in serum endotoxin and consequent arterial stiffening following high fat feeding in healthy, non-obese males. Second, we tested the hypothesis that VSL #3 would attenuate the rise in plasma TMAO concentrations following high fat feeding in healthy, non-obese males. In contrast to our first hypotheses, serum endotoxin concentrations and arterial stiffness did not change in response to high fat feeding or with VSL#3 treatment. Interestingly, VSL #3 significantly attenuated the increase in body mass (+ 1.4±0.4 vs. +2.3±0.3 kg; P < 0.05) and fat mass (+0.7±0.1 vs. + 1.4±0.3 kg; P < 0.05) following high fat feeding compared to the placebo. In contrast to our second hypothesis, probiotic supplementation did not attenuate the rise in plasma TMAO following high fat feeding. Future studies are necessary to elucidate the mechanisms responsible for the prevention of body mass and fat mass gain with VSL#3 supplementation following high fat feeding. In addition, studies are needed to determine whether higher doses of VSL #3, other single or multispecies probiotics, prebiotics, or synbiotics attenuate the production of the proatherogenic, TMAO. / Ph. D.

<p> Understanding the mechanisms of microbiome assembly during host development is crucial for successful modulation of the gut microbiome to improve host health and growth. Detailed characterization of the swine gut microbiome through meta-analysis allows us to understand the dynamics of microbial community succession, as well as the transient and natural variations between timepoints and animals. A total of 3,313 fecal samples from over 349 pigs covering 60 time points (from birth to market age) from 14 publications were included in the meta-analysis in Chapter 2. Alpha diversity continuously increased during early stages of animal growth and increased at a slower rate in the following stages. Random forest regression identified 30 OTUs as potential microbiota biomarkers for modeling swine gut microbiome development and the external validation suggested the generalization and benchmarking role of our models in application to future microbiome studies conducted in suckling and weaning pigs. In Chapter 3, a total of 924 fecal samples from 44 newborn piglets over 21 time points (day one of age until 41 days of age) were collected every two days and community composition, assembly, and succession was determined using the V4 region of the 16S rRNA gene. Alpha diversity continuously increased during the suckling stage, yet there was no significant increase in alpha diversity during days post-weaning. Post-weaning in-feed antibiotics consistently decreased the microbial diversity and changed the community structure in both low birth weight (LBW) and normal birth weight (NBW) piglets. Delayed gut microbial community maturation was observed in LBW piglets on post-weaning days compared with NBW. Heterogeneity of the gut microbial community between piglets linearly decreased over time, as revealed by the within-time Bray-Curtis dissimilarities. Intra-individual variance both in community structure and genus abundance indicates the importance of repeated measurements for reliable observations. Dirichlet multinomial mixtures analysis supported an age-dependent microbiome developmental pattern and identified microbial taxa that are age-discriminatory. Our study addresses ecological processes shaping the swine gut microbiome between piglets with contrasting birth weights and receiving post-weaning antibiotics. Persistent gut microbiota immaturity in LBW piglets suggests that efforts to accelerate microbial community succession might improve LBW piglet growth performance and disease resistance. </p>

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Inflammatory bowel disease (IBD) is associated with an inappropriate immune response to the gut microbiota and disruption of intestinal homeostasis. IBD patients and experimental animal models have consistently shown alterations in the gut microbiota composition. However, these studies have mainly focused on faecal microbiota samples taken after the onset of inflammation and IBD establishment. The colonic microbiota inhabits both the gut lumen and the mucus layer covering the intestinal epithelium. Thus, information about mucus-resident microbiota is not necessarily conveyed in the routine microbiota analyses of faecal samples. To address potential changes in microbial composition and function before the onset of IBD, we compared both mucus and faecal microbiota in the mdr1a-/- spontaneous model of colitis over times that we histologically defined as before onset of colitis, during and after colitis onset. We showed that alterations in microbiota composition preceded the onset of intestinal inflammation and that these changes were evident in the mucus, but not in faeces. This altered microbiota composition was coupled with a reduced inner mucus layer, indicating a compromised mucus barrier prior to colitis development. Upon emergence of inflammation, compositional differences were found in both mucus and faecal microbial communities. Spatial segregation of microbiota with intestinal mucosa was also disrupted on disease onset which we hypothesise contributes to a more severe intestinal pathology. Therefore, our data indicate that microbial changes start locally in the mucus and then proceed to the faecal matter concomitantly with colitis development. Next, we examined whether microbial gene functional potential and endogenous metabolite profiles followed alterations in gut microbiota taxonomic composition. Our findings showed that the microbial gene content was similar between mdr1a-/- mice and wild-type littermate controls, demonstrating stability of the gut microbiome at the face of ensuing gut inflammation. In further support of these findings, urinary metabolite analysis revealed that metabolite profiles were unaffected by intestinal inflammation. Metabolites previously reported to change in IBD were similar between mdr1a-/- and wild-type mice at stages preceding and during inflammation. We also found that changes in metabolite profiles did not correlate with colitis scores. However, metabolite changes could discriminate mdr1a-/- mice from wild-type controls, suggesting they could have value in predicting risk of IBD with a potential clinical use in at least a subset of individuals with MDR1A polymorphisms. To assess whether changes in antimicrobial proteins (AMPs) accounted for observed differences in mucus microbiota composition, we also investigated the expression of regenerating islet-derived protein 3 γ (Reg3γ), angiogenin 4 (Ang4), β-defensin 1 and resistin-like molecule beta (Relm-β) in the colon. We found similar levels of these AMPs as well as IgA-producing plasma cells between mdr1a-/- and wild-type mice, suggesting that other factors contribute to alterations in microbiota composition. Overall, our data indicate that the mdr1a-/- is a good model of colitis, as it enables us to look at pre-clinical changes in the gut microbiota. This work suggests the importance of mucus sampling for sensitive detection of microbiota changes. Furthermore, metabolite profiling may be a helpful way to discriminate genetic susceptibility to disease.

Objective: To determine the variations in the composition of the intestinal microbiota in asymptomatic children infected with Helicobacter pylori in comparison with children without the infection. Results: Children infected with H. pylori doubled their probability of presenting 3 of 9 genera of bacteria from the gut microbiota, including: Proteobacteria (p = 0.008), Clostridium (p = 0.040), Firmicutes (p = 0.001) and Prevotella (p = 0.006) in comparison to patients without the infection. We performed a nutritional assessment and found that growth stunting was statistically significantly higher in patients infected with H. pylori (p = 0.046). / Revisión por pares / Revisión por pares

There is an increasing interest in how therapeutic drugs could alter the human gut microbiota composition and function. While some knowledge is accumulating on the antimicrobial impact of some psychotropics on isolated strains or the gut microbiota of animal models, information about other classes of psychotropics and representative species from the human gut is poorly investigated. The antimicrobial effect of psychotropic drugs is usually neglected as a confounding factor when investigating gut microbiome biomarkers, knowing that patients are generally put in long-term medication. The purpose of the present study was to investigate (in vitro and ex-vivo) the antimicrobial activity of some oral commonly prescribed psychotropics from different therapeutic classes on colonic microbiota diversity and metabolism and the potential capacity of probiotics to alleviate related dysbiosis. The findings of this study revealed an important in vitro inhibitory activity of psychotropic drugs, which were also expressed as drastic alterations in gut microbiota composition ex-vivo. Indeed, the relative abundances of Firmicutes and Actinobacteria were lowered while the Proteobacteria population was increased. Families of Lachnospiraceae, Lactobacillaceae, and Erysipelotrichaceae were also declined by psychotropics (aripiprazole) treatment. These microbial changes were translated into a decrease of the major SCFA (butyrate, acetate, and propionate) at the metabolic level. The addition of a probiotic combination (Lactobacillus rhamnosus and Bifidobacterium longum) concomitantly with a psychotropic (aripiprazole) had a protective effect by attenuating the decline of microbiota composition and increasing the concentrations of SCFA. These findings provide evidence that psychotropics, through their antimicrobial effect, have the potential to alter the human gut microbiota composition and metabolism, while probiotics can mitigate the related dysbiosis.

No description available.

The prevalence of obesity is increasing globally. Obesity is characterized by increased fat mass and is a risk factor for type 2 diabetes (T2D). Obesity is associated with hyperglycaemia, hyperinsulinemia, insulin resistance and chronic inflammation. Currently, the most effective and durable treatment for obesity and its comorbidities is bariatric surgery. Bariatric surgery changes food intake, energy balance and the composition of gut microbiota. Bariatric surgery can lower blood glucose and put T2D into remission. It was unknown if bariatric surgery-induced changes in the gut microbiota was an independent yet sufficient factor to lower blood glucose. Fecal microbiota transplantation (FMT) was performed on conventional (specific-pathogen-free, SPF) and germ-free (GF) mice using fecal material obtained from patients before surgery and 12 months after bariatric surgery. We tested FMT into mice from the same patients before and after vertical sleeve gastrectomy (VSL) and biliopancreatic diversion with duodenal switch (BPD/DS). FMT did not alter body weight, fat mass, glucose tolerance or glucose transporter mRNA expression in all intestine segments in SPF mice. FMT lowered blood glucose during an oral glucose load in GF mice receiving bacteria after VSL and BPD/DS bariatric surgery. Post-BPD/DS surgery FMT decreased Glut1 transcript level in the ileum and increased Glut1 transcript level in the TA muscle of GF mice, but did not change GLUT1 protein levels. Post-BPD/DS surgery FMT also decreased goblet cell count, villus height and crypt depth in the ileum of GF mice. We conclude that changes in the gut microbiota caused by bariatric surgery is a standalone factor that can lower blood glucose and alter gut morphology. / Thesis / Master of Science (MSc) / Type 2 diabetes is a chronic disease that involves high blood sugar (i.e. glucose), which can damage many parts of the body leading to serious complications. Diabetes is a growing global problem and is the seventh leading cause of death. Obesity is one of the largest factors leading to type 2 diabetes. Bariatric surgery reduces obesity and is to date the most effective method to lower blood glucose and reverse type 2 diabetes. Bariatric surgery alters gut anatomy and the types of bacteria that inhabit the gut. Gut bacteria can change obesity and blood glucose levels, but it was not known if the bacterial community present after bariatric surgery was a factor that is sufficient to lower blood glucose. We found that transferring gut bacteria from humans after bariatric surgery into mice lowers the blood glucose and alters the gut barrier structure where food is absorbed. It is not yet clear how this happens, but these findings show that a change in gut microbes is a standalone factor that can alter host blood glucose. Finding the glucose lowering factor in bacteria may be a new treatment to combat type 2 diabetes.