<p dir="ltr">Dietary fibers have been observed to modulate the gut microbiome in ways that prevent and moderate human diseases and confer health benefits onto their human host. How dietary fibers do this is through their structure; gut microbes are equipped with a variety of differ- ent carbohydrate-active enzymes (CAZymes) that allow some to hydrolyze glycosidic bonds, thereby utilizing the dietary fiber. The more complex the dietary fiber, the more diverse the maintained gut microbiota may be, as specialist species may be required for complete hydrol- ysis. Therefore, increasing structural complexity of dietary fibers may increase gut microbial diversity and help prevent diseases. To understand if structural features impact the gut mi- crobiome, a set of resistant glucans varying in structures, including mixed-linkage -glucans, resistant maltodextrins (similar to type IV resistant starch) and polydextroses, which are comprised entirely of glucose, were used as substrates in an in vitro sequential batch fermen- tation using fecal microbiota form three healthy donors as inocula. I measured metabolic outputs, growth curves, and community structures by 16S rRNA amplicon sequencing, which I analyzed for through alpha and beta diversity differences and taxa that overrepresented and increased in each treatment. My results show that, depending on the donor and the resistant glucan, structure does significantly impact the concentrations of short-chain fatty acids (SCFAs) and other metabolites that are produced. Resistant glucan structure also impacts alpha and beta diversity to a degree and linear discriminant analysis (by LEfSe) results also support that specific species have preference towards substrates as well. Next, resistant glucans were supplemented into a high-fat diet, and compared these diets to a low- fat diet (LFD), high-fat diet with cellulose (HFD), and high-fat without cellulose (HWC) in a mouse study using C57BL/6J mice over 4 weeks. Increasing microbial diversity will not only increase diversity in the gut microbiome, but it will also provide protective effects in behavior such as helping to prevent anxiety. I measured weight, metabolic outputs, 16S community structure, changes in alpha and beta diversity, and differential abundances of OTUs and taxa by discriminant analysis Effect Size (LEfSe) and Metastats, and anxiety behaviors using open field and light/dark box tests. Microbial community structure was significantly different in treatment groups from controls. Anxiety for mice in tapioca dextrin 01 (TD01), tapioca dextrin 03 (TD03), and resistant maltodextrin (RMF) treatment groups were gen- erally increased, suggesting that the chemical structure of these resistant dextrins may alter the gut microbiome in ways that may influence behavior.</p><p dir="ltr">My overall results support the hypothesis that the fine structural features of dietary fibers do significantly impact the gut microbiome by selecting for specific microbiota, and may even impact cognition and behavior.</p>

While consumer awareness of benefits of adequate nutrition has noticeably surged in recent years, developing countermeasures against improper eating habits still represents a public health priority in view of the growing prevalence of diet-related diseases. Eating behaviours are complex phenomena driven by a spectrum of biological and environmental factors, wherein (chemo)sensory perception is reckoned amongst the most influential. Analogously, chemosensation is affected by a myriad of determinants, and this warrants the commonly observed large variation in how tastes and smells are perceived among individuals. Given how such variability intimately relates to dietary habits, deciphering its underlying mechanisms is paramount to promoting healthier food choices. In this vein, emerging evidence suggests that human eating behaviours can also be affected by interactions between the gastrointestinal microbiota and the chemosensory systems. Despite growing interest, the sensory-oriented microbiome field suffers from obvious limitations due to its recent emergence. As a result, little efforts has been devoted to elucidating: a) the associations between the oral microbiota and olfaction or known psychological mediators of sensory perception; b) the links between the distal gut microbiota and taste functioning; c) the consequences of interactions between chemosensation and the gastrointestinal microbiota on dietary intakes. Against this backdrop, this thesis aimed at expanding the current knowledge on the interplays between domains of sensory perception and the gastrointestinal microbiota and how these might mirror variations in habitual food habits. In detail, four studies probing the associations a) between a psychosocial correlate of sensory perception (food neophobia), olfaction (Chapter 2) and the oral microbiota (Chapter 3); and b) between distal gut (Chapter 4) or oral (Chapter 5) microbiota, taste functioning and dietary intakes are here presented. In Chapter 2 and 3, a healthy cohort of 83 individuals (57.8 % women; aged 22-68 yo) remotely filled out the common Food Neophobia Scale and the trait anxiety subscale of the State-Trait Anxiety Inventory prior to providing a salivary sample for subsequent metataxonomic analysis (16S rRNA gene sequencing). Next, volunteers were tested for orthonasal olfactory functioning via the Sniffin’ Sticks battery, and monitored for retronasal aroma release while consuming a strawberry jelly candy by nose-space analysis (Selected-Ion Flow-Tube Mass Spectrometry). In Chapter 4 and 5, instead, 100 young adult volunteers (52 % women; aged 18-30 yo) attended a 7-day lasting remote protocol where responsiveness to genetically-mediated bitterness of 6-n-propylithiuracil (PROP), hedonics and intensity of oral sensations elicited by ten commercially-available food products, a battery of food-related psychological traits, a 4-day food record, and one salivary and one stool sample (sequenced by targeting the 16s rRNA gene) were collected. Overall, results substantially strengthen past evidence suggesting: a) that pronounced neophobic tendencies translate into higher levels of (negative) emotional activation or arousal towards foods; b) the existence of homogenous groups of individuals with generalized hypergeusia towards oral stimulations; c) that hyperresponsiveness to a peculiar taste quality is a barrier to the intake of foods evoking such sensation; d) that habitual consumption of dietary fibers and simple carbohydrates can shape both the gut and oral microbial ecology, respectively. Intriguingly, food neophobia and poor olfaction were positively associated with oral microbial markers of dysbiosis (e.g., Porphyromonas gingivalis), whilst a Clostridia-enriched salivary microbiota co-occurred with low responsiveness to alarming oral sensations (astringency, bitter, sour) elicited by real foods. Similarly, an ample panel of commensal gut bacterial genera mainly allocated to the families Lachnospiraceae and Ruminococcaceae was found to be enriched in individuals exhibiting lower acuity to both tastes (bitter, salty, sour, sweet) and trigeminal sensations (astringent, pungent). Besides taxonomically annotating a range of microbial taxa tied to sensory perception, putative metabolic pathways used by salivary and gut microbial communities to modulate taste perception were inferred and discussed. To conclude, this thesis supports the notion that the gastrointestinal microbiota is an additional candidate to explain interindividual variations in taste and smell perception, and provides novel important insights into the aetiology of eating behaviours. More importantly, this work also offers methodological cues to robustly assess the associations between chemosensation and host-related non genetic factors, and paves the way for future interventional studies targeting the efficacy of sensory-related microbial taxa as potential modulators of dietary habits.

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Mucosal inflammation in conditions ranging from infective acute enteritis or colitis to inflammatory bowel disease (IBD) is accompanied by alteration in enterochromaffin (EC) cell numbers and serotonin (5-hydroxytryptamine; 5-HT) content in the gut. Previously we had shown that CD4+ T cells, via production of T helper (Th)2 cytokines, regulate EC cell biology in the Trichuris muris-infectious colitis model. I further examined the mechanisms of immuno-endocrine interactions in the context of intestinal inflammation. In chapter 3, utilizing human EC cell line and Trichuris muris-mouse model of infectious colitis we identified a critical role of interleukin (IL)-13, a key Th2 cytokine, in increasing EC cell numbers, tryptophan hydroxylase (TPH)1 expression (rate-limiting enzyme of mucosal 5-HT bio-synthesis), and 5-HT production. In chapter 4, we show that IL-13 driven intestinal inflammation is critically dependent on increased 5-HT production using dextran sulfate sodium (DSS) and dinitrobenzene sulphonic acid (DNBS) models of colitis. In DSS-induced colitis, we were the first to identify the increased production of IL-13 and its pathogenic role as IL-13 knockout (IL-13-KO) mice had less severe inflammation compared to wild-type, which was exacerbated following replenishment of 5-HT in IL-13-KO mice. In chapter 5, biopsy examination revealed, higher mucosal IL-13 expression accompanied inflammation in Crohn's disease (CD), which was additionally associated with increased TPH1, 5-HT receptor (5-HTR)3A, 5-HTR7 and decreased 5-HT transporter (5-HTT) expressions. Moreover, CD patients had elevated plasma and platelet-poor plasma 5-HT levels compared to healthy controls (HCs). Furthermore, 5-HTT polymorphism associated genotypes causing inefficiency in 5-HT re-uptake were more common in our patient cohort than HCs. The findings included in this thesis further emphasize the role of immuno-endocrine interactions in intestinal inflammation, which may be a step toward a better diagnosis or management or even a cure for a disease that is of growing concern, and in understanding IBD pathogenesis. / Dissertation / Doctor of Philosophy (PhD) / The gut produces most of the serotonin found in our body, where it regulates many normal functions. A group of special cells, named enterochromaffin cells, produces nearly all of the serotonin in the gut. In diseases of the gut, especially ones that involve inflammation resulting in symptoms like abdominal pain, diarrhea and bleeding, the number of these cells and serotonin concentration are different from that in the normal gut. I found that these changes are controlled by a particular protein produced by immune cells, called interleukin-13, and alteration in serotonin levels, in turn, contributes to the inflammatory process. Our laboratory experiments with cells and animals establish this connection between interleukin-13 and serotonin in gut inflammation. We further confirm this association between interleukin-13 and serotonin in human inflammatory bowel disease. Moreover, we identify a potential genetic cause of these changes in serotonin concentrations which may ultimately result in inflammatory bowel disease.

The composition of gut microbes affects host weight, immune function, and disease status, and is sensitive to diet, environment, and pharmaceutical exposure. The gut microbiome modulates the toxicity and bioavailability of chemical stressors, however the effects of chemicals on the gut microbiome of aquatic biota are largely unknown. The Waterloo and Kitchener wastewater treatment plants (WWTPs) release effluents containing antibiotics, pharmaceuticals, and other contaminants into the Grand River (ON) that may negatively affect the gut microbiome of downstream organisms. In this study done in Fall 2018, I collected freshwater mussels (Lasmigona costata), several species of insect larvae, and riparian spiders (Tetragnathidae) from sites upstream and downstream of these WWTPs. The gut microbiome was analyzed following the extraction, PCR amplification, and sequencing of bacterial DNA using the V3-V4 hypervariable regions of the 16S rRNA genetic barcode. Changes in the relative abundance of major gut microbiome phyla were observed in all targeted aquatic organisms downstream of WWTPs except Hydropsychidae. Shannon alpha diversity, a measure of bacterial abundance and evenness, differed significantly among sites for mussels (one-way ANOVA: F=7.894, p=0.001), spiders (F=4.788, p=0.01), Perlidae (F=3.1, p=0.0056), Hydropsychidae (F=3.674, p=0.0014), and Heptageniidae (F=2.715, p=0.0143), but not for Baetidae and Ephemerellidae. In sites downstream of the Waterloo WWTP, alpha diversity decreased in spiders, while in sites downstream of the Kitchener WWTP diversity decreased in mussels and Perlidae, while increasing for spiders. Bray-Curtis beta diversity, a measure of dissimilarity between bacterial communities, was significantly dissimilar among sites in all invertebrate taxa (Permanova: p<0.02). Upstream sites differed from downstream Waterloo sites in spiders, Perlidae, and Hydropsychidae (Adonis pairwise: p<0.05), while upstream mussels, spiders, Perlidae, and Hydropsychidae differed from downstream Kitchener sites (p<0.05). Additionally, effluent-derived bacteria were found in the microbiomes of aquatic invertebrates downstream of the WWTPs and not upstream. Taxa was also a significant driver of bacterial composition and diversity in invertebrates. These results indicate that the gut microbiome of downstream organisms differed from the bacterial composition observed in the same invertebrate taxa upstream of the WWTPs, potentially leading to altered host health. This adds to our understanding of how chemical stressors impact the gut microbiome of aquatic and riparian biota; however, future studies are needed to investigate linkages between the gut microbiome and health of these species. / Thesis / Master of Science (MSc)