Thesis (M.S.)--Duquesne University, 2003. / Title from document title page. Abstract included in electronic submission form. Includes bibliographical references (p. 59-61) and abstract.

Thesis (Ph. D.)--University of Hong Kong, 1994. / Includes bibliographical references (leaves 72-104).

Thesis (Ph. D.)--University of Hong Kong, 2005. / Title proper from title frame. Also available in printed format.

Thesis (Ph.D.) - University of Queensland, 2006. / Includes bibliography.

Thesis (Ph. D.)--Drexel University, 2006. / Includes abstract and vita. Includes bibliographical references (leaves 109-120).

Irritable bowel syndrome (IBS), majorly characterized by irregular bowel movements and abdominal pain, is one of the most prevalent functional gastrointestinal disorders (FGIDs) in the world. Disturbance of gut microbiota, closely linking with gut dysfunction, has been regarded as one of important pathogenetic factors for IBS. However, gut microbiota-driven mechanism underlying IBS remains unclear, which leads to inefficient and non-specific effects of current microbiota-oriented therapy. In this thesis, function-based microbiota investigation with combination of metagenomic and metabolomic analyses was separately performed in IBS cohort and model to precisely link pathogenic species with disordered GI motor function. A series of microbiota manipulation studies in rodents were conducted to explore bacteria-driven molecular mechanism. Firstly, a pilot study with 'omics' analyses revealed fecal microbial structure significantly varied in IBS patients with disorder GI motility relative to healthy controls (HC). Such changed IBS enterotype was functionally characterized by disturbed metabolism of bile acids (BAs) that are previously proved to regulate GI motor function. It indicates microbiota-driven GI dysmotility relevant to disturbance of BA metabolism in IBS. Secondly, a systematic review with meta-analysis was performed to comprehensively understand existing findings related to BA metabolism and its linkage with IBS. Results showed that abnormal BA excretion, previously reported in at least one IBS subtype, is associated with dysregulation of BA synthesis, marked with abnormalities of circulating indices 7α-hydroxy-4-cholesten-3-one (C4) and fibroblast growth factor 19 (FGF19). However, what's the role of gut microbiota in abnormal BA excretion is undetermined. Thirdly, to explore possible role of gut microbiota in abnormal BA excretion in IBS, BA metabolites and BA-related microbiome were simultaneously analyzed in stools of recruited subjects. Results found that total BA and microbiota-derived BAs were remarkably elevated in a quarter of IBS-D patients (BA+IBS-D) who exhibited more frequent defecation, higher level of serum C4 but lower level of serum FGF19 than those with normal BA excretion (BA-IBS-D). In line with metabolic results, abundances of BA-metabolizing bacteria, particularly Clostridium scindens (C. scindens) simultaneously expressed hdhA and bais that are responsible for BA 7α oxidation and dehydroxylation, were highly enriched in fecal metagenomes of such particular IBS-D population. These findings suggest the increased BA-metabolizing microbiome is associated with the dysregulated host BA synthesis in the subgroup of BA+IBS-D patients. Fourthly, by analyzing metabolites and bacteria related to BA metabolism, a neonatal maternal separation (NMS)-induced IBS-D rat model characterized by accelerated GI motility and excessive BA excretion were found to largely mimic gut microbial BA metabolism in BA+IBS-D patients. Specifically, intraluminal total and secondary BAs were significantly elevated in the large intestinal lumens (cecum, proximal colon and feces) of NMS rats, together with increased abundances of hdhA- and bais-expressing Clostridium species, including C. scindens. Moreover, quantitative polymerase chain reaction (PCR) analysis showed upregulated mRNA expression of cholesterol 7 α-hydroxylase (CYP7A1) whereas downregulated mRNA expression of small heterodimer partner (SHP) in the liver of NMS rats, indicating enhanced hepatic BA synthetic level. These observations based on such IBS-D model suggest the association of excessive BA-metabolizing microbiome and increased hepatic BA synthesis. Fifthly, to further clarify whether excessive BA-metabolizing bacteria contribute to enhanced hepatic BA synthesis and to explore the underlying molecular mechanism, we performed bacterial intervention in pseudo germ-free (GF) or/and specific pathogen free (SPF) mice by transplantation of human fecal microbiota and the signal strain C. scindens. Compared with GF mouse recipients of HC and BA-IBS-D fecal microbiota, BA+IBS-D fecal microbial recipients displayed shorter GI transit and increased subsistence of C. scindens in the cecal contents. In line with higher level of serum C4, taurine-conjugated BA contents and mRNA expressions of BA synthetase CYP7A1 and sterol 12α-hydroxylase (CYP8B1) were significantly elevated in the liver of BA+IBS-D recipients. These findings showed bioactive effects of BA+IBS-D fecal microbiota with enrichment of C. scindens on hepatic BA synthesis. Next, to further confirm the effects of the species C. scindens on host BA synthesis, we individually colonized C. scindens strains (ATCC 37504) to pseudo GF and SPF mice. Results showed both mice models with single strain colonization exhibited accelerated GI transit and higher contents of hepatic total and taurine-conjugated BAs compared with individual vehicles treated with PBS. Combining metabolic changes, the upregulated expressions of hepatic CYP7A1 mRNA in colonized mice indicate that C. scindens substantially promote hepatic BA synthesis in colonized mice. Furthermore, contents of taurine-conjugated BAs, served as natural antagonists of farnesoid X receptor (FXR) that negatively control of new BA synthesis, were elevated in ileal lumens of colonized mice. Expressions of FXR-targeted genes SHP and fibroblast growth factor 15 (FGF15) were consistently reduced in the liver and ileum tissues of colonized mice, respectively. Results suggest that suppression of FXR-mediated feedback signaling is involved in Clostridium-driven hepatic BA oversynthesis, which deserve the further investigation. Collectively, the works of this thesis integrating clinical and animal studies indicate that BA-metabolizing bacteria, particularly C. scindens, enhance hepatic BA synthesis and consequently leads to BA overexcretion. It provides novel bacteria-driven mechanism for enhanced GI motility, and supply a direction in precise microbiota-related pathogenesis and medication for IBS-D population in future.

This research investigated the role of the intestinal microbiota in shaping host food intake and body weight through immunomodulation, the impact of refined and unrefined diets, and though fermentable fibre induced gastrointestinal hormone secretion. Gut-derived lipopolysaccharide activating TLR4 has been proposed to contribute to obesity. To investigate this, TLR4-/- or CD14-/- mice and C57BL/6J controls were fed a high-fat or low-fat diet. Neither TLR4-/- or CD14-/- were protected against high-fat diet-induced obesity. High-fat diet increased hypothalamic expression of SerpinA3N and SOCS3 regardless of genotype; however, inflammatory gene expression was not increased. To investigate the use of chow control diets in obesity-associated microbiota changes, C57BL/6J mice were fed a chow diet, refined high-fat, or low-fat diet. Both high-fat and low-fat refined diets resulted in similar dramatic alterations in the composition of the intestinal microbiota at the phylum, family, and species level compared to chow, while only high-fat diet feeding resulted in obesity and glucose intolerance. The roles of colonic GLP-1 and PYY in mediating fermentable fibre in reducing food intake and body fat were investigated using GLP-1R-/- and PYY-/- mice fed a high-fat diet supplemented with inulin or cellulose. Inulin supplementation reduced body fat and food intake in C57BL/6J control mice while GLP-1R-/- and PYY-/- mice showed an attenuated response to dietary inulin. In summary, this research questions the role of TLR4 and LPS in diet-induced obesity. These results demonstrate the importance of the control diet used in studies of obesity in mice and indicate that many of the obesity-associated changes in the gut microbiota are due to comparing refined high-fat diets with chow diets. These results also provide evidence for an essential role for both GLP-1 and PYY in mediating the food intake and bodyweight-reducing effects of fermentable fibre.

No description available.

Microbiota are present in large numbers and as a diverse population within the gastrointestinal tract. There are approximately 400 different species of microbiota which may be beneficial, harmful or both, but each play an important role in the regulation and modulation of the hosts’ bowel processes (McOrist et al. 2008; Dethlefsen et al. 2008). Many of these colon microbiota allow for saccharolytic fermentation of non-digestible dietary fibres and carbohydrates into by-products and intermediates, followed by a subsequent conversion into short chain fatty acids (SCFAs) (mainly n-butyric acid, propionic acid and acetic acid) each of which play an important role in maintaining colon homeostasis (Topping & Clifton 2001). A balance of ‘good’ microbiota (e.g., Bacteroides spp./ Bifidobacteria spp.) and ‘bad’ microbiota (e.g., Veilonellae) and the optimal production of various SCFAs within the gut could possibly allow for proper functioning of the large intestine and assist in decreasing the onset of various colonic disorders such as Irritable Bowel Syndrome (IBS). The sample group for the study consists of male and female patients, with an average age of 40 to 50 years old, whom of which have been diagnosed with either constipation IBS (C-IBS) or diarrhoea IBS (D-IBS) via the Rome III criteria system for IBS diagnosis. DNA and SCFA extractions were optimised for human stool, colonic fluid and tissue biopsy sample obtained from the aforementioned patients. Optimization steps allowed for starting material with high analysis integrity. Different methods of microbiota analysis, such as ARISA, were investigated; however, real-time qPCR was selected as the best method to identify and quantify specific microbiota. Extracted SCFAs were separated via gas chromatography and identified and quantified via Mass Spectrometry. Significant changes in microbial content and SCFA profiles were found to be associated with healthy and IBS patients. Results obtained would however be influenced by external factors typical of clinical studies of this nature. This study allows for opportunities for future research into understanding IBS.

Human gastrointestinal tract is complex and highly dynamic environment, harboring trillions of microbes that collectively play a pivotal role in host metabolism, immune function, and the maintenance of general health. However, studying the gut microbes and their interplay with host requires measurements at multiple dimensions is challenging since we currently lack the tools to directly measure these microorganisms at many different levels, which hinders our ability to unravel the ecology of gut microbes and their mechanistic underpinnings in human health and disease. Here, I present a set of novel techniques to study gut microbe and host-microbe interactions at unprecedented resolution, providing tremendous innovative insights to comprehensively understand the gut microbes and their environment. First, I leverage a high-throughput automation system to build a machine learning guided culturomics platform, enabling rapid isolation and culturing of personalized gut strains. Second, to better characterize the functions of these non-model microorganisms, I describe a ribonuclease-based ribosomal RNA depletion approach for microbe, paving the way for high-throughput bacterial transcriptome profiling. Next, shifting from gut microbes to the interaction with the host, I develop a technique of fecal exfoliome sequencing to robustly profile host gastrointestinal transcriptome in a non-invasive way, providing a powerful approach to study the temporal behaviors of gut cells in health and disease. Finally, to study massive genetic variants in microbiome arena, I describe a template-mediated synthesis approach for rapid and efficient generation of genetic variants sequences and demonstrate its utility in a few cases. Taken together, these techniques provide in-depth novel measurements into the ecology and physiology of human gut microbes, collectively making up an exciting set of tools for future studies.