The intestinal tract microbiota – microbial community of the gut – is an important field in microbiology not only because of its critical role in the host development, but also increasingly large number of diseases are associated with certain state of the gut microbiota. The community structure and function of the gut microbiota is relatively well studied in humans and related higher vertebrates, but is severely understudied in fish. This is especially true for the coral reef fishes, who constitute the most diverse assemblage of vertebrates spread over a very local scale, and are essential for the resilience of the reefs. In order to bridge this gap in knowledge, this dissertation studied the community structure, interactions and functions of the gut microbial community from the surgeonfishes in the Red Sea – with special focus on the surgeonfish enteric symbiont Epulopiscium spp. Initially, I studied the composition of the gut microbiota of nine surgeonfish and three nonsurgeonfish species from the Red Sea using 454 pyrosequencing. Upon discovering the high abundance of Epulopiscium spp. in herbivorous surgeonfishes, I then proceeded to identify their phylogenetic diversity, distribution, as well as deducing their coevolutionary relationship with the host. Because Epulopiscium spp. undergo substantial changes in the cell size (grow up to ~600μm) and the DNA concentration (from 85 to over 250pg per cell) throughout their diel lifecycle, I also studied the temporal changes in their expression pattern using RNA-seq. Overall, this dissertation shed light on the complex structure, interaction and function of an important family of coral reef fish from the Red Sea through range of molecular techniques.

<p>    </p> <p>In the United States, colorectal cancer (CRC) is the third most common cancer and the third leading cause of cancer mortality in men and women. Recent epidemiological evidence has shown that there’s been a steady increase in young onset CRC, underlying a continued need to understand mechanisms that may be contributing to its development. One risk factor that continues to persist and rise is obesity. Obesity is a multifaceted disease characterized by various metabolic and physiologic changes that influence tumorigenesis. Another component that is altered in obesity and has been shown to contribute to CRC is the gut microbiota. Obesity associated gut microbiota is different relative to a lean counterpart and has been linked poor colonic health, which can increase risk for CRC. Researchers have shown that intestinal tumorigenesis is worse in diet induced obesity but given other related conditions like chronic inflammation, the role of the gut microbiota in obesity associated CRC risk has not been adequately isolated. To address this gap and to further explore the role of diet in this relationship given its importance in driving obesity and impacting gut microbiota composition, we performed two studies. First, we assessed the role of obesity and/or two different obesogenic diets on gut microbiota composition and intestinal permeability. We hypothesized that diet and obesity would affect gut microbial community composition and that obese mice would have higher intestinal permeability relative to lean mice regardless of diet. Our results indicated that both diet and obesity were significant predictors and had varying effects on species richness and community structure of the gut microbiota and significantly enriched multiple bacterial taxa. Second, to isolate the role of obesity- and/or diet- influenced gut microbiota on CRC development, fecal microbial transplantation was performed by transferring the intestinal content from mice in the first study into recipient mice before chemical induction of CRC. We hypothesized that the gut microbiota from obese mice on obesogenic diets would promote CRC independent from the development of obesity. Our results indicated that gut microbiota shaped by the obesogenic diets was associated with worse colonic tumor measurements, while the differences in gut microbiota due to obesity or leanness did not affect CRC outcomes. Overall, we have demonstrated that diet and obesity have significant effects on gut microbial communities, but only dietary-induced gut microbial changes promote CRC. These results highlight the importance of understanding dietary effects on gut microbiota in CRC development which improves our ability to determine better strategies of prevention and treatment. </p>

Previously, the exact phylogenetic relationship between the giant panda (Ailuropoda melanoleuca) and the red panda (Ailurus fulgens) has been unclear, but with the advent of molecular sequencing technologies, these two animals are now known to be distantly related. Although taxonomically distinct, these two panda species have several things in common, primarily their almost exclusively bamboo diet, but also their similar physical adaptations to their diet and their sympatry in some locations. What was unknown was if their similarities also extended to their gastrointestinal tract (GIT) microbiota. Using next-generation 16S rRNA parallel sequencing technologies, we uncovered several factors that impact bacterial communities of the pandas and also found that the two panda species harbor distinct microbial communities. In general, the Firmicutes and the Proteobacteria dominate both pandas’ gut microbiomes, with lesser contributions by the Actinobacteria and the Bacteroidetes. However, for the red panda, sex, age, and season significantly alter GIT microbiota. For giant pandas, we found that bacterial communities differed significantly between their normal fecal samples and mucus excretions. Together, these data display the plasticity of their bacterial communities, with several factors shaping GIT microbiota. As both species are highly threatened, understanding the relationship between the panda and their gut microbiome has given insight into the overall health of these uniquely herbivorous carnivores.

No description available.

Obesity is a growing problem that impacts both adults and children. Obesity is linked to the development of unfavorable health outcomes like excess fat accumulation in the liver, a problem known as non-alcoholic fatty liver disease (NAFLD). Brown adipose tissue (BAT), a thermogenic body fat that can be turned on by cold, produces heat by consuming circulating lipids and glucose in a futile cycle. Less active cold-stimulated BAT is linked to obesity and type 2 diabetes in adults but whether this relationship exists in children is unknown. In rodents, increases in BAT activity are associated with reductions in NAFLD, effects that may be mediated through changes in the gut microbiome and reductions in peripheral serotonin. Whether the gut microbiome and serotonin play a role in regulating BAT activity in adults and children is not known. In this thesis, we have utilized magnetic resonance imaging (MRI) proton density fat fraction (PDFF) to assess BAT in the supraclavicular (SCV) region after three hours and one hour of whole-body cold exposure in adults and children, respectively. In 60 adults (aged 18-57 years), we examined whether there is a relationship between cold-stimulated BAT activity and liver fat (assessed via MRI) and whether gut microbiota plays a role in connecting these two tissues. In children, we investigated, BAT activity after whole-body cold exposure in 26 boys (aged 8-10 years). We also explored if BAT activity was different between boys with and without overweight/obesity. Finally, in young boys, we measured the levels of serotonin in platelet-poor plasma and its metabolic end product 5-hydroxyindole acetic acid (5-HIAA) in the urine. We explored if these measures of circulating serotonin were related to cold-stimulated BAT activity and if they were different between boys with and without overweight/obesity. The findings from this research indicate that higher cold-stimulated BAT activity is associated with lower liver fat in adults, but that this relationship is unlikely mediated through changes in the gut microbiota. Additionally, boys with overweight/obesity have lower cold-stimulated BAT activity and lower 5-HIAA in their urine compared to those with normal weight. Moreover, circulatory serotonin is negatively related to total adiposity. However, circulating serotonin is not related to cold-stimulated BAT activity in this cohort. These findings are important as they indicate for the first time that increasing BAT activity in adults and children could potentially be a new avenue for the treatment of NAFLD and obesity. / Thesis / Doctor of Philosophy (PhD) / Obesity is a risk factor for the accumulation of extra liver fat, a problem known as non-alcoholic fatty liver disease (NAFLD). Brown adipose tissue (BAT) is a kind of body fat that rather than storing calories like white fat burns calories when switched on by cold. Studies in adults have shown that people with obesity and type 2 diabetes have less active BAT suggesting switching it on may be helpful to promote weight loss and lower glucose. However, whether this relationship exists in children is not known. In rodents, increased BAT activity has also been linked to reductions in NAFLD, effects that might involve a hormone called serotonin, or changes in the gut microbiome but whether this is important in children and adults is also not understood. In this thesis, we utilized magnetic resonance imaging (MRI) to examine BAT activity after whole-body cold exposure in adults (3 hours) and children (1 hour). In 60 adults (aged 18-57 years), we report that higher cold-stimulated BAT activity is linked to NAFLD, but gut microbiota does not seem to play a role in this relationship. In 26 boys (aged 8-10 years), BAT is less responsive to cold in boys with overweight/obesity compared to boys with normal weight. Additionally, serotonin is lower in boys with overweight/obesity compared to boys with normal weight. These findings suggest that increasing BAT activity in adults and children could potentially be a new avenue for the treatment of NAFLD and obesity.

No description available.

This study aimed to isolate and characterize in-vitro and under simulated colonic conditions, probiotic candidates isolated from food environment producing γ-aminobutyric acid (GABA), a major inhibitory neuromediator of the enteric nervous system with a potential role in modulating the immune system in many health disorders. Several lactic acid bacteria were isolated and detected for the presence of the gadB gene using PCR and GAD enzymatic assay. The most active strains with high and fast production kinetics were identified, characterized, and included Streptococcus thermophilus, Lactiplantibacillus plantarum, and Lactobacillus delbrueckii subsp. bulgaricus. The biological safety (i.e., sensitivity to antibiotics and the presence of virulence factors) and probiotic potential (i.e., resistance to gastrointestinal conditions and whole-genome sequencing) of identified bioactive strains was also confirmed in vitro. The growth, GABA production, and competitiveness of selected probiotic candidates (B. animalis, S. thermophilus, and L. bulgaricus) were investigated in the presence of human gut microbiota ex vivo in a model of a proximal colon mimicking physiological and microbiological conditions of the human large intestine. Supplementation with GABA-producing probiotic candidates did not affect the overall gut microbiota diversity over 48 h of treatment. However, we observed modulation of the microbiome composition, especially change of Bacteroides population, a key gut microbe associated with anti-depressive and anti-inflammatory activities. The level of microbiota-generated butyrate within 12 h of treatment was significantly increased compared to control. Results from this study demonstrated the probiotic potential of tested GABA-producing bacteria and their impact on gut microbiota structure and metabolism, suggesting their suitability for gut health-promoting application.

京都大学 / 新制・課程博士 / 博士(農学) / 甲第24906号 / 農博第2569号 / 新制||農||1102(附属図書館) / 京都大学大学院農学研究科森林科学専攻 / (主査)教授 大村 和香子, 教授 髙野 俊幸, 教授 飛松 裕基 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DGAM

Temperature represents a major driving force in biology as it influences essential functions across multiple levels of biological organization. The role of temperature is especially important for ectothermic animals, whose biotic processes are dependent on both body and environmental temperature. Assessing the relationship between temperature and organismal performance represents an important research direction as temperatures continue to warm under anthropogenic climate change. Chapters two and three are focused on a recently colonized population of the invasive Mediterranean House Geckos at the northern edge of their invasion front. These chapters examine the ecological and physiological factors that enable these lizards to persist in a cooler and more temperate environment than their native range. The thermal breadth of a reptile greatly influences its ability to tolerate a thermally variable environment, particularly when environmental options are limited for behavioral thermoregulation. These chapters explore the thermal performance of this species, and the results show that the eurythermality of these geckos promotes their rapid colonization of novel environments despite experiencing prolonged periods of cool temperatures. Chapters four, five, and six, by contrast, shift focus to larval amphibians to explore the constraints and factors underlying plasticity in acclimation to temperature extremes. As habitats continue to warm with climate change, ectotherms with limited capacity to thermoregulate, such as larval amphibians in shallow ponds, will be under a heightened threat of heat stress and mortality. Resultantly, identifying different factors that can increase organismal heat tolerance would reduce the risk of overheating and promote survival. Chapters four, five, and six explore this topic by measuring the critical thermal maximum (CTmax) of larval wood frogs. Chapter four focuses on the tradeoff between basal CTmax and plasticity of CTmax and its consequences for how a larval anuran responds to an acute heat shock. Chapter five examines the role a viral pathogen, ranavirus, has on larval CTmax. Surprisingly, a lethal dose of ranavirus did not reduce CTmax which goes against the common pattern of pathogenic infections lowering host heat tolerance. Lastly, chapter six explores the relationship between the gut microbiota and host CTmax with a particular focus on cross-species microbiota transplants. In line with our prediction, transplanting the gut microbiota of a heat-tolerant donor species promoted greater CTmax in the heat-sensitive recipient species.

Plant-based proteins have gained popularity because of their high nutritional value and more sustainable alternative to animal-based proteins. Soybean and chickpea are two widely consumed plant-based proteins, whereas tempeh is a popular plant-based fermented whole food product that is rich in protein. With the increase in the development of plant-based food products, there is little research into how plant proteins affect gut microbiota characteristics and metabolites. Therefore, there is a need to understand the underlying mechanisms surrounding the consumption of these foods. The purpose of this study was to investigate the health benefits of soybean, chickpea, and their tempeh counterparts’ consumption as whole foods on the gut microbiota and metabolites. Our results showed that soybean tempeh significantly increased the abundance of beneficial probiotic bacteria such as Roseburia and Ruminiclostridium 5 in the gut microbiota of mice. Additionally, soybean tempeh and soybean significantly increased Muribaculaeceae abundance, known to increase SCFA production in the colon. Lachnospiraceae NKA136 was significantly increased in soybean tempeh, soybean, and chickpea groups which may allow these foods to be used as a way of probiotic restoration. Our results showed that all dietary supplementation groups had significantly altered metabolic profiles compared to the control group. The soybean tempeh group had higher levels of peroxide (vitamin B6), myoinositol, and tetrahydrobiopterin while the chickpea tempeh group had higher levels of metabolites such as 3 hydroxyanthranilic acid. The soybean group had higher levels of metabolites such as 3-hydroxytryptophan (Oxitriptan) whereas the chickpea protein group had higher levels of metabolites such as 3-hydroxyanthranilic acid and oxitriptan. In conclusion, our study suggests that different plant-based foods can have distinct effects on gut microbiota and metabolic profiles in mice. These findings may have implications for human health and warrant further investigation into the effects of plant protein consumption on human metabolism.