京都大学 / 新制・課程博士 / 博士(工学) / 甲第24610号 / 工博第5116号 / 新制||工||1978(附属図書館) / 京都大学大学院工学研究科マイクロエンジニアリング専攻 / (主査)教授 土屋 智由, 教授 横川 隆司, 教授 安達 泰治, 教授 田畑 修(京都先端科学大学) / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DFAM

京都大学 / 新制・課程博士 / 博士(農学) / 甲第24672号 / 農博第2555号 / 新制||農||1099(附属図書館) / 学位論文||R5||N5453(農学部図書室) / 京都大学大学院農学研究科応用生命科学専攻 / (主査)教授 小川 順, 教授 井上 善晴, 教授 森 直樹 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

Type II Diabetes Mellitus (T2D) and cardiovascular diseases (CVD) are non-communicable chronic diseases that involves impairments in glucose metabolism and vascular function. Multiple factors may increase the risk for T2D, including but not limited to genetics, obesity and lifestyle, such as physical inactivity and diet. The gut microbiota, the human's largest population of microorganisms, plays an essential role in health and disease. The physiology and function of the gastrointestinal tract can be influenced by the diet. Phosphatidylcholine (PC), a source of choline in the diet, is rich in Western-type diets. Gut microbiota metabolize choline to trimethylamine (TMA) which circulates and is oxidized in the liver to form trimethylamine N-oxide (TMAO). As a result, ingestion of PC or choline could increase levels of TMAO. Preclinical studies indicate a role of TMAO in the development of atherosclerosis. Likewise, multiple observations support a potential role of TMAO in the development of insulin resistance and T2D. Much of the research has been conducted on rodent models, while others are observational human studies. Whether acute and short-term increases in TMAO contribute to impairments in insulin sensitivity in humans remains unknown. To address this, we performed two studies utilizing a double-blind, placebo controlled, crossover design. Eligible participants consumed a 1000mg/day dose of choline bitartrate and placebo (maltodextrin) the night before each testing session (for the acute choline study) or for 4 weeks (for the short-term choline ingestion study). Oral glucose tolerance test, continuous glucose monitoring, flow-mediated dilation, and applanation tonometry was performed the day after the acute choline load and before and after the short-term choline ingestion period. We hypothesized that gut microbiota-generated increase in TMAO will impair insulin sensitivity, glucose tolerance, endothelial function and arterial stiffness in healthy sedentary humans. Following acute choline ingestion, significant increases in plasma TMAO (p = 0.013) and choline (p = 0.003) were evident. There was no statistically significant difference in insulin sensitivity, glucose tolerance or in any of the endothelial function and arterial stiffness measurements. Four weeks of 1000mg choline ingestion per day, significantly increased plasma (p = 0.042) and urine (p = 0.008) TMAO concentrations compared to the placebo. However, no significant differences were observed for any other measurements of insulin sensitivity, glucose tolerance, glycemic variability, endothelial function, and arterial stiffness. More research is needed to elucidate the mechanisms behind the mechanistic observations between elevated TMAO concentrations and T2D and CVD. / Doctor of Philosophy / Type 2 diabetes mellitus (T2D) and cardiovascular diseases (CVD) increase the risk of all-cause mortality. Choline is a nutrient that can be found in foods such as red meat, dairy, fish, and eggs. Choline is metabolized from bacteria in our gut and a metabolite called trimethylamine (TMA) is formed. TMA is then oxidized in the liver and trimethylamine-N-oxide (TMAO) is produced. A Western-type diet is rich in red meat, dairy, fish, and eggs and has been shown to increase production of the compound TMAO. Preclinical studies have suggested a causal role of TMAO in atherosclerosis and T2D and elevated plasma TMAO concentrations have been associated with an increased risk for CVD and T2D in observational studies. However, the causal nature of this relationship in humans is unknown. The studies described herein aimed to investigate the effects of increases in TMAO on insulin sensitivity and vascular function in healthy adults. The first study tested the effect of increasing TMAO on insulin sensitivity, glucose tolerance, and vascular function following an acute choline load (1000mg) and placebo (carbohydrate) the night before each testing session. In the second study, we examined the effect of increasing TMAO on insulin sensitivity, glucose tolerance, and vascular function in healthy adults, following a short-term choline load (1000mg/day) and placebo (carbohydrate) for 4 weeks. Acute and short-term choline ingestion significantly increased plasma TMAO concentrations. No significant differences were observed following acute or short-term choline ingestion for any measurement of insulin sensitivity, glucose tolerance 24-hout glycemic variability, vascular function., and arterial stiffness.

Necrotic enteritis (NE) is a major enteric disease in commercial poultry and manifests itself in clinical and subclinical forms. Despite years of research, NE is still among the leading diseases with the greatest economic impact on poultry production. Subclinical forms lead to poor performance (reduced feed intake, weight gain and eventually higher feed conversion ratio) but usually occurs with low mortality rates. The use of antibiotic growth promoters (AGPs) is proving to be an effective tool in maintaining gut health and modifying gut microbiota, thus improving broiler performance and reducing NE. Removal of AGPs has led to an increase in NE occurrence, particularly the subclinical forms. The lack of alternative strategies to control NE is mainly due to limited insight into the relationship between NE pathogenesis, the host microbiome and its immune responses. Therefore, key to overcoming NE is to define the cellular and molecular mechanisms that are involved in the progression of the disease, especially with regard to mucosal immune responses and gut microbiome. Also, assessing the impact of these changes on gut cell metabolism and function is of great importance. This information would be a valuable guide to prevent the onset or alleviate the negative impact of NE on bird's health and performance. In a series of experiments conducted for this project, the effect of single or multi-strain probiotics as well as multi-component additives were tested during NE challenge in order to define the cellular and molecular mechanisms that are involved in the progression of the disease. Results of these experiments revealed that challenging broilers with a 'naturally occurring' NE led to differential expression of tight junction (TJ) proteins in the jejunum compared to non-challenged birds. Supplementation of certain additives reduced NE lesion scores, improved performance and increased mRNA abundance of claudin-3, a key epithelial TJ protein. Multi-strain probiotics and multi-component additives (including a symbiotic and a product containing probiotics, prebiotics and essential oils) were more effective than single-strain probiotics or prebiotics. The aforementioned additives were also more effective in modulating immune responses to NE, especially by decreasing the mRNA abundance of IFN-γ and IL-10 in the jejunum. Furthermore, supplementation of these additives led to an increase in the expression of nutrient transporters (SGLT-1) and regulators of energy metabolism (PGC-1α, mTOR and AMPK); thus, improving nutrients absorption and metabolism. Microbial profiling using 16S rRNA sequencing showed that supplementation of each specific additive led to a signature-like microbiome in the ileal scrapings of broilers. However, supplementation of multi-component additives (including a symbiotic and a product containing probiotics, prebiotics and essential oils) modified the ileal microbiome in association with lower NE lesion scores, better performance and modulated immune responses. These additives reduced the relative abundance of bacteria such as ASF356, Bacteroides, Clostridium sensu stricto 1, Faecalibaculum, Lachnospiraceae UCG-001, Muribaculum, Oscillibacter, Parabacteroides, Rikenellaceae RC9 gut group, Ruminococcaceae UCG-014, and Ruminiclostridium 9 and increased the relative abundance of Lactobacillus compared to NE challenged birds. Collectively, these data indicate that during a subclinical naturally occurring NE, the use of multi-strain probiotics or multi-component additives, compared to single-strain probiotics or prebiotics, would be a more promising strategy in alleviating the effect of this enteric disease. / Doctor of Philosophy / Necrotic enteritis, an enteric disease, is one of the major diseases that negatively impacts the poultry industry and producers' profitability. The growing ban on the use of antibiotics that were used to prevent this disease has increased the number of necrotic enteritis outbreaks worldwide. Having a better understanding of the cellular and molecular mechanisms that are involved in the onset of this disease is of crucial importance and could lead to finding more effective ways to control this disease without drugs. The gut is the site of digestion and absorption of nutrients so any damage would lead to poor bird performance. In a series of experiments conducted for this project, several combinations of beneficial bacteria and nutrient sources that help bacterial growth in the gut (prebiotics) improved gut health leading to better performance during the grow-out period (days 0-42) when birds reach market age. These supplements protected the gut lining and reduced damages due to necrotic enteritis with less severe lesions. Barrier function of the gut was also improved by supplementing the diet with combination of beneficial bacteria and nutrients that help their growth in the gut. There are special types of proteins (called tight junctions) that seal up the space between intestinal cells (enterocytes) and prevent pathogens in the gut lumen from entering the body, thus preventing inflammation and disease. This helps the body to use the absorbed nutrients for growth rather than spending energy to fight pathogens, which collectively results in better growth performance. Concurrent supplementation of beneficial bacteria plus nutrients that help their growth balanced the immune responses in the gut by increasing the copy number of cytokines. Cytokines are proteins that orchestrate immune responses that the host mounts against pathogens. Certain cytokines regulate such responses by preventing the immune system from overreacting and mounting unnecessary reactions, thus preserving energy and nutrients for growth while reducing inflammation. Nutrient uptake from the gut lumen is facilitated by nutrient transporter proteins that reside on intestinal cells (enterocytes). Birds concurrently supplemented with beneficial bacteria and nutrients that help their growth in the gut increased the abundance of these proteins, resulting in improved nutrient uptake and performance compared to the control birds. Co-supplementation of beneficial bacteria and nutrient sources that help their growth modified the type and number of bacteria that are present in the gut lumen. The modified bacterial community were able to produce metabolites such as butyrate and propionate, which are beneficial for the health and growth of the intestinal cells, thus improving the bird's health and its performance. Overall, compared to beneficial bacteria alone, co-supplementation of beneficial bacteria with the nutrients that help their growth in the gut significantly reduced intestinal lesions and improved performance of broiler chickens during the production period. Moreover, dietary addition of these supplements improved gut barrier function by regulating the gene expression of tight junction proteins and gut mucosal immune responses as well as modifying the bacterial community of the gut. Therefore, such combination supplements hold promise in controlling necrotic enteritis in poultry and sustain good overall performance that translates into higher profitability to producers.

Systemic lupus erythematosus (SLE) is a multi-system autoimmune disease with no known cure. The crosstalk between the gut microbiota and the immune system plays an important role in the tolerance induction to self-antigens both in the intestinal mucosa and at the systemic level. The MRL/lpr mouse model exhibits lupus-like symptoms early in life due to multiple SLE susceptible loci of the MRL background, plus the Faslpr mutation that offers an accelerated model. Recently, we experienced a loss of disease phenotype in our in-house colony compared to the previous published phenotype of MRL/lpr mice. We thus compared mice newly obtained from The Jackson Laboratory (JAX) with our in-house MRL/lpr mice and found that the phenotypic drift, most significantly the attenuation of glomerulonephritis, was present in both colonies. In addition, while JAX mice and mice in our colony are genetically identical, there were minor differences in disease that might be due to differences in splenic microRNAs and the gut microbiota. Once confirming that our MRL/lpr mouse model was as good as that from JAX, we continued our investigation of the role of Lactobacilli in the pathogenesis of lupus-like disease in MRL/lpr mice. We previously published that the mixture of Lactobacillus reuteri (L. reuteri), L. oris, L. johnsonii, L. gasseri, and L. rhamnosus significantly attenuated disease in MRL/lpr mice by restoring the imbalance between regulatory T cells and T helper-17 cells. To further understand the role of Lactobacillus spp., we treated MRL/lpr mice with the combined culture supernatant of the 5 strains containing secreted metabolites, given that the metabolites may induce an immunosuppressive response. The results showed significant attenuation of the inflammation of the spleen and renal lymph nodes similar to the effect of the bacteria themselves. There was also a trending decrease of double-stranded DNA autoantibodies with the combined supernatant. We thus tested the strains individually but none was able to recapitulate the effect of the bacterial mixture. This suggests cell-to-cell contact among different strains of lactobacilli may be required in ameliorating the disease. With these results, we now have a better understanding of the role of probiotic Lactobacillus spp. against SLE. Future investigations will focus on the potential therapeutic effect of Lactobacillus spp. as a combination. Additionally, our group generated a Cx3cr1-deficient MRL/lpr mouse which exhibits a distinct phenotype of exacerbated glomerulonephritis with concurrent change of the gut microbiota composition compared to Cx3cr1+/+ MRL/lpr littermates. Interestingly, upon correction of the gut microbiota with Lactobacillus administration, the phenotype of exacerbated glomerulonephritis was reversed, suggesting that CX3CR1 controls glomerulonephritis in MRL/lpr mice through a gut microbiota-dependent mechanism. In addition, a collaborative project revealed that Cx3cr1 deficiency-mediated pathogenic mechanisms also contributed to SLE-associated cardiovascular disease in MRL/lpr mice. The results of these studies will lead to the identification of new therapeutic targets for the treatment of two severe manifestations, glomerulonephritis and cardiovascular disease, that together account for most of the morbidity and mortality in SLE. / Doctor of Philosophy / Systemic lupus erythematosus (SLE) is an autoimmune disease with no known cure. Commensal microbiota, mostly bacteria living in our gut, and the immune system have a strong relationship in maintaining a healthy state of the gut as well as the whole body. Alterations in the gut microbiota, known as dysbiosis, can facilitate SLE in human and animal models. Current treatments for SLE are primarily focused on using immunosuppressants, but the side effects are still a concern. The use of long-term nonselective immunosuppressant conducts a higher incidence of severe infections in SLE patients. It is thus necessary to develop new approaches and treatments against SLE. My dissertation research is focused on understanding how commensal bacteria influence in the pathogenesis of SLE. My studies have shown that environmental factors can manipulate the gut microbiota leading to different disease outcomes. In addition, following upon previously published studies from our laboratory, I have delineated the mechanism how a mixture of probiotic Lactobacilli can exert a beneficial effect against lupus. Finally, I have revealed a new, CX3CR1-mediated mechanism through which the gut microbiota controls kidney disease in the MRL/lpr lupus-prone mouse model.

Neurodevelopmental disorders, such as autism spectrum disorders, schizophrenia, and attention deficit hyperactivity disorder, are a heterogeneous set of developmental disorders affecting the central nervous system. Studies into their etiology remain challenging, as neurodevelopmental disorders frequently present with a wide range of biological, behavioral, and comorbid symptomologies. Increasing epidemiological reports of antibiotic use during pregnancy as a significant correlate of subsequent mental disorder diagnosis in children suggest a mechanism of influence via the maternal gut-fetal brain axis. Importantly, antibiotics cause dysbiosis of the gut microbiome and disrupt the delicate composition of the microbial inoculum transferred from mother to child, which is critical for development of the immune system and holds implications for long-term health outcomes. The research objective of this dissertation is to reveal a causal mechanism of maternal microbial influence on neurodevelopment by examining the brain's resident immune cells, microglia, and corresponding behavioral outcomes in a mouse model of antibiotics-driven maternal microbiome dysbiosis (MMD). We identify early gross motor deficits and social behavior impairments in offspring born to MMD dams, which paralleled hyperactivated microglia in brain regions specific to cognition and social reward. The MMD microglia also exhibited altered transcriptomic signatures reflective of premature cellular senescence that support evidence of impaired synaptic modeling found in MMD brains. We report that these deficits are rescued in the absence of Cx3cr1, a chemokine receptor expressed ubiquitously on microglia, to highlight a pathway in which maternal microbiota may signal to neonatal microglia to undergo appropriate neurodevelopmental actions. Finally, we characterize Lactobacillus murinus HU-1, a novel strain of an important gut bacterium found in native rodent microbiota, and demonstrate its use as a probiotic to restore microglial and behavioral dysfunction in MMD offspring. / Ph. D. / Population studies on neurodevelopmental disorders, such as autism spectrum disorders, schizophrenia, and attention deficit hyperactivity disorder, highlight antibiotic use during pregnancy as a major correlate of subsequent diagnoses in children. These findings support a growing body of evidence from animal and human studies that the microbial ecosystems (“microbiome”) found in and on our bodies play significant roles in mental health, including mood, cognition, and brain function. Importantly, antibiotics during pregnancy create an imbalance of the gut microbiome (“dysbiosis”) and disrupt the microbial inoculum transferred from mother to child, which is critical for maturation of the infant immune system and holds implications for long-term health outcomes. Thus, the research objective of this dissertation is to identify a mechanism of influence from the mother’s gut to the neonate’s brain by examining the brain’s resident immune cells (“microglia”) in a mouse model of antibiotics-driven maternal microbiome dysbiosis (MMD). We uncover autism-like behavioral deficits and dysfunctional microglia in MMD offspring, and characterize signaling cues specific to microglia by which improper neurodevelopment may be taking place. We also reveal that the detrimental effects of MMD are reversed in mice born to mothers pretreated with a probiotic candidate, Lactobacillus murinus HU-1, to suggest maternally-derived Lactobacillus may help to mediate proper neurodevelopment.

During acute and chronic infectious diseases hosts develop complex immune responses to cope with bacterial persistence. Depending on a variety of host and microbe factors, outcomes range from peaceful co-existence to detrimental disease. Mechanisms underlying immunity to bacterial stimuli span several spatiotemporal magnitudes and the summation of these hierarchical interactions plays a decisive role in pathogenic versus tolerogenic fate for the host. This dissertation integrates diverse data from immunoinformatics analyses, experimental validation and mathematical modeling to investigate a series of hypotheses driven by computational modeling to study mucosal immunity. Two contrasting microbes, enteroaggregative Escherichia coli and Helicobacter pylori, are used to perturb gut immunity in order to discover host-centric targets for modulating the host immune system. These findings have the potential to be broadly applicable to other infectious and immune-mediated diseases and could assist in the development of antibiotic-free and host-targeted treatments that modulate tolerance to prevent disease. / Ph. D.

Abdominal pumping is a well-known behavior in insects, thought to function largely in respiratory processes. In particular, the abdominal pump is considered to produce ventilation of air in the tracheal system, but the mechanistic link between abdominal movement and flow of air is not well understood. In this thesis, we explore the relationship between the abdominal pump and ventilation of air using pupal and adult forms of the darkling beetle Zophobas morio. First, we investigated the mechanical linkage between abdominal pumping and active ventilation in pupae by simultaneously measuring abdominal movement, hemolymph pressure, CO2 emission, and deformation of tracheal tubes. This study revealed that pupae with low metabolic rates do indeed exhibit tracheal compression, which is coincident with abdominal pumping and pressure pulsation. However, more than 63% of the abdominal pumps and associated pressure pulsations did not lead to tracheal compression. This result can be explained by the status of the spiracles; when the system is closed, little compression in the tracheae can occur. Therefore, we conclude that abdominal pumping in insects does not necessarily lead to ventilation and may serve other functions, such as producing hemolymph flow for circulation. Insects have an open circulatory system, with flow driven largely by the small dorsal vessel. Within the open coelom, hemolymph pressure should be mostly uniform, suggesting that abdominal pumping does not produce hemolymph flows within the main body cavity. We tested this assumption by simultaneously measuring hemolymph pressure in different locations in the coelom. Within the abdomen and thorax, hemolymph pressure is nearly uniform, as expected. However, hemolymph pressures are significantly different between the abdomen and thorax. This suggests that the coelom is compartmentalized, and that abdominal pumping can induce hemolymph flow within the coelom. Throughout these experiments, we faced a common difficulty inherent to flow-through respirometry systems: they are incapable of providing direct, instantaneous measurement of gas concentration. Previous methods are not able to reconstitute the rapid dynamical changes in respiratory signals that are required for precise temporal analysis. Therefore, we developed two new methods to accurately recover instantaneous gas exchange signals, based on new models of the impulse response of the system. These methods enabled us to accurately recover fast- changing respiratory signals with a higher fidelity than previously possible. Using these methods, we demonstrate the synchronization of respiratory data with other physiologically relevant signals, such as pressure and abdominal movement. This research was supported by NSF grant #0938047 and the Virginia Tech Institute for Critical Technology and Applied Science (ICTAS). / Ph. D.

The gut-brain axis describes a paradigm wherein the trillions of microorganisms inhabiting the gastrointestinal tract engage in bidirectional communication with the host central nervous system. Adaptive immunity represents an important intermediate in this dynamic crosstalk; previous work in our lab has demonstrated that T-lymphocytes, a main class of immune effector cells, contribute to neurodevelopmental processes and behavioral outcomes across the lifespan. Parallels between the phenotype of T-cell deficient and germ free mice led us to hypothesize that bidirectional T-cell-microbe communication is critical for normal neurodevelopment, and that T-cell deficiency impacts the neural circuitry underpinning behavior via disruption of the gut-brain axis. The main objective of this thesis was to elucidate the mechanisms by which T-cells mediate developmental gut-brain signalling. The first installation examined the gut microbiome, gut metabolome, and neurochemical profile in wild-type and T-cell deficient mice from adolescence to adulthood, demonstrating that absence of T-cells impacts the developmental trajectory of functional microbiome output and levels of neuroactive molecules in the brain. Experiment two investigated the impact of T-cell deficiency on gut-brain communication through the lens of host gene expression in the parenchyma and the intestine. T-cell deficient mice showed significant changes in genes related to intestinal immunity and barrier function, in addition to decreases in microglia-related genes in the prefrontal cortex during early life. The final experiment transitioned into a wild-type model to measure the co-evolution of T-cell subsets in mucosal and central immune compartments with composition and diversity of the microbiota. We demonstrated a parallel diversification of the gut microbiome and the functional T-cell repertoire, whereby emergence and proliferation of specific T-cell subsets is linked to compositional shifts in dominant microbial communities across development. Together, our results demonstrate the importance of T-cells for normal development of the holo-organism, with implications for the developmental wiring of functional brain circuitry. / Thesis / Doctor of Philosophy (PhD) / Modern medicine has increasingly placed emphasis on the mind-body connection. This has been exemplified by a series of recent discoveries surrounding the importance of the gut microbiome in maintaining our physical and mental health. One of the key channels through which the microbiome communicates with the host is through the immune system, an equally complex network of cells and proteins that protect the body against invading pathogens. Indeed, these systems evolve alongside each other and engage in constant crosstalk throughout the lifespan, with downstream impacts on the developing brain. This thesis sought to further explore the role of T-cells, a key component of the adaptive immune system, in coordinating gut-microbiome-brain interactions across development. The first experiment examined the microbiome as well as small molecules in the gut and brain of normal mice and mice lacking T-cells. The second experiment built on this work to examine how T-cells influence the expression of different genes in the gut and brain. Finally, the third experiment mapped different populations of T-cells and microbiome composition from the first week of life to adulthood, to better understand how they interact at different stages of development. This work will offer insight into how T-cells talk to the microbiome and how they transmit signals from the gut to the brain, with implications for understanding neurodevelopmental disorders and how they arise.

No / Inflammatory bowel diseases are associated with increased risk of developing colitis-associated colorectal cancer (CAC). Epidemiological data show that the consumption of ω-3 polyunsaturated fatty acids (ω-3 PUFAs) decreases the risk of sporadic colorectal cancer (CRC). Importantly, recent data have shown that eicosapentaenoic acid-free fatty acid (EPA-FFA) reduces polyp formation and growth in models of familial adenomatous polyposis. However, the effects of dietary EPA-FFA are unknown in CAC. We tested the effectiveness of substituting EPA-FFA, for other dietary fats, in preventing inflammation and cancer in the AOM-DSS model of CAC. The AOM-DSS protocols were designed to evaluate the effect of EPA-FFA on both initiation and promotion of carcinogenesis. We found that EPA-FFA diet strongly decreased tumor multiplicity, incidence and maximum tumor size in the promotion and initiation arms. Moreover EPA–FFA, in particular in the initiation arm, led to reduced cell proliferation and nuclear β-catenin expression, whilst it increased apoptosis. In both arms, EPA-FFA treatment led to increased membrane switch from ω-6 to ω-3 PUFAs and a concomitant reduction in PGE2 production. We observed no significant changes in intestinal inflammation between EPA-FFA treated arms and AOM-DSS controls. Importantly, we found that EPA-FFA treatment restored the loss of Notch signaling found in the AOM-DSS control and resulted in the enrichment of Lactobacillus species in the gut microbiota. Taken together, our data suggest that EPA-FFA is an excellent candidate for CRC chemoprevention in CAC.