The human gut microbiome is the collection of all organisms and their genetic content that inhabit the gastrointestinal tract. An overwhelming number of studies have associated the gut microbiota with health and disease, but with little consensus on which specific bacterial groups are important for causing or maintaining either state. A majority of microbiome studies only identify associations between the gut microbiome and health status, and determining causation requires the isolation and growth of bacterial isolates for further experiments. The goal of this thesis is to demonstrate that the combination of culture-based and culture-independent methods describes greater complexity and diversity in the human gut microbiota than observed by either approach alone. In the first study, a method of culture-enriched molecular profiling could capture the majority of bacterial groups found in fecal samples. Additionally, when compared to culture-independent 16S rRNA gene sequencing, culture detected more bacterial taxa. This method was applied to the targeted culture of the commensal Lachnospiraceae family. The second study explored the diversity in the isolated Lachnospiraceae strains, and compared the genetic diversity of the strains to reference genomes, revealing functional and genetic heterogeneity within the bacterial family. The third study characterized the intra-species phenotypic and genetic diversity in Escherichia coli. E. coli diversity was extensive between individuals, but also within-individuals, in both the phenotypes and genetic profiles. Lastly, a method of culture-enriched metagenomics was applied to a murine IBS microbiota transfer model to identify bacterial members of the microbiota and their functional pathways that may be responsible for the development of gastrointestinal and behavioural IBS phenotypes, although no bacterial groups could be conclusively associated with symptoms. Together, the work described demonstrates that culture and culture-independent methods are complementary, and provides more resolution into the structure and diversity of the human gut microbiome than either approach in isolation. / Thesis / Doctor of Philosophy (PhD) / Bacteria that inhabit the human intestine are important for health, and are involved in several diseases; therefore, it is critical to determine the roles of specific bacteria. I describe a method that results in the growth and recovery of most bacteria in stool, which allows them to be studied in detail. The differences, both in behaviour and in DNA sequences, found within two different bacterial groups were characterized, and extensive variability was observed between closely related bacteria. I studied which bacteria and their functions might be important in Irritable Bowel Syndrome (IBS) by using our method for growing stool bacteria combined with sequencing of all DNA in the stool, but could not find strong support for specific bacteria causing IBS symptoms. This work shows how the ability to grow and isolate bacteria, combined with studying their DNA, allows for better understanding of their functions in the human intestine.

京都大学 / 新制・課程博士 / 博士(理学) / 甲第23749号 / 理博第4839号 / 新制||理||1692(附属図書館) / 京都大学大学院理学研究科生物科学専攻 / (主査)准教授 半谷 吾郎, 教授 湯本 貴和, 教授 古市 剛史 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DFAM

The collection of microbes that inhabits the human gastrointestinal tract is known as intestinal microbiota, and an enormous body of work has shown that their activities contribute to health and disease. Ulcerative colitis (UC), which is a type of inflammatory bowel disease, is considered to arise due to a disruption in the balance between the immune system and microbiota. However, there is little consensus on the mechanism of action and microbes involved in the disease manifestation. In this work, I applied culture-enriched metagenomics (CEMG) to characterize the dynamics of gut microbiota in healthy individuals and UC patients. I showed that CEMG provides a higher resolution to study these microbial communities, and we used this approach to understand microbial colonization after fecal microbiota transplantation (FMT) therapy in UC patient. I showed that sequencing approaches alone did not reveal consistent engraftment across FMT responders. Using CEMG and a collection of bacterial whole-genome sequences, I showed patient-specific microbial strain transfer and a signature of commonly engrafted genes only in patients who responded to FMT. In this work, I also investigated the dynamics of a highly abundant bacteriophage, crAssphage, in an FMT donor and implemented a new method to detect bacteriophage engraftment post-FMT using SNP analysis. Finally, it has been suggested that antibiotic treatment before FMT may increase the efficacy of FMT. However, in this work, I show that while antibiotics alter the microbiome, there was no difference in the composition of the microbiome of antibiotic vs placebo group post-FMT. This is consistent with the randomized controlled trial results that shows pretreatment with antibiotics does not improve FMT outcome. Together, this work demonstrate the importance of in-depth microbiome analysis applied to culture-dependent and -independent sequencing to characterize microbial changes post-FMT. / Dissertation / Doctor of Philosophy (PhD) / Many bacteria reside in the human gut, and they are essential in our health and in disease. It is evident that these bacteria are associated with inflammatory bowel disease, but we do not yet know how and what bacteria are involved in this disease. In this work, I describe a method to study these bacteria from stool that relies on growing them and investigating their DNA. I showed that our approach helped us recover a greater diversity of these bacteria and their genetic content in healthy individuals and patients with inflammatory bowel disease compared to methods that use only DNA based approaches. Using this method, we could better understand why some patients responded to a treatment consisting of transferring stool content from healthy donor to patient. I also investigated a group of viruses that infect bacteria and implemented a new computational method based on DNA sequencing to test whether these viruses transfer to the patient after receiving the fecal therapy. We also found that antibiotic treatment before fecal therapy in patients with inflammatory bowel disease does not improve the patient’s recovery.

Background: The introduction of solid foods is an important dietary event during infancy and is associated with a time of dramatic shifts in gut microbial composition. The influence of solid food introduction on gut bacterial dynamics remains understudied. Methods: 15 healthy, full-term, vaginally born, and breast-fed infants of the Baby, Food and Mi sub-study of the Baby & Mi Study were investigated. Caregivers were asked to collect daily stool samples and food diaries for 17 days, commencing three days prior to the introduction of solids. Additional stool samples were available up to one year as part of the Baby and Mi study. The exposure of interest, nutritional patterns, was analyzed using food composition output from ESHA’s Food Processor. The number of food items and food groups introduced were used to calculate dietary diversity scores. The outcome of interest, gut bacterial dynamics, was analyzed using RStudio. Results: The mean (SD) age at the introduction of solid foods is 5.5 (0.66) months (n = 15). Over the study period, the proportion of estimated energy intake from solid foods was low (7.5%; SD 6.74%) (n = 14). Alpha diversity increased over time and was highest at 1 year. The gut microbial community influenced by dominant bacterial taxa changed with increasing age. With introduction of solids, individual community composition changed, though to a varying extent. Shannon alpha diversity was directly associated with calories from carbohydrates, particularly daily fiber intake. The infant’s dietary diversity score was directly associated with alpha diversity and was also positively associated with the degree of change occurring in this time period. Conclusion: Fiber intake and the dietary diversity scores had the closest relationships to the gut microbiome’s alpha diversity and community structure in infants at the time of solid food introduction. / Thesis / Master of Science (MSc) / The introduction of solid foods is an important life-event during infancy. This is also when the gut microbiome is developing to its mature state. Since nutrition is an important factor influencing the microbiome, investigating the dietary choices at the introduction to solid foods is the aim of the following study. Here, daily stool samples and food diary entries were collected for 15 healthy, breast-fed infants. It is important to measure the diversity of the bacteria in the gut of an individual (alpha) and between people (beta), as well as bacteria present. Carbohydrates drive the change in alpha diversity, especially fiber. Feeding infants a diet with many different foods shows increased alpha diversity and change in the microbiome immediately after introduction. Interestingly, the infant gut microbiome reacts to fiber in a manner comparable to the adult gut microbiome, i.e. increased bacterial diversity, which is associated with better health outcomes in adults.

No description available.

Epilepsy is one of the most common neurological disorders worldwide. This neurological disorder is characterized by spontaneous recurrent seizures and impacts about 65 million people globally. As there is no cure for epilepsy, the treatment goal for patients is seizure management, and ultimately seizure freedom. The first line of defense in seizure management is anti-epileptic drugs, which aim to restore the excitatory and inhibitory balance in the brain. Unfortunately, about 30% of people with epilepsy are drug resistant, a number which has remained unchanged despite the increasing amount of anti-epileptic drugs. This leads patients to seek alternative treatments, which include surgery, vagus nerve stimulation, or diet alterations such as the ketogenic diet. Due to the invasiveness of surgeries, difficulty to maintain specialty diets, or lack of effectiveness of these treatments in some patients, additional therapies are needed. The gut-brain axis is a bidirectional communication network connecting the central and enteric nervous systems. Part of this network includes communication via the gut microbiota. The gut microbiota consists of all the microorganisms living in the gut, including bacteria, viruses, and fungi. It is involved in aiding nutrient absorption, promoting the maturation of immune cells and functions, and protection against pathogens. There is growing interest in the role of the gut microbiome in human health and disease. Studies have shown that patients with epilepsy have altered gut microbiomes compared to healthy controls, and that gut microbiome alteration can impact seizure frequencies. These exciting findings have ignited research on the potential therapeutic role of the gut microbiome in epilepsy. Although studies have explored the impact of alterations in the gut microbiome on seizure activity, they have not studied how anti-epileptic drugs may contribute to this relationship. Thus, this dissertation explores the role of the commonly prescribed anti-epileptic drug topiramate on the gut microbiome. Fecal samples of mice treated with topiramate were analyzed using 16S ribosomal RNA gene sequencing. Analysis revealed that topiramate ingestion increased the probiotic bacteria Lactobacillus johnsonii in the gut microbiome. In addition, cotreatment of topiramate and Lactobacillus johnsonii reduced seizure susceptibility in a pentylenetetrazol-kindling seizure model. Moreover, cotreatment increased the butyrate producing family Lachnospiraceae and subsequently increased the neuroprotective SCFA, butyrate in the gut microbiome. Importantly, cotreatment also resulted in an increased GABA/glutamate ratio in the cortex of mice that underwent pentylenetetrazol-kindling. These results are the first to demonstrate that the anti-seizure effect of topiramate may be facilitated by the modulation of the gut microbiota via increasing butyrate and altering the GABA/glutamate ratio in the cortex. Lastly, this work highlights the potential for probiotics as an adjuvant therapy in seizure management. / Doctor of Philosophy / Epilepsy is one of the most common neurological disorders worldwide. This neurological disorder is characterized by spontaneous recurrent seizures and impacts about 65 million people globally. As there is no cure for epilepsy, the treatment goal for patients is seizure management, and ultimately seizure freedom. The first line of defense in seizure management is anti-epileptic drugs, which aim to restore the excitatory and inhibitory balance in the brain. Unfortunately, about 30% of people with epilepsy are drug resistant, a number which has remained unchanged despite the increasing amount of anti-epileptic drugs. Due to this unmet need, epilepsy patients utilize alternative treatments, which include surgery, vagus nerve stimulation, or diet modifications such as the ketogenic diet. Due to the invasiveness of surgeries, difficulty to maintain specialty diets, or lack of effectiveness of these treatments in some patients, additional therapies are needed. The gut microbiota consists of all the microorganisms living in the gut, including bacteria, viruses, and fungi, which can be both harmful and helpful. In healthy individuals, the gut microbiota coexists in a balance that prevents diseases and helps the host, however, disruptions in this balance can lead to susceptibility to several diseases. As a result, researchers are increasingly interested in the role of the gut microbiota in human health and disease. In epilepsy, the gut microbiome is altered compared to healthy individuals, and gut microbiome alterations can impact seizure activity. This has led researchers to investigate the potential therapeutic role of the gut microbiome in epilepsy. Although studies have explored the impact of alterations in the gut microbiome on seizure activity, they have not studied how anti-epileptic drugs may contribute to this relationship. Thus, this dissertation explores the role of the commonly prescribed anti-epileptic drug topiramate on the gut microbiome. The results demonstrate that topiramate increases probiotic bacteria in the gut microbiome of mice. Moreover, this probiotic bacterium facilitates topiramate in reducing the susceptibility to seizures in a mouse model by resulting in a beneficial gut microbiome and restoring excitatory and inhibitory balance to the brain. These results are the first to demonstrate that the anti-seizure effect of topiramate may be facilitated by the gut microbiome. Lastly, this work highlights the potential for probiotics as an adjuvant therapy in seizure management.

Development of type 2 diabetes (T2D) is preceded by prediabetes, which is a metabolically "atypical" state associated with chronic low-grade inflammation, overweight and obesity, lack of exercise, and detrimental changes to the gut microbiome. Dietary intake and exercise are modifiable lifestyle factors for reducing T2D risk; however, several questions remain unanswered related to the efficacy and role of prebiotics and exercise, and their respective influences on gut microbiome composition, intestinal permeability, insulin sensitivity and metabolic flexibility. Sedentary to recreationally active overweight and obese adults 40-75 years old at-risk for T2D were recruited (n=22) and randomized to either supplementation with inulin, a prebiotic dietary fiber, (10g/d) or maltodextrin while consuming a controlled diet for six weeks. At baseline and week 6, participants completed a stool collection, a 4-sugar probe test, an intravenous glucose tolerance test (IVGTT), and high-fat meal challenge with skeletal muscle biopsies to evaluate changes in the gut microbiome composition, intestinal permeability, insulin sensitivity and metabolic flexibility, respectively. There were no baseline group differences (all p>0.05). Following the intervention, Bifidobacteria operational taxonomic units increased in the intervention group ([placebo: Δ 9.5 ± 27.2 vs inulin: 96.3 ± 35.5][p=0.03]). There were no other group differences over time in any other outcome variables with the exception of changes in metabolic flexibility. Secondarily, a systematic review of literature was conducted to determine the influence of exercise engagement on gut microbiome composition. Overall, exercise interventions appeared to diversify taxa within the Firmicutes phylum, and specifically in several taxa associated with butyrate production and gut barrier function. Due to unclear risk of bias in all studies and low quality of evidence, additional research is needed using well- designed trials. In summary, the respective influences of prebiotics and exercise on human gut microbiome composition and their subsequent effects on metabolic function and disease risk are not well understood. / PHD / Type 2 diabetes (T2D) is common in the United States. Prediabetes occurs before T2D, and goes frequently undiagnosed, yet lifestyle changes (e.g. dietary changes and exercise engagement) may prevent or delay the development of T2D. Gut bacteria is a newer area of research that may have an important role in disease prevention. Several dietary supplements, such as pre- and probiotics, and their influence on gut bacteria have been studied, but the effectiveness of the prebiotic inulin for delaying or preventing T2D is unknown. Additionally the effects of exercise on gut bacteria and its role for T2D prevention is still not well understood. To address these questions, sedentary to recreationally active overweight and obese adults 40-75 years old at increased risk for T2D were recruited (n=22) and randomly assigned to either supplementation with inulin (10g/d) or maltodextrin and all consumed a six week standardized diet. At baseline and week 6, all participants completed a stool collection, a 4-sugar probe test, a high-fat challenge (HFC), and intravenous glucose tolerance test (IVGTT), and changes were evaluated in the gut microbiome, intestinal permeability, and indicators of metabolism, respectively. At week 6 Bifidobacteria, which is associated with improved gut health, increased in the inulin group ([placebo: Δ 9.5 ± 27.2 vs inulin: 96.3 ± 35.5][p=0.03]). There were no other differences over time for any other measurements with the exception muscle metabolism meal response. A systematic review of currently available research was also conducted to determine the influence of exercise engagement on gut microbiome composition. Overall, exercise engagement appeared to increase bacteria that is associated with better gut health. These findings are preliminary, and most evidence is from animal studies. Therefore, more research is needed to confirm these changes in humans. In summary, the roles of prebiotics and exercise on gut bacteria and human health are not well understood.

Despite the association of the human gut microbiome and various diseases, a systematic definition of what constitutes a healthy human gut microbiome has not been established. This is crucial for microbiome research as it provides a basis for evaluating whether a given microbiome sample may deviate from the homeostasis state and is thus prone to the development of chronic diseases. This work aims to propose one such definition by using species/strain-resolved Genome-scale (GEM) models of metabolism. More specifically, we have constructed sample-specific GEMs from 30 healthy subjects using the taxonomic profiling of fecal metagenomic samples. We then computationally simulated these GEMs under a relevant diet (a supplemented typical Western diet) to determine which microbes in each sample contribute to the production of 17 key metabolites curated from literature and reported to be produced and secreted by the gut microbiota of healthy subjects. Beyond this pilot study, we plan to expand our analyses by creating samples-specific GEMs for a large-scale database of all publicly available metagenomic data from healthy subjects (~2,500 samples so far). We will additionally identify a core set of microbial species/strains that are necessary to perform all essential functions of a healthy microbiome. Taken together, this project offers a new paradigm to establish a healthy baseline microbiome definition by identifying generalized and personalized microbial blueprints that could serve as viable markers of health.

Most animals contain chronic microbial infections that inflict no harm on their hosts. Recently, the gut microflora of humans and other animals have been characterized. However, little is known about the forces that shape the diversity of these bacterial communities. In this work, comparative genomics was used to investigate the evolutionary dynamics of host-adapted bacterial communities, using Wolbachia infecting arthropods and Lactobacteria infecting bees as the main model systems. Wolbachia are maternally inherited bacteria that cause reproductive disorders in arthropods, such as feminization, male killing and parthenogenesis. These bacteria are difficult to study because they cannot be cultivated outside their hosts. We have developed a novel protocol employing multiple displacement amplification to isolate and sequence their genomes. Taxonomically, Wolbachia is classified into different supergroups. We have sequenced the genomes of Wolbachia strain wHa and wNo that belong to supergroup A and B, respectively, and are present as a double-infection in the fruit-fly Drosophila simulans. Together with previously published genomes, a supergroup comparison of strains belonging to supergroups A and B indicated rampant homologous recombination between strains that belong to the same supergroup but were isolated from different hosts. In contrast, we observed little recombination between strains of different supergroups that infect the same host. Likewise, phylogenetically distinct members of Lactic acid bacteria co-exist in the gut of the honeybee, Apis mellifera, without transfer of genes between phylotypes. Nor did we find any evidence of co-diversification between symbionts and hosts, as inferred from a study of 13 genomes of Lactobacillus kunkeei isolated from diverse bee species and different geographic origins. Although Lactobacillus kunkeii is the most frequently isolated strain from the honey stomach, we hypothesize that the primary niche is the beebread where the bacteria are likely to contribute to the fermentation process. In the human gut, the microbial community has been shown to interact with the immune system, and likewise the microbial communities associated with insects are thought to affect the health of their host. Therefore, a better understanding of the role and evolution of endosymbiotic communities is important for developing strategies to control the health of their hosts.

Studying the microbiome in natural populations could improve our understanding of the biological factors that influence microbiome variation. If host genetic variation is important in microbiota assembly, then understanding genetic divergence among natural populations could be informative. Despite advances in sequencing technology, we have not yet taken full advantage of this technology in natural populations. Here we integrate genome-wide population genomic and microbiome analyses in wild threespine stickleback (Gasterosteus aculeatus) fish distributed throughout western Oregon, USA. We found that gut microbiome varied in diversity and composition more among than within wild host populations. Furthermore, this among population variation was better explained by host population genetic divergence than by environment and geography. We also identified a subset of gut microbial taxa that were most strongly sorted both across environments and across genetically divergent populations. We believe this study contributes generalizable methods and findings in host systems. This thesis includes supplemental materials. / 2021-04-30