Doctor of Philosophy, The Ohio State University, 2024, Microbiology

Human-associated microbiomes refer to the diverse communities of microorganisms, including bacteria, archaea, microbial eukaryotes, and viruses that reside in various niches within a human host, such as the gut, skin, mouth, and respiratory tract. These microbiomes play crucial roles in the host's health, influencing processes like digestion, immune function, physiological development, and protection against pathogens. The composition of these microbial communities is influenced by factors such as genetics, diet, environment, and lifestyle. Disruptions in the balance of these microbiomes, known as dysbiosis, have been linked to a range of health issues, including infections, autoimmune diseases, and metabolic disorders. Understanding host-associated microbiomes is critical for developing targeted therapies and interventions to maintain or restore health. Most studies have focused on bacteria due to their dominance in the human host and available tools for investigation. Accumulating evidence suggests microbial eukaryotes in the microbiome play pivotal roles in host health, but our understandings of these interactions is limited to a few readily identifiable taxa because of technical limitations in microbial eukaryote exploration. In the chapter 2, we combined cell sorting, optimized eukaryotic cell lysis, and shotgun metagenomic sequencing to accelerate discovery and analysis of host-associated microbial eukaryotes. Using synthetic communities with a 1% microbial eukaryote representation, the eukaryote optimized cell lysis and DNA recovery method alone yielded a 38-fold increase in eukaryotic DNA. Automated sorting of eukaryotic cells from stool samples of healthy adults increased the number of microbial eukaryote reads in metagenomic pools by up to 28-fold compared to commercial kits. Read frequencies for identified fungi increased by 10,000x on average compared to the Human Microbiome Project (HMP) and allowed for the identification of novel taxa, de novo assemb (open full item for complete abstract)

Committee: Virginia Rich (Advisor); Karen Dannemiller (Committee Member); Vanessa Hale (Committee Member); Matt Anderson (Committee Member) Subjects: Microbiology

Master of Science, The Ohio State University, 2024, Microbiology

The human gut microbiome is the collection of the microbiota that reside in the human intestinal tract. Imbalances in the gut microbiome are associated with multiple diseases, so studying this is important for preventing and treating these conditions. These imbalances can have multiple causes, such as changes in core temperature. Previous work has indicated that the gut microbiome could play a role in mitigating negative effects of temperature on epithelial tissues, which could have profound effects on human health. Research into the human gut is normally performed by way of animal models, or by using a synthetic model involving the use of human cells on transwells. The goal of this study was to collect preliminary data to determine if gene expression in gut epithelial cells is influenced by the presence of a fecal sample at hypoxic, hyperthermic conditions. An experiment was performed on 36 gut-on-a-chips over the course of 48 hours at three different temperature levels: 30°C, 37°C, and 42°C. Next-Generation Sequencing (NGS) was performed to determine gene expression in the human epithelial cells when comparing the introduction of a fecal sample to the chip in low-oxygen conditions at 42°C. Most genes in the host cells were upregulated when exposed to the fecal sample, with the majority being involved in immune system responses, as well as cell growth and differentiation, host metabolism, and enzymatic activity, which is consistent with what would be expected when the gut bacteria are present. The gut-on-a-chip can be used to study temperature effects on the human epithelial cells, as well as test ways to counteract any negative effects that come with this shift. Future studies can elucidate the role that the gut microbiome may play in the response of the human body to changes in core temperature.

Committee: Karen Dannemiller (Committee Chair); Joshua Hagen (Committee Member); Justin North (Committee Member) Subjects: Biology

Master of Sciences, Case Western Reserve University, 2020, Biology

The “mycobiome" refers to the composition of both bacterial and fungal communities in the human gut microbiome and has been the focus of disease-state correlations investigated by researchers and pursued with commercial interests by biotech startups. A microbiome startup currently sells direct-to-consumer at-home microbiome sequencing kits and probiotics that aim to balance the gut biofilm that contributes to the dysbiosis-associated conditions. This company has expressed an interest in developing new business strategies to leverage their intellectual and technical strengths. This thesis is composed of two parts: The first section is a scientific and technical investigation of the micro- and myco-biome, sequencing techniques and strategies (16S, ITS, WGS, and Shotgun Metagenomic Sequencing) that play a role in the characterization and identification of fungal and bacterial colonies in the gut. These strategies aim to overcome challenges in characterizing and quantifying microbiota composition. Next, this sequencing data can form a robust database of patient data that plays a role in disease identification, and this thesis identifies some of the bioinformatic analyses to achieve this goal. The section concludes with how insights derived from patient data can be used in the optimization of cohort design in clinical trials for various diseases. The second section investigates three different business models that a microbiome startup has expressed interest in exploring for future development: (1) medical foods; (2) a therapeutic pipeline; and (3) a data-licensing and discovery platform for drug development. A detailed analysis of the market dynamics, competitive landscape, regulatory issues, and other nascent concerns was performed for each potential vertical as a foundation to develop future business strategy of a microbiome-related startup. The thesis is concluded on a holistic analysis of the scientific and technical assets and business opportunities and str (open full item for complete abstract)

Committee: Christopher Cullis (Committee Member); Emmitt Jolly (Committee Member); Neema Mayhugh (Committee Member) Subjects: Biology; Entrepreneurship

Master of Science, The Ohio State University, 2020, Food Science and Technology

Tomato consumption has been associated with a number of health benefits, many of which are reduced risks for chronic diseases prominent in the US. Considerable attention has been paid to the health benefits to lycopene, the red-colored carotenoid in tomatoes. However, whole tomato has been shown to provide more benefit than lycopene alone. The tomato fruit is a complex system containing thousands of small molecules, many of which have not been studied for their action in the human body. This research aims to investigate two ways in which tomato phytochemicals may influence human health. The first of these is elucidation of tomato steroidal glycoalkaloid absorption and metabolism after tomato consumption. Steroidal glycoalkaloids are an understudied class of secondary plant compounds that have recently been shown to be absorbed from the diet and deposited in tissue, and have bioactive properties in vitro and in vivo. There is little information regarding what happens to these compounds once they are consumed from tomatoes. In order to understand potential bioactivity of tomato steroidal glycoalkaloids, it is important to know how these compounds are metabolized and distributed. To investigate tomato steroidal glycoalkaloids in vivo, we conducted a parallel study in weaned piglets (aged three weeks), a physiologically relevant model for humans, fed a control diet (n=10) or a diet containing 10% tomato powder (n=10) for two weeks. Blood plasma samples were analyzed for tomato steroidal glycoalkaloids via UHPLC-QTOF-MS. Nine masses were putatively identified as steroidal alkaloids or their metabolites. It was found that most sugar moieties are cleaved, and the remaining aglycones undergo phase I and II metabolism, namely hydroxylation and sulfonation. This information provides a basis for further research on understanding the bioactivity of tomato steroidal glycoalkaloids in humans and their potential for health benefit. The second study was an exploration of effects of (open full item for complete abstract)

Committee: Jessica Cooperstone Ph.D. (Advisor); Rachel Kopec Ph.D. (Committee Member); Devin Peterson Ph.D. (Committee Member) Subjects: Food Science

Doctor of Philosophy, Miami University, 2024, Biology

CHAPTER 1: Nutrient excretion by fish supports a variable but significant proportion of lake primary productivity over 15 years. This chapter analyzes the long-term importance of excretion from gizzard shad for primary production in a midwestern reservoir using a supply:demand (S:D) approach and considers environmental and population variables that best predict the S:D ratio. Gizzard shad excretion supported a variable proportion of phytoplankton phosphorus demand, and it supported more demand during the summer than spring. Stream discharge, temperature, and gizzard shad population biomass best predicted S:D during the spring, while the biomass of the young-of-year best predicted S:D in the summer. CHAPTER 2: Combined influence of parasites and temperature on nutrient excretion rates and body stoichiometry of a freshwater fish. The rates of excretion from fish and the ratios of the nutrients excreted are expected to change as aquatic ecosystems warm. An experiment examined the excretion rates from bluegill under three climate scenarios and a range of natural parasite intensity. Carbon and phosphorus excretion increased with temperature but declined with parasite load, and the C and N concentrations in fish bodies declined with parasite load. CHAPTER 3: Ontogenetic changes in the gut microbiomes of Gizzard Shad and Bluegill and their relationship to nutrient excretion. The microbial communities within the guts of animals contribute to their health, but little is known about how these communities change with development and contribute to ecosystem processes. We conducted an exploratory study to learn about the gut microbiome of larval, young-of-year, and adult gizzard shad and bluegill as well as the relationship between microbiomes and excretion. We found that the two fish species had similar microbial communities as larvae, but the communities were different in the adults. The guts of adult gizzard shad contained taxa that are believed to fix nitrogen as well as s (open full item for complete abstract)

Committee: Michael Vanni (Advisor); Melany Fisk (Committee Member); Matthew Saxton (Committee Member); Roxane Maranger (Committee Member); Christopher Myers (Committee Member); María González (Committee Member) Subjects: Biogeochemistry; Biology; Environmental Science; Limnology; Science Education

Master of Science, The Ohio State University, 2024, Food Science and Technology

In the human gut, there are trillions of microorganisms shaping complex networks, so-called ‘human gut microbiota'. The members of human gut microbiota are linked to each other by metabolic interactions and the functions encoded in their genome, which is called ‘human gut microbiome'. The gut microbiome interacts with humans, the host, in various paths. For example, their metabolites modulate cellular physiology by being attached to surface receptors or involving in epigenetic modifications. In addition, cellular components of gut microorganisms work as a ligand of pattern recognition receptors, which is important in host immunological modulation. Moreover, those kinds of exposures in a proper time window of the human growth stage are crucial in early life development. Hence, gut microbiome affects human health from one's birth to death. There are multiple factors affecting the human gut microbiome, which can be classified into two, internal (e.g., genetic) and external (e.g., environmental, social, behavioral, cultural) factors. Based on the internal attributes of the host, gut microbiota colonizes and changes via interacting with external factors. Among external factors, delivery mode, breastfeeding, antibiotics treatment, lifestyle, and diet have been studied extensively. Yet, the most important factors affecting gut microbiome has been agreeable to be diet in many studies. As an energy source of gut microbiota, foods, administered into large intestine shapes gut microbial composition. Properties of macronutrients and micronutrients in food, such as digestibility and physicochemical characteristics are important in shaping gut microbiome. However, since many people still do not have such profound knowledge of nutrition, their dietary behavior is determined by social factors, including socioeconomic status, demographical, belief and philosophy, culture, or religion. Therefore, the objective of this thesis was examining how such social and environmental (open full item for complete abstract)

Committee: Jiyoung Lee (Advisor); Vanessa Hale (Committee Member); Ahmed Yousef (Committee Member) Subjects: Food Science

Doctor of Philosophy, The Ohio State University, 2024, Microbiology

Signal transduction is an essential part of how bacteria sense and respond to their internal and external environments. Signal transduction is mediated by three different types of systems: one-component systems, two-component systems, and chemosensory systems. Each system receives an input through a sensory domain resulting in the creation of a signal that leads to a cellular response. Extracytoplasmic sensory domains are important for how bacteria sense their external environment. Two major families of extracytoplasmic domains are the Cache Superfamily and the Four Helical Bundle Superfamily. We are interested in studying signal transduction is the human gut microbiome. The human gut is extremely diverse and varies between individuals making it difficult to study. Human gut commensals are widely unexplored because many of the organisms in the microbiota cannot be cultured. Here, we begin to explore signal transduction pathways that are found in common bacterial commensals found in the human gut microbiota. We identify thousands of extracellular sensory domains, and we characterize binding motifs for several dCache_1, sCache_2, and Cache _ 3-Cache _ 2 domains. By better understanding extracellular sensory domains in these organisms, we can learn more about what molecules in the gut contribute to commensal proliferation. Interestingly, in the gut commensal Akkermansia muciniphila, the only Verrucomicrobiota member commonly found in the gut, we have found only one histidine kinase that potentially contains a putative extracytoplasmic sensory domain. Structural modeling suggests that this hypothetical domain resembles a dCache domain. This domain should be further investigated to determine its functionality.

Committee: Igor Jouline (Advisor); Jesse Kwiek (Committee Member); Patrick Bradley (Committee Member); Irina Artsimovitch (Committee Member) Subjects: Microbiology

Doctor of Philosophy, The Ohio State University, 2024, Food Science and Technology

Food safety inadequacies constitute a substantial global hazard, not only influencing human health but also bearing serious implications for animal health and environmental sustainability. The sources of food contaminants are diverse, ranging from polluted food production environments during food production to deficient practices in transportation, and inadequate storage conditions. The pollutants that contaminate our food supply can be broadly classified into physical, chemical, and biological. Among biological contaminants, pathogens and microbe-derived metabolites are largely responsible for precipitating foodborne diseases. The built environment—comprising agricultural lands, livestock, aquaculture farms, food industry and consumers settings,—is deeply impacted by microbial threats. It is crucial to provide an effective and environmentally friendly method to modulate biological threats. In the meantime, from a personal environment, it is not only essential to minimize the contact with hazards, but also important to seek an effective and convenient way to mitigate the harmful impacts of the exposure in our daily life. This method should encompass reinforcing human health defenses. This dissertation presents an innovative exploration of two effective approaches aimed at protecting health under a high-risk (cancerous) condition in a personal environment with diet intervention and controlling biological contamination at a built environment level with an environmentally friendly technique. Chapter 2 and 3 investigate the effectiveness of polyphenol-rich diet, black raspberry (BRB), on gut microbiota and their function, with a particular focus on its application for negating harmful effects from carcinogen exposure in high-risk populations. For this, we applied a carcinogenesis mouse model and simulated black raspberry ingestion to determine whether this diet can be an effective way for health risk intervention at a host level. 16s rRNA sequencing and metagenomic (open full item for complete abstract)

Committee: Jiyoung Lee (Advisor); Ahmed Yousef (Committee Member); Rafael Jimenez-Flores (Committee Member); Jessica Cooperstone (Committee Member) Subjects: Food Science

Doctor of Philosophy, Case Western Reserve University, 2024, Molecular Medicine

The gut microbiome constitutes billions of microorganisms consisting of bacteria, viruses, fungi, and archea which colonize the gastrointestinal tract. These microbes have a profound impact on host physiology due to their ability to modulate immune responses, metabolize dietary compounds, and produce metabolites which can enter circulation. As a result, the microbiome can influence the pathogenesis of various diseases, including alcohol-associated liver disease (ALD). ALD remains one of the most prevalent liver diseases worldwide, contributing to increases in mortality through its ability to affect multiple organs in the host. Recently, much attention has been brought to the role of alcohol-induced disruptions to the microbiome, and the subsequent modulations which either prevent or promote the progression of this disease. However, the vast mechanisms by which the microbiome can influence disease means that much is still left unanswered in regard to this axis. In this dissertation, our objective was to further elucidate mechanisms by which ALD-associated disruptions to the microbiome influence the course of disease. To do so, we employ clinical data from patients with ALD along with novel methodologies of targeting microbial metabolites for the elucidation of microbiome-related mechanisms in mice exposed to ethanol. In Chapter 2, we use mass-spectrometry to profile changes in circulating microbial metabolites in patients with ALD. We find that meta-organismal metabolites are decreased in patients with severe ALD and the exploration of bulk RNA-seq datasets unveil that this is potentially a result of dysregulated hepatic phase II metabolism in patients with ALD. In Chapter 3, we use synthetic bacterial communities to test the effects of the deletion of a bacterial tryptophanase gene. Here, we identify bacterial species susceptible to ethanol as well as a mechanism by which bacterial tryptophanase expression protects against ethanol administration through the promotio (open full item for complete abstract)

Committee: Mark Brown (Advisor); Laura Nagy (Advisor); Daniela Allende (Committee Member); Philip Ahern (Committee Member); Christine McDonald (Committee Chair) Subjects: Biomedical Research; Immunology; Microbiology; Molecular Biology

Doctor of Philosophy, Case Western Reserve University, 2024, Biomedical Engineering

Intracortical microelectrodes (IMEs) are a type of brain-computer interface that allows for the recording of neural signals to communicate between the brain and computers. IMEs can be used to restore motor function in people with spinal cord injury, treatment of neurological disorders, and are a strong basic science tool for understanding the brain. Unfortunately, implanted IMEs consistently see a steady decline in recording ability over time, leading to failure of the device. Damage to the blood-brain barrier (BBB) from IME implantation is a key contributor to device failure. After BBB breach, neurotoxic molecules invade the brain and cause a downstream cascade of neuroinflammation and oxidative stress that further damages the BBB, brain tissue, and the IME itself. Attempts to minimize BBB damage to improve neuroinflammation and IME longevity have shown limited success. Given the lack of solutions to the chronic stability of neural recordings, further investigation into understanding and minimizing the effects of BBB damage is warranted. In my dissertation, I investigate multiple strategies to mitigate and expand our understanding of how BBB damage can impact IME performance. Thermal damage to underlying vasculature because of cranial drilling has been shown to impact BBB permeability. To combat this, I developed a standardized surgical approach to limit surgeon variability and reduce thermal damage on the BBB. Next, I utilized the antioxidant dimethyl fumarate to promote BBB healing and reduce oxidative stress, resulting in acute improvements to IME function without long-term stability. Lastly, I investigated what unknown molecules enter the brain through the permeable BBB and contribute to neuroinflammation. I was the first to discover that gut-derived bacteria invade the site of implantation through the damaged BBB, which can be modulated with antibiotics to alter neuroinflammation and IME performance. New therapeutics can be developed utilizing this connecti (open full item for complete abstract)

Committee: Jeffrey Capadona (Advisor); Anirban Sen Gupta (Committee Chair); A. Bolu Ajiboye (Committee Member); Andrew Shoffstall (Committee Member); Gary Wnek (Committee Member) Subjects: Biomedical Engineering; Engineering

Doctor of Philosophy (Ph.D.), Bowling Green State University, 2024, Biological Sciences

Host responses to synthetic phenethylamines have been linked with alterations in the gut microbial profile. A novel gut commensal, Proteus mirabilis (P. mirabilis) strain Roy1, was discovered to be enriched in the cecal contents of a rat treated with the synthetic phenethylamine, 3,4-methylenedioxymethamphetamine (MDMA). The genomic DNA of this bacterium was subjected to Illumina sequencing, revealing a draft genome sequence of approximately 3.9 Mbps and comprises 3,602 coding sequences (CDSs). To identify functionally significant genes, a comparative genome analysis was conducted between P. mirabilis Roy1 and thirty different P. mirabilis genomes available in the NCBI database. The pan-genome comparisons indicated that P.mirabilis Roy1 shared approximately 75% of its core genome with the P. mirabilis referencestrains. Furthermore, the comparative analysis revealed unique genes contributing to its successful colonization and proliferation in the gastro-intestinal tract (GIT). Rats subjected to MDMA treatment exhibited diarrheal symptoms. The strain-specific genes detected in P. mirabilis Roy1 might have aided in bypassing the intestinal emptying process. The unique gene repertoire includes genes involved in inter/intraspecies competition, intestinal adherence, and pathogenicity. Interestingly, these gene sets closely resembled genes found in various Escherichia coli (E. coli) strains, suggesting that they may have been acquired from the rat's gut contents. The direct contributions of P. mirabilis Roy1 in driving phenethylamine-induced responses require further experimental validations. Phage therapy has emerged as a treatment option for bacterial infections. However, its efficacy against drug-induced responses has not been addressed. Therefore, phages specific to P. mirabilis strain Roy1 were isolated. For orally administered phages to be therapeutically effective, they need to endure the passage through gastric fluid, including surviving at low pH levels. Thus, aci (open full item for complete abstract)

Committee: Vipaporn Phuntumart Ph.D. (Committee Co-Chair); Raymond Larsen Ph.D. (Committee Co-Chair); Jon Sprague Ph.D. (Committee Member); Scott Rogers Ph.D. (Committee Member); Zhaohui Xu Ph.D. (Committee Member); Jeremy Oehrtman Ph.D. (Other) Subjects: Bioinformatics; Microbiology; Molecular Biology; Pharmacology

PhD, University of Cincinnati, 2023, Medicine: Immunology

Hematopoiesis is a complex and tightly regulated biological system in which the stem cells and progenitors balance between mature lineage outputs and self-renewal. Environmental stimuli, genetic predispositions, and host responses together control and alter underlying transcriptional network. Various animal models and single-cell multi-omics approaches have been developed to unravel the network and mechanisms associated with it. This dissertation characterizes relationship between gut microbiome (environmental stimuli) and host; describes human and murine hematopoietic stem cells and progenitors; and demonstrates methods to incorporate with biological models to derive insightful biological readouts. Microbiome models have informed our understanding of microbiome-dependent metabolites, their role in homeostatic hematopoiesis, and nominated some metabolites as potential therapeutics. However, conclusions about gut microbiota-induced biological functions have been called into question after recent results from metabolite clinical trials and conflicting findings across studies. To systematically evaluate the impact of durably different gut microbiome on homeostatic hematopoiesis, we analyzed three C57BL/6 mouse microbiome models with defined flora, and contrasted with germ-free and standard-pathogen-free C57BL/6 mice. Metagenomics and metabolomics confirmed distinct microbial species present, their relative diversity, and associated changes in physiology and serum metabolites. We find that a minimal microbiome composition restores the majority of metabolites absent in germ-free mice, but community complexity controls metabolite abundance and perturbs metabolite pathways and transcriptional signatures. However, immunophenotyping reveals comparable innate and adaptive immune populations across models. Bone marrow transplant reveals normal homeostatic HSC function, and in vitro assays reveal similar neutrophil innate immune function across models. Thus, defined flo (open full item for complete abstract)

Committee: H. Leighton Grimes Ph.D. (Committee Chair); Daniel Lucas Ph.D. (Committee Member); Jose Cancelas-Perez M.D. Ph.D. (Committee Member); Nathan Salomonis Ph.D. (Committee Chair) Subjects: Immunology

Doctor of Philosophy (Ph.D.), Bowling Green State University, 2023, Biological Sciences

Globally abused phenethylamine drugs can cause “phenethylamine-induced-hyperthermia” (PIH), a serious health concern associated to sequela of complications including rhabdomyolysis, coagulopathy, kidney failure and death. In general, PIH is known to occur via activation of host sympathetic nervous system (SNS) leading to increased release of norepinephrine (NE) post phenethylamine exposure. NE then acts as signal to activate pathways which generate heat in various thermogenic tissues or prevent heat loss through vasoconstriction. Besides NE, recent research from our laboratory pointed towards potential involvement of gut bacteria in PIH, shown by altered PIH following gut microbial modulations such as via antibiotic treatment or fecal microbial transplantation (FMT). Here, we aimed to investigate the functional role of gut microbiome and bile acids as signal in PIH. We applied targeted LC-MS/MS, first time to our knowledge, to quantify serum concentrations of three important bacteria metabolized/associated bile acid species (BAs): cholic acid (CA), chenodeoxycholic acid (CDCA) and deoxycholic acid (DCA) prior to and post (hyperthermic dose of) 3,4-methylenedioxymethamphetamine (MDMA) (a phenethylamine) treatment. Male Sprague-Dawley rats were provided either sterile or antibiotic-water for five days prior to MDMA (20 mg/kg, sc)/saline administration. On day six BAs and body temperatures were measured at 0 minute before and 30 minutes and 60 minutes post MDMA/Saline challenge. We found all three focal BAs in serum to deplete significantly in MDMA treated rats compared to saline group at 60-minute, exactly the same time point when peak rise in core body temperature occurred, indicating contribution of these three BAs in PIH. While prior antibiotic cocktail (vancomycin, bacitracin and neomycin) treated groups had greatly reduced serum level of all three BAs and reversal of hyperthermia after MDMA. We also inferred metagenomic functions applying PICRUSt2 on 16S rRNA ge (open full item for complete abstract)

Committee: Christopher Ward Ph.D. (Committee Chair); Benjamin Ward Ph.D. (Other); Raymond Larsen Ph.D. (Committee Member); Vipaporn Phuntumart Ph.D. (Committee Member); Jon Sprague Ph. D. (Committee Member) Subjects: Biology

MS, Kent State University, 2023, College of Arts and Sciences / Department of Biological Sciences

Cyanobacterial Harmful Algal Blooms (CyanoHABs) are prevalent in both freshwater and marine environments and are notorious for producing cyanotoxins and forming dense, visible blooms. Specifically, MCs, which are primarily synthesized by Microcystis, Anabaena, and Planktothrix, stand out as cyclic peptides characterized by a unique amino acid, ADDA, that is pivotal for their toxic effects. Despite robust monitoring and mitigation strategies, incidents related to surging MC concentrations occur frequently. Moreover, conventional water treatment facilities might fall short of completely eliminating MCs, potentially leaving traces in drinking water distributed globally. This poses specific public health risks, making the ramifications of cyanotoxin exposure a subject of ongoing research and heightened public health alertness. Gut microbiome, a diverse community of microorganisms inhabiting the gastrointestinal tract, is a crucial component of human health. With trillions of bacteria contributing to these processes, it is involved in vital processes like digestion, immunological control, and nutrition synthesis. However, this intricate system could be disturbed, leading to several health issues, especially if disturbed by the exposure to MC-LR exposure. Guided by this idea, the primary aim of this thesis was to dissect the potential dynamics of gut microbiome alterations in mice during MC-LR exposure through drinking water. This thesis aimed to understand the relationship between consumption or exposure to MC-contaminated water and changes in the gut microbiome. The first part of this study focused on short-term (weeks) exposure to low MC concentrations. Here, we hypothesized that even brief MC exposure would cause significant alterations in the gut microbiome community and its structure. However, our short-term study found no significant changes in gut microbiome diversity or community structure after MC-LR exposure. There were changes in the microbial taxa but (open full item for complete abstract)

Committee: Xiaozhen Mou Dr. (Advisor); Sangeet Lamichhaney Dr. (Committee Member); Wilson Chung Dr. (Committee Member) Subjects: Biology; Ecology; Environmental Science; Microbiology

Master of Science (MS), Bowling Green State University, 2023, Biological Sciences

Microbes in the gut have diverse roles in influencing the host metabolism, including nutrient provision, immune system protection, and gut barrier integrity. The main objective of this study was to investigate the impact of fecal microbial transplantation (FMT) from alcohol Non-preferring (NP) rats on alcohol drinking behavior and the gut microbiome of selectively bred alcohol-preferring (P) rats. The rats were given choices between 15%, 30% alcohol solutions and water. FMT was conducted using a mixture of powdered feces and chow to facilitate the transfer of the gut microbiota. Fecal samples were collected at various time points, including before, during and after FMT, and were analyzed through sequencing to evaluate the composition and alteration in the gut microbiome over time. The R programming language and KBase were used to analyze the operational taxonomic units (OTUs) and to assess the changes in microbial composition and abundance within the gut microbiome of P rats following FMT. The results showed a significant reduction in total alcohol consumption (measured as g/kg/day) in the P rats after FMT, suggesting that the gut microbes influenced drinking behavior. Furthermore, alpha diversity analysis was conducted using the Shannon diversity index (SDI) and observed OTUs. The results revealed that alpha diversity was higher in the pre-FMT samples compared to post-FMT samples, suggesting that FMT contributed to a decrease diversity, more stable and uniform bacterial community composition among the P rats. To assess the dissimilarity between bacterial communities, beta diversity analysis was performed through non-metric multidimensional scaling (NMDS). The NMDS plot which is based on Bray-Curtis dissimilarity index showed less variation in P rats after FMT. Further analysis demonstrated that the gut microbiota of the P rats through FMT from NP rats led to significant increase in the relative abundance of Bacteroidetes and decrease in Lachnoclostridium. Ot (open full item for complete abstract)

Committee: Vipaporn Phuntumart Ph.D. (Committee Chair); Christopher Ward Ph.D. (Committee Member); Howard Casey Cromwell Ph.D. (Committee Member) Subjects: Biology; Microbiology; Molecular Biology

Master of Science (MS), Wright State University, 2023, Biochemistry and Molecular Biology

Pomegranate is known to have antioxidant and prebiotic qualities that have been shown to promote the growth of beneficial bacteria while reducing inflammation in the gut. Inflammation in the gut is an issue that results in many health problems including obesity and colon cancer. In this study, an experimental group received a daily pomegranate supplement for three weeks where a control group did not receive any supplement. After sequencing gDNA isolated from fecal samples from both before and after the trial period there was a significant difference between the two groups. The largest amount of variability is attributed to the individual the sample came from. However, pomegranate did significantly contribute to a change in the gut microbiome. Multiple different genera were changed between the pre and post-pomegranate trial samples. Two of these genera, Limosilactobacillus and Enterococcus, are both lactic acid bacteria. Lactic acid bacteria are known to have anti-inflammatory qualities within the gut. Other genera, including Collinsella are reduced during the trial period. Collinsella promotes inflammation in the gut that can lead to many intestinal diseases including irritable bowel syndrome and ulcerative colitis. Overall, this study shows that pomegranate consumption results in a significant change to the gut microbiome by promoting anti-inflammatory bacteria while reducing pro-inflammatory bacteria. The changes in the gut by pomegranate consumption helps protect against inflammatory associated diseases including type 2 diabetes and irritable bowel disease.

Committee: Oleg Paliy Ph.D. (Advisor); Weiwen Long Ph.D. (Committee Member); Kwang-Jin Cho Ph.D. (Committee Member) Subjects: Biochemistry; Microbiology; Molecular Biology

Doctor of Philosophy, Case Western Reserve University, 2023, Molecular Medicine

Cardiovascular diseases (CVD) and their thromboembolic complications, including myocardial infarction and stroke, are the leading cause of death worldwide. Despite tremendous advances in understanding CVD pathogenesis that have led to important drug discoveries, patients still suffer from a substantial residual cardiovascular event risk. Understanding the drivers for residual risk is critical to identify new therapeutic targets and improve CVD outcomes. Untargeted metabolomics studies have proven to be a powerful discovery platform for metabolites that contribute to CVD events independent of traditional risk factors. In chapter 1, we discuss the role of the microbiome in CVD. The discovery of metaorganismal metabolites that are both clinically and mechanistically linked with thromboembolic complications has paved the way for new therapeutic concepts that include gut microbial metabolic pathways as drug targets to alleviate residual cardiovascular event risk. In chapter 2, we found that the metaorganismal metabolite trimethylamine N-oxide (TMAO) induces vascular endothelial tissue factor that contributes to a pro-thrombotic state. This adverse phenotype could be reversed using a drug that inhibits TMA(O) production without the bleeding risk that is observed with drugs that directly inhibit the coagulation system. Chapter 3 describes how low levels of cardiac troponin T that leak into the circulation in the absence of acute myocardial injury can be used to predict residual cardiovascular event risk in patients with prediabetes, a population that is increasing and for whom risk stratification is an unmet clinical need. Chapter 4 shows how an untargeted metabolomics approach identified endogenous levels of the non-nutritive sweetener erythritol to be associated with residual cardiovascular event risk. Following validation of this association in independent large clinical cohorts, mechanistic studies provided evidence that both endogenous and postprandial levels of eryth (open full item for complete abstract)

Committee: Thomas McIntyre (Committee Chair); Stanley L Hazen (Advisor); Mark Bown (Committee Member); Scott Cameron (Committee Member) Subjects: Epidemiology; Experiments; Medicine; Nutrition

Doctor of Philosophy, The Ohio State University, 2022, Environmental Science

Antibiotic resistance (AR), or the ability of bacteria to evade the effects of antibiotics, is a global public health crisis that limits the effectiveness of antibiotics in treating infections. AR is governed by mechanisms in bacteria that serve competitive and ecological purposes. These mechanisms are encoded by genes that can be transmitted from resistant to susceptible bacteria within a population via horizontal gene transfer (HGT) while in the presence of selective pressure. While AR is ancient and ubiquitous, anthropogenic use of antibiotics in medicine and livestock drive the proliferation of AR in bacteria. Due to the interconnected complex nature of AR spread between human, animals and environment domains, AR should be studied from One Health perspective. Historically, AR has been studied from a clinical and agricultural aspect, but the role of the environment as a reservoir of clinically relevant AR genes and bacteria is under-studied. It has been postulated that the environment plays a critical role in the spread and maintenance of AR, due to the large amount of antibiotics, AR genes, and AR bacteria that enter the environment via human and animal feces. Therefore, it is necessary to characterize AR in the environment and the potential implications for human and animal health. Chapter 1 is a literature review that summarizes the issue of AR from an environmental and microbial ecology perspective. The scope of the AR crisis from a public health perspective is described, however this review focuses on the role of anthropogenic pollution in promoting the dissemination of AR genes in bacteria, focusing on animal- and human-originated contamination. Differences in the resistome, or the collection of AR genes in a community, between animals, humans, and the environment are described. Finally, due to the interconnected nature between the microbiome and resistome, this review discusses the principles of microbial community ecology in relating those t (open full item for complete abstract)

Committee: Jiyoung Lee (Advisor); Thomas Wittum (Committee Member); Mark Weir (Committee Member); Michael Bisesi (Committee Member) Subjects: Environmental Science; Microbiology; Public Health

Master of Science (MS), Wright State University, 2022, Biochemistry and Molecular Biology

The benefits of intermittent fasting have been studied across many facets of health. It is known that physiologically fasting results in a metabolic switch from liver-derived glucose to adipose cell derived ketones to be used as energy and signaling molecules. Fasting down-regulates inflammation, increases expression of antioxidant defenses, and activates pathways for DNA repair and autophagy. While fasting or intermittent feeding effects on host physiology have been identified, the relationship between fasting and gut microbiome is not as well known. In times of gut rest, resident microbes undergo detoxication and motility, and in times of activity, gut microbes undergo DNA repair, energy metabolism, and cell growth. These daily fluctuations of microbial composition and function are mainly influenced by feeding patterns, and a change of these feeding patterns results in dysbiosis. In this study, we used an in vitro system to simulate the conditions of the human colon to evaluate gut microbiome fluctuations when switched to a once-per-day feeding pattern also known as intermittent feeding. This study found that intermittent feeding results in a significant increase in three beneficial genera (Mitsoukella, Bifidobacterium, Phoceaicola) and decrease in two detrimental genera (Gemmiger and Desulfovibrio) across all vessels. Cell density, community diversity, and short chain fatty acid production were all decreased by intermittent feeding. It appears that intermittent feeding has both beneficial and harmful effects on the human gut microbiota

Committee: Oleg Paliy Ph.D. (Advisor); Hongmei Ren Ph.D. (Committee Member); Michael Craig Ph.D. (Committee Member) Subjects: Microbiology

Doctor of Philosophy, Miami University, 2022, Microbiology

Choline, a quaternary amine, is found in a wide variety of foods such as dairy, egg-based dishes, and red meat. Moreover, this compound also occurs in the marine environment and is a non-competitive substrate for methanogens. This compound, in our gut, is degraded into trimethylamine (TMA), which is further oxidized in the liver to form trimethylamine N-oxide (TMAO). Increased concentrations of TMAO lead to heart risks such as atherosclerosis. Canonical choline degradation pathways that cleave choline to generate TMA via choline trimethylamine lyases (CutC) have been well studied. However, there is an alternate pathway that uses methyltranferases to degrade quaternary amines by removing a methyl group. Many of these methyltransferases belong to the superfamily COG5598, which includes both pyrrolysine (pyl)-containing TMA methytransferases, MttBs, and non-pyl MttB homologs, which lack the pyrrolysine residue. Some of these non-pyl-MttB homologs have been shown to demethylate quaternary amines such that an alternative demethylated product is formed instead of TMA. The goal of the work presented in this dissertation was to elucidate choline utilization pathways in Citrobacter amalonaticus CJ25 (CJ25), a novel gut bacterial isolate, and a brackish water methanogen isolate Methanococcoides methylutens Q3c (Q3c). These two microbes are explored because of their ability to utilize choline as the sole energy and carbon source for growth. CJ25 did not encode any CutC in the genome and was able to still utilize choline. Genomic and proteomic data pointed in the direction of a pyruvate formate lyase, which was not a CutC, to be playing a role in choline degradation in CJ25. Furthermore, Q3c also did not encode the canonical CutC but instead utilized a demethylation pathway to metabolize choline. NMR, proteomic, and in silico studies provided strong evidence of a non-pyl homolog of the monomethylamine methyltransferase, MtmB, carrying out choline utilizat (open full item for complete abstract)

Committee: D.J. Ferguson (Advisor); Rachael Morgan-Kiss (Committee Member); Carole Dabney-Smith (Other); Xin Wang (Committee Member); Annette Bollmann (Committee Member) Subjects: Climate Change; Microbiology