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OBJECTIVE: Using preliminary data from the Binge-Eating Genetics Initiative (BEGIN), we evaluated the feasibility of delivering an eating disorder digital app, Recovery Record, through smartphone and wearable technology for individuals with binge-type eating disorders. METHODS: Participants (n = 170; 96% female) between 18 and 45 years old with lived experience of binge-eating disorder or bulimia nervosa and current binge-eating episodes were recruited through the Recovery Record app. They were randomized into a Watch (first-generation Apple Watch + iPhone) or iPhone group; they engaged with the app over 30 days and completed baseline and endpoint surveys. Retention, engagement, and associations between severity of illness and engagement were evaluated. RESULTS: Significantly more participants in the Watch group completed the study (p = .045); this group had greater engagement than the iPhone group (p's < .05; pseudo-R effect size = .01-.34). Overall, binge-eating episodes, reported for the previous 28 days, were significantly reduced from baseline (mean = 12.3) to endpoint (mean = 6.4): most participants in the Watch (60%) and iPhone (66%) groups reported reduced binge-eating episodes from baseline to endpoint. There were no significant group differences across measures of binge eating. In the Watch group, participants with fewer episodes of binge eating at baseline were more engaged (p's < .05; pseudo-R = .01-.02). Engagement did not significantly predict binge eating at endpoint nor change in binge-eating episodes from baseline to endpoint for both the Watch and iPhone groups. DISCUSSION: Using wearable technology alongside iPhones to deliver an eating disorder app may improve study completion and app engagement compared with using iPhones alone.

Microorganisms are key players in the ecosystem functioning. In this thesis, we developed a framework to preprocess raw microbiome data, build a correlation network, and analyze co-occurrence patterns between microbes. We then applied this framework to a marine microbiome dataset. The dataset used in this study comes from a year-long time-series to characterize the microbial communities in our coastal waters off the Cal Poly Pier. In analyzing this dataset, we were able to observe and confirm previously discovered patterns of interactions and generate hypotheses about new patterns. The analysis of co-occurrences between prokaryotic and eukaryotic taxa is relatively novel and can provide new insight into how marine microbial communites are structured and interact.

Mycobacterium ulcerans is an acid-fast bacillus that is the causative agent of Buruli ulcer, a necrotizing skin disease. The transmission route for M. ulcerans is unknown, but many insects have been posited as part of the web, including Belostomatids, Naucorids, and Culicids. Aedes albopictus was selected for use in a set of experiments where the first-generation larvae were inoculated with M. ulcerans, and mosquitoes were reared throughout the third generation to interrogate presence and quantity of the bacteria. Using qPCR, second and third generations displayed positivity (22% and 5.6% respectively). 16S V4 sequencing was used to obtain microbiota for all life stages as well as environmental samples, and many relationships between generations, life stages, and treatments displayed statistical significance in alpha diversity, beta diversity, and relative abundance of microbiomes. This study opens multiple avenues of further investigation into the transmission web of Buruli ulcer.

Ideally, a nutritional biomarker serves as an objective measure of the intake of a particular food or nutrient, may provide a reflection of health and disease processes, and can aid in the development of personalized nutritional recommendations. However, few food biomarkers have been validated and most have yet to be critically appraised in the literature. With the increased use of metabolomics in population-based studies, it is important to identify the sources of variability in nutritional biomarkers that may be attributed to intrinsic physiologic characteristics and extrinsic factors so that exposure-outcome associations can be examined more accurately. Additionally, circulating metabolites are associated with obesity-related changes in gut microbiome but there has been limited integration of metabolomics with microbiome in childhood obesity, and even less is known in non-white populations. This dissertation presents a series of studies that provide direct support for utility of nutritional biomarkers in population-based studies. The first study, presented in Chapter 2, contributes to the growing literature on food-based biomarkers by generating a comprehensive list of metabolites associated with a comprehensive list of all individual foods and food groups, and rated the evidence based on interstudy repeatability and study design. Chapter 3 identifies sources of variability in serum metabolite concentrations in White Europeans and South Asian pregnant women, thereby guiding appropriate statistical modeling when utilizing metabolomics in nutritional epidemiological studies. Chapter 4 provides results from a multi-omics integration analysis of serum metabolites and amplicon sequence variants of 16S ribosomal RNA genes to identify biomarkers that discriminate children with and without obesity. Collectively, the results showed that a specific food/food group may give rise to many metabolites, however in several cases, a single metabolite can be a good indicator of food intake. Dietary factors explained the highest proportion of variability in exogenous food-based biomarkers relative to non-dietary factors, whereas the contribution of non-dietary factors was either similar or lower for metabolites that can either be produced endogenously, biotransformed by gut microbiota, and/or derived from more than one food source. Most of the circulating metabolites differed by ethnicity (South Asian and White Europeans). Biomarkers with good evidence can be considered direct surrogates for food intake, however, they can be influenced by several non-dietary factors, which require appropriate consideration during the statistical analyses of the data. Finally, the results showed notable differences in serum metabolome and specific gut bacterial species, and between specific metabolites and bacterial species related to childhood obesity. Obesity related metabolic pathways such as glutamate and carnitine metabolism may provide insight into the metabolic processes related to early onset of obesity in childhood. / Dissertation / Doctor of Philosophy (Medical Science)

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It is well known that the elderly often manifest chronic low-grade inflammation. This phenomenon, called “inflamm-aging,” is postulated to contribute to increased susceptibility towards infectious diseases and an overall increase in frailty. We have proposed examining the gut microbiome as a potential mediator of these changes. Gut microbial communities influence the host immune system; often dictating an individual’s health status. Thus, harmful gut microbiome changes, termed dysbiosis, are associated with poor health in the elderly. We first sought to understand the key immunological, physiological and microbiome changes occurring with age (Chapter 3). Our data reveals immune impairments in aged mice, with increased intestinal permeability, systemic inflammation and alterations in the functions of myeloid cell populations. However, our aged germ-free (GF) mice are protected from these outcomes, indicating that the old microbiome may play a strong role in these age-associated impairments. To study this further, we have colonized young and old GF mice with the “young” or “old” microbiota in order to determine whether the relationship between microbial dysbiosis with age and health status is correlative or causative (Chapter 4). Interestingly, young GF mice colonized with old microbiota have significantly increased permeability, systemic inflammation and an influx of Ly6Chigh monocytes when compared to those colonized with the young microbiota. By using transgenic mice (TNF-/- mice), or by reducing systemic TNF levels via therapeutics, we were able to reduce some aspects of microbial dysbiosis and age-associated inflammation (Chapter 5). Our data suggests that harmful changes to the gut microbiome composition with age initiate a cycle of negative events that ultimately result in increased inflammatory myeloid cell recruitment, increased intestinal permeability and an overall increase in systemic inflammation in old mice. By identifying these key changes, we can work towards developing effective therapeutics that promotes healthy aging and protection against infectious diseases. / Thesis / Master of Science (MSc) / Élie Metchnikoff first coined the term “dysbiosis” when he described the imbalance in microbial populations that could result anywhere in the body. Since then, numerous studies have examined the role of the intestinal microbiota in defense against pathogens. Metchnikoff also suggested that the gut composition and function is altered with age and this can in turn; increase the host’s susceptibility towards infectious diseases. My research aims to characterize the role of microbial dysbiosis on the immune defects with age. To do so, I will be utilizing a unique set of mice, called gnotobiotic mice. These mice are housed under specific germ-free conditions and contain no microbiome. Thus, they provide us with the ideal model to study the effects of the microbiome on immune function. The findings from these studies will help in the development of preventative and therapeutic alternatives to provide the elderly with more years of healthy, independent living.

Over 1.1 billion people smoke worldwide despite the association of smoking with numerous diseases including chronic obstructive pulmonary disease (COPD). The decline in lung function observed in COPD patients is thought to be related to smoke-induced inflammation. COPD patients are also at increased risk of acquiring lung bacterial infections that are associated with exacerbations, characterized by worsened disease symptoms and inflammation. The focus of this thesis is on how cigarette smoke impacts bacterial-host interactions and bacterial community interactions to promote infection and disease. In chapter 3.1, we sought to understand how cigarette smoke primed the lungs towards an amplified inflammatory response to bacterial infection reflective of COPD exacerbations that accelerate disease progression. We present a novel finding that exacerbated neutrophilia elicited by nontypeable Haemophilus influenzae (NTHi) lung challenge in smoke-exposed mice occurred dependent on IL-1α. Smokers and patients with COPD are additionally at increased risk of acquiring bacterial infection that may be related to impaired containment of nasally colonizing pathogens. In chapter 3.2, we found that cigarette smoke predisposed mice to invasive pneumococcal disease (IPD) following nasal pneumococcal colonization associated with attenuated nasal inflammatory responses. To our knowledge, this is the first study to describe the progression from asymptomatic nasal pneumococcal colonization to the development of IPD in the context of cigarette smoking. It has been suggested that smokers have higher rates of pathogen colonization as a consequence of cigarette smoke-induced nasal microbiome dysbiosis. The last study in chapter 3.3 advanced knowledge in the field by testing this hypothesis. We observed that cigarette smoke alone did not alter the mouse nasal microbiome and concluded that microbiome dysbiosis observed in smokers likely occur as a consequence of nasal pathogen colonization. Overall, work presented in this thesis advanced our understanding of how cigarette smoking alters bacterial-host interactions to promote infection and disease. / Thesis / Doctor of Philosophy (PhD) / Over 1.1 billion people smoke worldwide and can develop chronic obstructive pulmonary disease (COPD), a serious inflammatory disease compromising lung function. Additionally, smokers and COPD patients have higher rates of bacterial infection. The goal of this thesis is to understand how smoking impacts our ability to combat infection. Lung infection in COPD patients causes exacerbation, with worsened disease symptoms. Using mouse models, we learned how smoking causes increased lung inflammation following bacterial infection, contributing to damage reflective of COPD exacerbations, and identified a potential intervention. We elucidated smokers may have increased infections due to impaired immune responses in the nose, a major pathogen entry point. It is thought smoking reduced beneficial bacteria that counter pathogen acquisition in the nose. We confirmed smoking did not impact these bacteria, directing research focus towards other ways smokers acquire pathogens. Overall, this thesis advanced knowledge and will help efforts to control disease in smokers.

Systemic Lupus Erythematosus (SLE) stands as a multifaceted autoimmune disorder, characterized by a spectrum of clinical manifestations and the generation of autoantibodies against self-antigens. Our focus was on the pivotal role of B cells in the development of SLE. The study also underscored the significant contribution of regulatory B (Breg) cells in the context of SLE, suggesting their potential as key regulators of the disease process. Our results provided a deeper understanding of the intricate interplay between B cells and SLE, offering insights that were valuable for both scientific research and future designs of therapeutic approaches. Cutting-edge single-cell RNA sequencing was employed to analyze the differences in splenic Breg subsets and their molecular profiles across different stages of lupus development in mice. Transcriptome-based changes in Bregs during active disease were confirmed through phenotypic analysis. These findings provided crucial insights into the dynamic role of B cells in the pathogenesis of SLE. In addition, we delved into the intricate connection between SLE and the gut microbiota. A literature review offered a comprehensive analysis of current research, with a particular emphasis on potential interactions between bacterial flagellin and Toll-Like Receptor 5 (TLR5) on immune cells. These interactions garnered substantial attention due to their potential implications in the pathogenesis of SLE. We synthesized existing research, providing valuable insights into the complex interplay between SLE and the microbiota and suggesting promising avenues for further investigation and potential therapeutic interventions. In the final study, we explored lupus-like disease in mice with global Tlr5 deletion, initially expecting disease attenuation. Surprisingly, the results revealed an exacerbation of lupus-like symptoms, particularly in female mice lacking Tlr5. Future research will seek to uncover the mechanisms by which Tlr5 deletion modulates interactions between the host and the gut microbiota, ultimately contributing to the exacerbation of lupus-like disease. / Doctor of Philosophy / Systemic Lupus Erythematosus (SLE) is characterized by a range of health issues and the body attacking itself. In this exploration, we journey through the intricate landscape of SLE, uncovering key players and unexpected twists. In this dissertation, we journeyed through the intricate landscape of SLE, uncovering key players and unexpected twists. In this dissertation, we closely examined these immune cells, revealing how different types of B cells contributed to SLE's development. We also introduced the enigmatic regulatory B (Breg) cells, which acted as potential peacekeepers in this autoimmune reaction. Our results illuminated the complex relationship between B cells and SLE, offering insights that benefited both researchers and those seeking new treatments. We employed cutting-edge technology, single-cell RNA sequencing, to scrutinize the genetic fingerprints of B cells in mice with SLE. The results unveiled changes in Breg cells during active disease, providing critical clues about how B cells impacted SLE progression. In addition, this dissertation took us into the microscopic world of our gut inhabitants, the microbiota. We dived into a treasure trove of research, focusing on how interactions between bacterial flagellin and various microbiota elements affected immune cells through a special receptor called Toll-Like Receptor 5 (TLR5). These interactions, like hidden clues, had piqued scientists' interest for their potential role in SLE development. We synthesized existing research, offering valuable insights into the complex interplay between SLE and our microbiota. The discussion also suggested promising paths for future research and potential therapies. In the final study, we encountered a plot twist. We anticipated that deleting the Tlr5 gene would improve lupus-like disease in mice. To our surprise, the opposite happened. Lupus-like symptoms worsened, especially in female mice lacking Tlr5. Clinical signs included enlarged spleens and lymph nodes, increased immune cell activity, and kidney inflammation. But Tlr5 deletion didn't change the mice's metabolism or the leaky gut. Instead, it reshaped their gut's microbial residents. Future research aimed to uncover how Tlr5 deletion altered the interactions between the host and gut microbes, ultimately making lupus-like disease more severe. In a nutshell, this journey through SLE's complex world provided a deeper understanding of its intricacies. We met the B cells, explored the microbiota, and encountered surprises along the way. These discoveries were vital pieces of the puzzle, bringing us closer to unlocking the secrets of SLE and, perhaps, finding new ways to manage and treat this challenging autoimmune disorder.

Les communautés bactériennes sont constituées d’un grand éventail d’espèces pouvant interagir entre elles dans des environnements spatialement hétérogènes tels que le sol, les plantes ou l'intestin humain. À quel point ces interactions stimulent ou entravent la diversité du microbiome demeure inconnu. Historiquement, deux hypothèses ont été proposées pour expliquer comment les interactions interespèces pourraient influencer la diversité. L’hypothèse ‘l’écologie contrôle’ (EC) prédit une relation négative, dans laquelle l'évolution ou la migration de nouvelles espèces est freinée à mesure que les niches se saturent. En revanche, l’hypothèse ‘la diversité engendre la diversité’ (DBD) prédit une relation positive, où la diversité existante favorise l'accumulation d'une plus grande diversité à travers des interactions telles que la construction de niche. De nombreuses études ont investigué ces modèles chez les vertébrés ou les plantes, et certaines les ont testés sur des bactéries en culture ; mais le modèle qui régit les communautés bactériennes naturelles demeure inconnu. En utilisant les données du gène ARN ribosomique 16S provenant d’un large éventail de microbiomes, j'ai montré une relation positive générale entre la diversité des taxons et la diversité des communautés de niveaux taxonomiques plus élevés. Cette observation est conforme à l’hypothèse du DBD, mais cette tendance positive plafonne à des niveaux élevés de diversité en raison des limites physiques de la niche. Ensuite, j'ai observé que le modèle DBD restait valide à une résolution plus fine, en analysant la variation génétique intra espèce dans les métagénomes des microbiomes intestinaux humains. Conformément au DBD, j'ai observé que le polymorphisme génétique ainsi que le nombre de souches intra espèces étaient positivement corrélés avec la diversité Shannon de la communauté. Dans le chapitre 3, j'ai examiné les interactions antagonistes entre V. cholerae et ses phages virulents et la manière dont ces interactions affectaient le cours de l’infection et la diversité génétique de V. cholerae chez les patients infectés. J'ai quantifié les abondances relatives de V. cholerae et des phages virulents associés dans plus de 300 métagénomes provenant de selles de patients atteints de choléra, tout en tenant compte de leur exposition aux antibiotiques. Les phages et les antibiotiques ont supprimé V. cholerae et ont été associés à une déshydratation légère chez les patients. J'ai également investigué les mécanismes de défense contre les phages dans V. cholerae et découvert que les éléments connus de résistance aux phages (integrative conjugative elements, ICEs) étaient associés à de faibles rapports phage: V. cholerae. J’ai pu montrer aussi que lorsque les ICEs ne sont pas détectés, la résistance aux phages semble être acquise par l’accumulation de mutations ponctuelles non synonymes. Mes résultats valident que les phages virulents sont un facteur qui protège contre le choléra tout en sélectionnant la résistance dans le génome de V. cholerae. / Bacterial communities harbor a broad range of species interacting within spatially heterogeneous environments such as soil, plants or the human gut. The extent to which these interactions drive or impede microbiome diversity is not well understood. Historically, two hypotheses have been suggested to explain how species interactions could influence diversity. The ‘Ecological Controls’ (EC) hypothesis predicts a negative relationship, where the evolution or migration of novel species is constrained as niches become filled. In contrast, the ‘Diversity Begets Diversity’ (DBD) hypothesis predicts a positive relationship, with existing diversity promoting the accumulation of further diversity via niche construction and other interactions. Many studies investigated these models in vertebrates or plants, some focused on cultured bacteria, but we still lack insights into how natural communities are assembled in the context of these two hypotheses. Using 16S RNA gene amplicon data across a broad range of microbiomes, I showed a general positive relationship between taxa diversity and community diversity at higher taxonomic levels, consistent with DBD. Due to niche’ limits, this positive trend plateaus at high levels of community diversity. Then, I found that DBD holds at a finer resolution by analyzing intra-species strain and nucleotide variation in sampled metagenomes from human gut microbiomes. Consistent with DBD, I observed that both intra-species polymorphism and strain number were positively correlated with community Shannon diversity. In Chapter 3, I investigated the antagonistic interactions between V. cholerae and its virulent phages and how these interactions affect the course of the infection and the within V. cholerae genetic diversity in natural infections. I quantified relative abundances of Vibrio cholerae (Vc) and associated phages in 300 metagenomes from cholera patients stool, while accounting for antibiotic exposure. Both phages and antibiotics suppressed V. cholerae and were inversely associated with severe dehydration. I also looked at V. cholerae phage-defense mechanisms and found that known phage-resistance elements (integrative conjugative elements, ICEs) were associated with lower phage:V. cholerae ratios. In the absence of detectable ICEs, phages selected for nonsynonymous point mutations in the V. cholerae genome. My findings validate that phages may protect against severe cholera while also selecting for resistance in the V. cholerae genome within infected patients.