Thesis advisor: Catherine Y. Read / Background. Clostridium difficile infections (CDI) account for 20-30% of healthcare-acquired infections, resulting in serious patient and economic burdens. CDI incidence has grown rapidly due to overuse of antibiotics and an aging population, posing a significant public health threat. Fecal microbiota transplantation (FMT) using donor stool has demonstrated clinical efficacy rates up to 94% and long-term restoration of a healthy intestinal microbiome. Challenges with donor screening, lack of research about optimal stool donor characteristics and intestinal microbiome composition, and a poorly fit screening model, create barriers to the availability of FMT. Purpose. This study aimed to generate essential information about FMT donor characteristics predictive of passing the screening and donor intestinal microbiome compositions associated with FMT clinical efficacy. The primary aims were to 1) identify previously unstudied characteristics of prospective FMT donors that are predictive of passing a stool bank’s screening process; and 2) determine whether donor intestinal microbial diversity is related to FMT clinical efficacy in preventing recurrent CDI. Methods. This study was conducted as a secondary analysis on a cohort of previously screened donors (n=770). Aim 1 was tested through a logistic regression of donor characteristics (gender, age, body mass index, frequency of bowel movements, diet, tobacco and alcohol use, and seasonality) with screening outcomes. Aim 2 was tested through a simple regression evaluating donor intestinal microbial diversity and rates of FMT clinical efficacy. Results. One donor characteristic in the logistic regression, frequency of bowel movements (p = 0.018), was significantly predictive of whether a donor passed the screening. Specifically, donors who had fewer than two bowel movements per day were more likely to pass. All other characteristics were not predictive. Similarly, the linear regression evaluating alpha diversity and FMT clinical efficacy was not significantly predictive of clinical efficacy (p = 0.140). Conclusion. Findings were used to support recommendations for improving prospective donor screening that nurses and other clinicians can implement to decrease challenging logistics, reduce costs and barriers, and potentially increase FMT clinical efficacy. / Thesis (PhD) — Boston College, 2019. / Submitted to: Boston College. Connell School of Nursing. / Discipline: Nursing.

In the gastrointestinal (GI) tract, goblet cells are the major source of mucins, the main structural components of the mucus layer, which functions as the front line of innate defense. The GI tract contains trillions of commensal microbes, and these microbes can manipulate mucin production by activating different signalling cascades initiated by pattern recognition receptors (PRRs), including bacterial sensing Toll-like receptors (TLRs). In addition, sterile α motif pointed domain-containing ETS transcription factor (SPDEF) is a transcription factor that modulates goblet cell differentiation and positively regulates mucin production. During helminth infections, due to the co-existence of parasites and microbiota in close proximity of goblet cells in the gut, it is likely that helminth-microbiota interactions play an important role in mucin production. Indeed, goblet cell hyperplasia and increased mucin production are observed in many enteric helminth infections, including Trichuris muris, and these processes play key roles in host infection clearance. However, it should be noted that the role of microbiota within this axis is not yet understood. Here, we hypothesize T. muris-induced altered microbiota modulates goblet cell differentiation and mucin production via SPDEF-mediated transcriptional regulation and TLR2 signalling. C57BL/6 mice were gavaged with ~300 T. muris eggs. Mice were sacrificed 36 days post-infection. Microbiota from these T. muris-infected and non-infected mice were transferred into two groups of germ-free (GF) mice. Microbiota analysis revealed that treatments in both experiments (infection with T. muris and microbiota transfer from T. muris-infected mice into GF mice) significantly account for the among-sample variations in the composition of the gut microbiota between groups (p <= 0.001). In GF mice, transfer of T. muris-infected microbiota significantly increased goblet cell numbers and TLR2 expression as well as upregulated Muc2 expression compared to MSc Thesis –Yousefi Y; McMaster University – Medical Sciences v GF mice with non-infected microbiota. Antibiotic-treated (ABX-treated) TLR2 knockout (KO) mice after receiving microbiota from T. muris-infected mice showed significantly decreased expression of Muc2 and Muc5ac compared to ABX-treated wild-type (WT) mice receiving the same microbiota. To investigate whether SPDEF is a driving factor for Muc2 production in response to T. muris microbiota stimulation, we next transferred T. muris-infected microbiota into antibiotic-treated SPDEF KO and WT mice. We observed a slight, though not significant, the influence of SPDEF on the stimulation of mucin production by T. muris microbiota. These findings reveal important interactions among parasites, resident microbiota, and host in relation to goblet cell response in the gut. In addition, this study provides new information on TLR2-based innate signalling in the regulation of goblet cell biology and mucin productio / Thesis / Master of Science (MSc)

Major depressive disorder (MDD) is a highly heterogeneous disorder, with some patients displaying immune activation and altered intestinal microbiota composition when compared to healthy controls. In recent years, the transfer of fecal microbiota pooled from several MDD patients has been used to model depression in recipient rodents. However, we have previously observed the induction of donor-specific phenotypes in mice receiving microbiota from individual irritable bowel syndrome and generalized anxiety disorder patients. Therefore, we assessed the efficacy of fecal microbiota transplant (FMT) using individual versus pooled MDD patient microbiota to induce depressive-like behaviour in recipient rodents. We observed that pooling microbiota from several patients abrogated microbial features unique to individual donors. Mice that received pooled microbiota displayed different behavioural and immune phenotypes when compared to mice that received individual patient microbiota. Two individual MDD microbiota donors, patients MDD1 and MDD5, altered the behaviour of recipient mice when compared to controls. We identified several microbial species that may underlie the anxiety- and depressive-like behaviours observed in MDD1 and MDD5 mice. Additionally, altered expression of neural and immune genes was observed along the gut-brain axis of mice colonized with MDD1 microbiota. As microglia activation may play a role in our model, we developed a protocol for the isolation and phenotyping of adult mouse microglia that will facilitate future research efforts. Overall, our results demonstrate the heterogeneity of the microbial underpinnings of MDD and support the use of individual patient microbiota in future FMT experiments. / Thesis / Master of Science (MSc)

The oral microbiome is a key component of the human body and has been associated with several habits and diseases. Despite its important role in health, it remains relatively understudied, compared to the gut microbiome. To deepen our understanding of the oral microbiome and its links to host conditions, the main aim of my PhD thesis was to characterize the lifestyle, environmental and genetic determinants of the salivary microbiome using data from CHRISMB, a convenience sample within the Cooperative Health Research in South Tyrol (CHRIS) study. With more than 1,900 samples, CHRISMB is one of the largest salivary microbiome data resources in the world. First, I studied the association between the salivary microbiome and smoking status and degree of exposure both from the compositional and predicted metabolism perspective. I found associations with 44 genera, 11 of which were also proportionally affected by the degree of exposure to tobacco. Intriguingly, these associations highlight a novel role of salivary microbiome metabolism in cardiovascular diseases through periodontium degeneration via the nitrate reduction and extracellular matrix degradation pathways. My second contribution focused on the role of geography, family relatedness, and genetics in shaping CHRISMB diversity. I investigated the associations between household, municipality and altitude of residence, heritability, and genetic marker associations (mbGWAS). I confirmed that cohabitation is a strong driver of microbiome similarity, while municipality and altitude of residence did not show strong associations. Siblings living apart had a more similar microbiota than unrelated and non-cohabiting individuals. Sixteen out of 142 taxa had a significant heritability component, while 34 had a significant household component. A mbGWAS Gene-level analysis resulted in one association between rare variants in the SRFBP1 and LOX genes locus and Selenomonas noxia. This work confirmed that host genetics and familial relationships has a modest but significant association with the salivary microbiome composition and that the environment and lifestyle are strongly associated. In summary, this thesis deepens our understanding of population-level factors associated with salivary microbiome variability, which can help design future hypothesis driven studies.

Tesis por compendio / [ES] El análisis del control genético del hospedador sobre su microbiota ha sido señalado recientemente como un tema prometedor en diferentes campos de estudio. La relación entre el holobionte hospedador-microbioma y los fenotipos en el ganado lechero podría conducir a nuevos conocimientos en los programas de selección genética. Dentro de esta tesis doctoral, se realizó la estimación y análisis a través de diferentes enfoques estadísticos con el objetivo de desentrañar el control genético del hospedador sobre la microbiota en ganado lechero. Además, se analizó el rasgo de concentración de metano como un fenotipo potencial para ser incluido en el programa de mejora de ganado lechero español. Mayor abundancia relativa de la mayoría de los eucariotas (principalmente protozoos ciliados y hongos) y algunas arqueas (Methanobrevibacter spp. Methanothermus spp. y Methanosphaera spp.) fueron factores de riesgo para ser clasificadas en la categoría alta. Se propuso un conjunto de modelos de ecuaciones estructurales (SEM) de tipo recursivo dentro de un marco de Cadenas de Markov Monte Carlo (MCMC) para analizar conjuntamente la relación hospedador-metagenoma-fenotipo. Se estableció un modelo bivariado no-recursivo como punto de referencia. La heredabilidad de CH4 se estimó en 0,12 ± 0,01 en ambos modelos, recursivo y no recursivo. Asimismo, las estimaciones de heredabilidad para la abundancia relativa de los taxones se superpusieron entre los modelos y variaron entre 0.08 y 0.48. Las correlaciones genéticas entre la composición microbiana y el CH4 variaron de -0,76 a 0,65 en el modelo bivariado no recursivo y de -0,68 a 0,69 en el modelo recursivo. Doce matrices de relación de microbiota (K) fueron construidas a partir de diferentes métricas de distancia del microbioma, con el objetivo de comparar su desempeño dentro de un marco de estimación de componentes de varianza para CH4 y toda la microbiota. Análisis de simulación (n = 1000) y datos reales fueron desarrollados considerando cuatro modelos posibles: un modelo genómico aditivo (GBLUP), un modelo de microbioma (MBLUP), un modelo de efectos genéticos y microbioma (HBLUP) y un modelo de efectos de interacción genético, microbioma y genético × microbioma (HiBLUP). Un nuevo término "Holobiabilidad" fue definido para referirse a la proporción de la varianza atribuible a los efectos del holobionte hospedador-microbioma. Las estimaciones a partir de datos reales usando HiBLUP variaron dependiendo de la K utilizada y estuvieron entre 0.15-0.17, 0.15-0.21 y 0.42-0.59 para heredabilidad, microbiabilidad y holobiabilidad, respectivamente. El conjunto de datos de microbioma fue agregado a través de análisis de componentes principales (PCA), en pocos componentes principales (PCs) que fueron utilizados como aproximaciones del metagenoma central. Parte de la variabilidad condensada en estos PC está controlada por el genoma de la vaca, con estimaciones de heredabilidad para el primer PC (PC1) de ~ 0,30 en todos los niveles taxonómicos, con una gran probabilidad (> 83%) de que la distribución posterior sea > 0,20 y con un intervalo de mayor densidad posterior al 95% (95% HPD) no conteniendo cero. La mayoría de las estimaciones de correlación genética entre PC1 y metano fueron grandes (>0,70) en todos los niveles taxonómicos, con la mayor parte de la distribución posterior (> 82%) siendo > 0,50 y con su 95% HPD no conteniendo cero. Estos resultados sugieren que todo el metagenoma del rumen regula recursivamente las emisiones de metano en las vacas lecheras, y que tanto el CH4 como las composiciones de la microbiota están parcialmente controladas por el genotipo del hospedador. Las variables agregadas (PC) propuestas podrían ser usadas en programas de mejora de animales para reducir las emisiones de metano en las generaciones futuras. / [CA] L'anàlisi del control genètic de l'hoste sobre la seva microbiota s'ha assenyalat recentment com un tema prometedor en diferents camps d'estudi. La relació entre el holobiont hoste-microbioma i els fenotips en bovins de llet podria conduir a nous coneixements en els programes de cria. Dins d'aquest doctorat es van realitzar tesis, estimacions i anàlisis mitjançant diferents enfocaments estadístics amb l'objectiu de desentranyar el control genètic de l'hoste sobre la microbiota en bestiar lleter. A més, es va analitzar el tret de concentració de metà com a fenotip potencial a incloure en el programa espanyol de cria de bestiar lleter. La major abundància relativa de la majoria dels eucariotes (principalment protozous i fongs ciliats) i algunes arquees (Methanobrevibacter spp. Methanothermus spp i Methanosphera spp.) Van ser factors de risc per classificar-se en les categories altes. Es va proposar un conjunt de models d'equacions estructurals (SEM) de tipus recursiu dins d'un marc de cadena Markov Monte Carlo (MCMC) per analitzar conjuntament la relació hoste-metagenoma-fenotip. Es van establir models no recursius com a referència. L'heretabilitat del CH4 es va estimar en 0,12 ± 0,01 en ambdós models, recursius i no recursius. De la mateixa manera, les estimacions d'heretabilitat de l'abundància relativa dels tàxons es van superposar entre models i van oscil·lar entre 0,08 i 0,48. Les correlacions genètiques entre la composició microbiana i el CH4 van oscil·lar entre -0,76 i 0,65 en els models bivariables no recursius i de -0,68 a 0,69 en els models recursius. Dotze matrius de relació de microbiota (K) de diferents mètriques de distància de microbiomes, amb l'objectiu de comparar el seu rendiment dins d'un marc d'estimació de components de variància per CH4 i anàlisi de microbiomes sencers en simulació (n = 1000, 25 rèpliques) i es van realitzar dades reals , considerant quatre possibles models: un model genòmic additiu (GBLUP), un model de microbioma (MBLUP), un model d'efectes genètics i microbiomes (HBLUP) i un model d'efectes d'interacció genètics, microbiomes i genètics × microbiomes (HiBLUP). Es va definir un nou terme "Holobiabilitat" per referir-se a la proporció de la variància fenotípica atribuïble als efectes holobiont del microbioma host. Les estimacions de dades reals mitjançant HiBLUP van variar en funció de la K utilitzada i van oscil·lar entre 0,15-0,17, 0,15-0,21 i 0,42-0,59 per heretabilitat, microbiabilitat i holobiabilitat, respectivament. El conjunt de dades de microbiomes es va agregar mitjançant l'anàlisi de components principals (PCA) en pocs components principals (PC) que es van utilitzar com a proxies del metagenoma principal. Part de la variabilitat condensada en aquestes PC està controlada pel genoma de la vaca, amb estimacions d'heretabilitat per a la primera PC (PC1) de ~ 0,30 a tots els nivells taxonòmics, amb una gran probabilitat (> 83%) de la distribució posterior> 0,20 i amb un 95% més alt interval de densitat posterior (95% HPD) que no conté zero. La majoria de les estimacions de correlació genètica entre PC1 i metà eren grans (>0,70) en tots els nivells taxonòmics, amb una gran part de la distribució posterior (> 82%)> 0,50 i amb un 95% de HPD que no contenia zero. Aquests resultats suggereixen que tot el metagenoma del rumen regula recursivament les emissions de metà en vaques lleteres i que tant el CH4 com les composicions de microbiota estan parcialment controlades pel genotip de l'hoste. Les variables agregades proposades (PC) es podrien utilitzar en programes de cria d'animals per reduir les emissions de metà en les generacions futures. / [EN] The analysis of the host genetic control over its microbiota has recently been pointed out as a promising theme in different fields of study. The relationship between the host-microbiome holobiont and phenotypes in dairy cattle could lead to new insights in breeding programs. Within this Ph.D. thesis, estimation and analysis through different statistical approaches were performed aiming to unravel the host genetic control over the microbiota in dairy cattle. Besides, methane concentration trait was analyzed as a potential phenotype to be included in the Spanish dairy cattle breeding program. Higher relative abundance of most eukaryotes (mainly ciliate protozoa and fungi) and some archaea (Methanobrevibacter spp. Methanothermus spp and Methanosphera spp.) were risk factors for being classified in the high categories. a set of structural equation models (SEMs) of a recursive type within a Markov chain Monte Carlo (MCMC) framework was proposed to jointly analyze the host-metagenome-phenotype relationship. Non-recursive models were set as benchmark. Heritability of CH4 was estimated at 0.12 ± 0.01 in both, the recursive and non-recursive, models. Likewise, heritability estimates for the relative abundance of the taxa overlapped between models and ranged between 0.08 and 0.48. Genetic correlations between the microbial composition and CH4 ranged from -0.76 to 0.65 in the non-recursive bivariate models and from -0.68 to 0.69 in the recursive models. Regardless of the statistical model used, positive genetic correlations with methane were estimated consistently for the 7 genera pertaining to the Ciliophora phylum, as well as for those genera belonging to the Euryarchaeota (Methanobrevibacter sp.), Chytridiomycota (Neocallimastix sp.) and Fibrobacteres (Fibrobacter sp.) phyla. Twelve microbiota relationship matrices (K) from different microbiome distance metrics were built, aiming to compare its performance within a variance component estimation framework for CH4 and whole microbiome analysis on simulation (n = 1000, 25 replicates) and real data were performed, considering four possible models: an additive genomic model (GBLUP), a microbiome model (MBLUP), a genetic and microbiome effects model (HBLUP) and a genetic, microbiome and genetic × microbiome interaction effects model (HiBLUP). A new term "Holobiability" was defined to refer to the proportion of the phenotypic variance attributable to the host-microbiome holobiont effects. Estimates from real data using HiBLUP varied depending on the K used and ranged between 0.15-0.17, 0.15-0.21 and 0.42-0.59 for heritability, microbiability and holobiability, respectively. The microbiome dataset was aggregated through Principal Component Analysis (PCA) into few principal components (PCs) that were used as proxies of the core metagenome. Part of the variability condensed in these PCs is controlled by the cow genome, with heritability estimates for the first PC (PC1) of ~0.30 at all taxonomic levels, with a large probability (>83%) of the posterior distribution being > 0.20 and with the 95% highest posterior density interval (95%HPD) not containing zero. Most genetic correlation estimates between PC1 and methane were large (>0.70) at all taxonomic levels, with most of the posterior distribution (>82%) being >0.50 and with its 95%HPD not containing zero. These results suggest that rumen's whole metagenome recursively regulate methane emissions in dairy cows, and that both CH4 and the microbiota compositions are partially controlled by the host genotype. The purposed aggregated variables (PCs) could be used in animal breeding programs to reduce methane emissions in future generations. / This research was financed by RTA2015-00022-C03-02 (METALGEN) project from the national plan of research, development and innovation 2013-2020 and the Department of Economic Development and Competitiveness (Madrid, Spain). We thank the regional Holstein Associations and farmers collaborating in the project. Computational support from the High-Performance Computing Centre in Galicia (Spain) is acknowledged. Alejandro Saborío-Montero acknowledges the scholarship from Universidad de Costa Rica for his doctorate studies which partially conducted to the progress of this study. / Saborío Montero, A. (2021). Study of the Host Genetic Control over the Ruminal Microbiota and their Relationships with Methane Emissions in Dairy Cattle [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/172633 / TESIS / Compendio

Memoria para optar al Titulo Profesional de Médico Veterinario / La microbiota intestinal corresponde a las poblaciones bacterianas que habitan en el sistema gastrointestinal de los animales y humanos, esta participa directamente en la estimulación del sistema inmune, en la síntesis de vitaminas y en la inhibición de poblaciones bacterianas nocivas para el huésped. En la producción avícola destaca el uso de variados antimicrobianos para el tratamiento de diversas enfermedades infecciosas, el efecto de estos antimicrobianos sobre la microbiota intestinal en términos de resistencia y variaciones poblacionales ha sido escasamente estudiado en aves de postura. Por esto es que el objetivo del presente trabajo fue estudiar la variación de poblaciones intestinales de Escherichia coli, Enterococcus spp. y Lactobacillus spp. en aves de postura expuestas a un tratamiento con enrofloxacino y además medir la variación en los niveles de resistencia bacteriana en las poblaciones de E. coli y Enterococcus spp. en su rol de bacterias indicadoras de resistencia. Se utilizaron 30 gallinas ponedoras raza leghorn las cuales fueron separadas en un grupo tratado (n=15) y control (n=15), el grupo tratado recibió enrofloxacino 5% por vía oral y el grupo control un placebo (agua destilada) durante 10 días. A los 3, 7 y 15 días posteriores al tratamiento se obtuvieron muestras de contenido intestinal a partir de íleon y ciego de los animales, las cuales se sembraron y cultivaron en los diferentes medios de cultivo para el posterior conteo de colonias intestinales. A partir de estas muestras se aislaron 99 cepas de E. coli y 90 cepas de Enterococcus spp. para el análisis de la variación en los niveles de resistencia frente a amoxicilina, cefotaxima, enrofloxacino, ácido nalidíxico, estreptomicina, oxitetraciclina y sulfametoxazol + trimetoprim para E. coli; y frente a amoxicilina, enrofloxacino, eritromicina y oxitetraciclina para Enterococcus spp. En el caso del conteo de colonias bacterianas solo se encontraron diferencias significativas posteriores al tratamiento en las colonias de Lactobacillus spp. En el caso de los niveles de resistencia posteriores al tratamiento con enrofloxacino para las cepas de E. coli, estos aumentaron respecto del grupo control frente a amoxicilina, enrofloxacino, ác nalidíxico, estreptomicina y sulfametoxazol + trimetoprim. En el caso de las cepas de Enterococcus spp. la resistencia se incrementó solo en el caso de enrofloxacino, mientras que para eritromicina y oxitetraciclina disminuyeron respecto al control. De acuerdo a estos resultados se puede concluir que la utilización de antimicrobianos afecta directamente a la microbiota intestinal tanto en términos de variación en las poblaciones bacterianas como también en relación a los niveles de resistencia antimicrobiana de estas mismas

The determination of a symbiotic association as beneficial requires good assessment of the costs and benefits involved in the maintenance and transmission of these microbes across generations. In social insects, symbiotic associations are complex as they may involve a network of interactions between individual and colony that result in stable associations over evolutionary time. My goal was to investigate the roles of behavior and morphology as integrators that have enabled the benefits of harboring gut microbes to reach both adult and growing brood in a colony. To achieve this goal, I used turtle ants (Cephalotes), a group that has co-evolved with their gut microbes since the Eocene (Sanders et al. 2014) and that shows a variety of morphological and behavioral specializations likely connected to this symbiotic association. In my dissertation I present evidence that the specialized behavior and morphology of Cephalotes are indeed strongly associated with mechanisms that ensure stability of ant-gut microbe interactions over evolutionary time. In Appendix A, I show that a valve between the crop and midgut (proventriculus) of C. rohweri works as a filtration organ, capable of excluding possible pathogens from the mostly liquid diet consumed by turtle ants. In addition, the proventricular filter is also associated with the structuring of the gut microbiota, dividing it in at least two great groups: one upstream and another downstream of the proventriculus. Through behavioral observation and microscopy, we also suggest that the formation of the proventricular filter is only complete after young and sterile workers (callows) are inoculated with the core group of symbiotic bacteria. In Appendix B, I present results confirming that the compartmentalization of gut microbiota is also present in the congener C. varians. I compare these results with previously published data, defining the meta-communities of the gut microbiota, and demonstrate that the previously recognized core microbiota is composed of compartment-specific microbial communities and lineages. This compartmentalization of the gut microbiota is similar to the one found in highly specialized herbivores, both vertebrates and invertebrates. In addition, I also sampled the infrabuccal pocket, a characteristic oral cavity found in ants and that has largely been ignored in studies of gut symbiosis. Based on my results, I provide compelling evidence that hindgut microbes are inoculated into food particles trapped in the infrabuccal pocket, aiding in digestion of this substrate. Moreover, I suggest that trophallaxis olays a central role in inoculation of food and individuals, and might be responsible for the transmission of nutrients that are predicted to result from the gut bacteria metabolism. Finally, in Appendix C I characterize abdominal trophallaxis in C. rohweri to gain insight on its role in the context of symbiotic associations with gut microbes. I show that the hindgut contents, including bacteria, can be transmitted via abdominal trophallaxis. This interaction is found to occur between all combinations of major and minor workers, in addition to callows. The rate of solicitation of abdominal trophallaxis is higher when individuals are protein starved, indicating that hindgut content may also be nutritive. Using shotgun metagenomic data, we show that the microbiota present in the infrabuccal pocket (mostly hindgut bacteria) are indeed capable of re-utilizing nitrogen and synthesizing essential amino acids, in addition to breaking down plant material. We also report that oral trophallaxis is a possible route for transmission of crop-specific bacteria for callows, as this group has performed oral trophallaxis at a relatively higher rate than older workers. Put together, these results highlight the importance of nestmate interactions and gut morphology in the establishment and maintenance of symbiotic microbes in a social insect, introducing a new model for explaining the evolution and functioning of ant-gut microbe symbiosis.

Metabolic syndrome (MetS) is a group of obesity-related metabolic abnormalities that predisposes to type II diabetes mellitus (T2DM) and cardiovascular disease. The dramatic increase in incidence of obesity and MetS over the last 25 years amidst relatively constant host genetics supports the role for non-genetic factors such as gut microbiota composition as an important contributor to the development of these disorders. Microbiota can interact with the host, in a manner influenced by genetics and diet that result in low-grade chronic inflammation. A critical risk factor for the pathogenesis of obesity and its related MetS involves alteration of gut microbiota composition with increased innate immune system activation in the intestine increasing risk. Diet-induced obesity is often modeled by comparing mice fed high-fat diet (HFD), which is made from purified ingredients, vs. normal chow diet (NCD), which is a low-fat assemblage of relatively unrefined plant and animal products. The mechanism by which HFD promotes adiposity is complex but thought to involve low-grade inflammation and altered gutmicrobiota. Here, I investigated the extent to which physiological effects to which HFD-induced adiposity is driven by fat content per se vs. other factors that differentiate HFD vs. NCD or other compositionally-defined diets (CDD) and, moreover sought to define the mechanisms that drove such effects. Relative to NCD, HFD, and to a lesser but nonetheless significant extent, CDD induced increased adiposity in addition to a rapid and marked loss of cecal and colonic mass, indicating that both lipid content and other aspects of HFD are obesogenic.CDD-induced effects were not affected by adjusting dietary protein levels/types but could be largely eliminated by exchanging insoluble fiber (cellulose) for soluble fiber (inulin). Moreover, replacing cellulose with inulin in HFD protected mice against decreased intestinal mass, hyperphagia and increased adiposity. Such protective effects of inulin correlated with increased levels of short-chain fatty acids, which are the products of bacterial fermentation of inulin. Lack of a microbiota, achieved by use of germ-free mice prevented generation of SCFA and eliminated the beneficial effects of inulin. Together, these results indicate that HFD-induced obesity is promoted by its lack of soluble fiber, which, when present, supports microbiota-mediated intestinal epithelia homeostasis that prevents inflammation driving obesity and MetS.

<p>Despite a largely static DNA sequence, our genomes are incredibly malleable. Comparative studies of chromatin features between different cell types, tissues, and species have revealed tremendous differences in how the genome is accessed, transcribed, and replicated. However, how the dynamics of chromatin accessibility contribute to development, environmental response, and disease status has only begun to be appreciated. In this work we identified chromatin accessibility changes by DNase-seq in three diverse processes: in granule neurons of the developing cerebellum, with intestinal epithelial cells in the absence of a normal microbiota, and with myelogenous leukemia cells in response to histone deacetylase inhibitor treatments. In all cases, we coupled these analyses with RNA-seq assays to identify concurrent transcriptional changes. By mapping the changes to these genome-wide signals we defined the contribution of local chromatin structure to the transcriptional programs underlying these processes, and improved our understanding of their relation to other chromatin changes like histone modifications. Furthermore we demonstrated use of the strongest accessibility changes to identify transcription factors critical for these processes by finding enrichment of their binding motifs. For a few of these key factors, depletion or overexpression of the protein was sufficient to regulate the expression of predicted target genes or exert limited chromatin accessibility changes, demonstrating the functional significance of these proteins in these processes. Together these studies have informed our understanding of the role chromatin accessibility changes play in development and environmental responses while also proving their utility for key regulator identification.</p> / Dissertation

Suite à l’interdiction de l’utilisation des antibiotiques facteurs de croissances dans l’alimentation animale en 2006, des méthodes alternatives sont proposées aux éleveurs, notamment les phytobiotiques. Cependant, l’efficacité de ces molécules, telle que décrite dans la littérature, est variable, et leur modes d’action est mal connu. Nous avons pu mettre en évidence un effet important des conditions d’élevage dans la réponse des poulets aux deux modèles de phytobiotiques étudiés. Ils améliorent les performances zootechniques des animaux placés dans des conditions défavorables à leur croissance. Dans des conditions très dégradées, l’utilisation couplée de phytobiotiques portant des activités biologiques variées s’est avéré plus efficace. De plus, les modèles étudiés comprenant de nombreuses molécules exerçant une activité antibactérienne in vitro, nous avons étudié in vivo la réponse du microbiote digestif à leur ingestion par l’animal. Des modifications du microbiote digestif ont été observées et pourraient en partie expliquer l’amélioration de leur croissance. / The banning of antibiotic growth promoters for livestock feeding led to the development of several alternatives, including phytobiotics. However, their efficiency as growth promoters is inconstant between scientific studies and their mechanisms of action are poorly known. In the present work, the rearing conditions strongly affect the efficiency of two phytobiotics models. They improved the chickens’ growth performance when the rearing conditions were unfavorable to the growth. When strongly deteriorated, the combination of phytobiotics showing various biological activities was more efficient. As the phytobiotics used in the present study contains numerous molecules with an in vitro antibacterial activity, the impact of those phytobiotics on chickens’ digestive microbiota was studied in vivo. Changes in chickens’ digestive microbiota were observed which could partly explain the chickens’ growth improvement.