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

<p>Consumption of soy foods has been shown to provide beneficial health outcomes such as reduction of menopause symptoms, reduced risk of breast cancer and prostate cancer, improved cardiovascular health, and improved bone health. The mechanism hypothesized to be driving these outcomes is the conversion of the soy isoflavone daidzein into the metabolite equol by bacteria in the gut microbiome. Equol is an exclusively microbially produced metabolite with a high binding affinity to mammalian estrogen receptors. Not all humans harbor equol-producing microbes in their gut, and less than half of the population can be classified as equol producers. To date, soy feeding research published suffers from confounding factors that make assessing the causal impact of equol production in health difficult due to: (i) large interpersonal variation of the human microbiome and human genomes and that (ii) all lab-raised rodent models harboring natural microbiomes are highly efficient equol producers. In this study, we sought to establish a gnotobiotic mouse model harboring synthetic bacterial communities with divergent equol-producing capacities by designing two communities: the Equol(-) community and Equol(+) community. The Equol(-) community was designed to include ten bacterial strains commonly found within a human microbiome without equol-producing capacity<em>.</em> To create the Equol(+) community, the equol-producing bacteria <em>Adlercreutzia equolifaciens</em> was added to the Equol(-) community<em>.</em> Female and male germ-free C57BL/6 mice were colonized with either the Equol(-) or Equol(+) community for 4 weeks. Daidzein was administered by dietary supplementation (1.5% wt/wt daidzein) in a semi-purified diet containing fermentable fiber starting two weeks prior to bacterial colonization. As expected, equol was detected in the serum of mice colonized with the Equol(+) community, but not detectable in those colonized with the Equol(-) community. There were no sex differences detected in equol production. 16S rRNA gene sequencing of mouse cecal content revealed that ~50-80% of the strains from each community colonized within the mice at detectable levels. Strain-specific qPCR improved the detection of strains not observed consistently through 16S rRNA gene sequencing. Our results demonstrated that this model is reliable in producing the expected equol producing and non-equol producing phenotypes when colonized with the Equol(+) and Equol(-) communities, respectively. This model system can be utilized in a broad range of future studies to conclusively determine the causal impact of endogenous equol production in many areas, such as cardiometabolic health and bone health.</p>

Yes / Background: The changes that occur in the microbiome of aging individuals are unclear, especially in light of the imperfect correlation of frailty with age. Studies in older human subjects have reported subtle effects, but these results may be confounded by other variables that often change with age such as diet and place of residence. To test these associations in a more controlled model system, we examined the relationship between age, frailty, and the gut microbiome of female C57BL/6 J mice. Results: The frailty index, which is based on the evaluation of 31 clinical signs of deterioration in mice, showed a near-perfect correlation with age. We observed a statistically significant relationship between age and the taxonomic composition of the corresponding microbiome. Consistent with previous human studies, the Rikenellaceae family, which includes the Alistipes genus, was the most significantly overrepresented taxon within middle-aged and older mice. The functional profile of the mouse gut microbiome also varied with host age and frailty. Bacterial-encoded functions that were underrepresented in older mice included cobalamin (B12) and biotin (B7) biosynthesis, and bacterial SOS genes associated with DNA repair. Conversely, creatine degradation, associated with muscle wasting, was overrepresented within the gut microbiomes of the older mice, as were bacterial-encoded β-glucuronidases, which can influence drug-induced epithelial cell toxicity. Older mice also showed an overabundance of monosaccharide utilization genes relative to di-, oligo-, and polysaccharide utilization genes, which may have a substantial impact on gut homeostasis. Conclusion: We have identified taxonomic and functional patterns that correlate with age and frailty in the mouse microbiome. Differences in functions related to host nutrition and drug pharmacology vary in an age-dependent manner, suggesting that the availability and timing of essential functions may differ significantly with age and frailty. Future work with larger cohorts of mice will aim to separate the effects of age and frailty, and other factors. / This work was supported by the Canadian Institutes of Health Research (CIHR) through an Emerging Team Grant to RGB, CIHR Operating Grants to Langille et al. Microbiome 2014, 2:50 Page 10 of 12 http://www.microbiomejournal.com/content/2/1/50 SEH (MOP 126018) and RAR (MOP 93718), and a CIHR Fellowship to MGIL. Infrastructure was supported by the Canada Foundation for Innovation through a grant to RGB. RGB also acknowledges the support of the Canada Research Chairs program.

Bovine respiratory disease (BRD) is the leading cause of morbidity in feeder and stocker cattle, resulting in large impacts on economics of stocker and feedlot operations. One of the most effective means of controlling BRD is the mass administration of antimicrobials (AM) at arrival or “metaphylaxis”, potentially leading to increased antimicrobial resistance (AMR). Mannheimia haemolytica (MH), the most commonly isolated bacterial pathogen in BRD cases in feedlot cattle, has been shown to have integrative-conjugative elements (ICE), which are mobile genetic elements that have the ability to integrate themselves in the host genome. Notably, these ICE have been shown to contain multiple antimicrobial resistance genes (ARG) conferring resistance to antimicrobial classes used for BRD treatment. ICE have also been shown to be transferred between different genera. Since these ICE contain genes for resistance to multiple AM classes, administration of one AM could increase pressure for bacteria to transfer ICE for resistance to multiple drug classes; therefore, mass administration of AM may lead to increased isolation of multidrug resistant (MDR) MH and increase presence of resistance genes in the metagenome. Many NGS studies to date have used low numbers of cattle or pooled samples due to cost. Pooling is an acceptable strategy to increase number of units sampled, however sequencing depth per individual sample is decreased, and there is little evidence comparing pools to individual samples. In a trial involving high risk stocker cattle, tulathromycin metaphylaxis was associated with increased isolation of MDR MH, and this was associated with ICE related genes. Using pooled DNA extracted from NPS in these animals, which were shown to be acceptable for group level comparisons, metaphylaxis also increased ARG richness and diversity in these heifers; however, BRD treatment and time had a greater effect on the mircrobiome and resistome. Further work is needed to improve MH strain classification. These finding highlight the complexity of AMR research, because though tulathromycin had a clear effect on odds of isolation of MDR MH, metaphylaxis’ effects on the resistome and microbiome were more complex, and time and BRD contributed to greater change.

Les produits cosmétiques sont des substances utilisées pour entretenir ou modifier l'aspect des parties superficielles du corps humain (telles que la peau, les ongles ou les cheveux). Dans de nombreux pays d’Afrique et d’Asie et dans certaines communautés africaines immigrantes, plusieurs femmes et parfois des hommes utilisent des produits contenant des agents actifs tels que le mercure, l’hydroquinone et le propionate de clobétasol pour éclaircir leur peau. Ces principaux agents sont toxiques et leur présence dans les cosmétiques est règlementée, voire interdite, dans plusieurs pays. Dans notre étude, nous avons déterminé les concentrations de ces ingrédients dans plusieurs produits utilisés en Afrique de l’Ouest et au Canada. Nous avons également exploré l’effet de ces produits sur le microbiome cutané. Nos résultats révèlent que 68 à 84% des crèmes et 7.5 à 65% des savons dépassent les normes lorsqu’on considère l’interdiction de mercure, d’hydroquinone et de propionate de clobétasol et les concentrations déclarées sur les étiquettes ne sont pas souvent fiables. Selon la diversité de Shannon, il semble y avoir plus d’équitabilité, et donc moins de dominance dans le groupe des femmes utilisant les crèmes éclaircissantes que dans le groupe des femmes qui ne les utilisent pas. Par ailleurs, nous n’avons pas trouvé de différences significatives au niveau du microbiome cutané du groupe avec crèmes et sans crèmes au niveau du phylum et du genre. Cependant, d’autres méthodes plus approfondies avec plus d’échantillonnage pourraient révéler à des échelles plus fines (espèces, souches, etc.) l’effet de ces produits sur le microbiome cutané. / Cosmetics are substances used to maintain or change the appearance of external parts of the human body (such as skin, nails or hair). In many countries of Africa and Asia and in some immigrant African communities, many women and sometimes men use products containing active agents such as mercury, hydroquinone and clobetasol propionate to lighten their skin. These main active agents are toxic and their presence in cosmetics is regulated or even banned in several countries. In our study, we determined the concentrations of these ingredients in many products used in West Africa and Canada. In addition, we also explored the effect of these products on the skin microbiome. Our results reveal that 68 to 84% of cream and 7.5 to 65% of soaps exceed the standards when considering mercury, hydroquinone and clobetasol propionate ban in lightening products and concentrations of the three compounds declared on labels of soaps and creams usually did not correspond to concentrations actually measured. According to Shannon diversity index, there seems to be more evenness, less dominance in group of African women with creams than in those without cream. Moreover, we have not found significant differences in the skin microbiome of the group with creams and the one without creams at the phylum and genus level. However, additional detailed studies with more sampling methods could reveal at finer scales (species, strains, etc.) the effect of these products on the human skin microbiome.

Les diatomées sont des algues microscopiques qui contribuent à hauteur de 25% environ à la production primaire planétaire. Les diatomées sont très souvent entourées d’une flore bactérienne, avec laquelle de nombreuses interactions ont été documentées. Les génomes de diatomées contiennent par ailleurs de nombreux gènes dont l’origine prédite est bactérienne.Nous avons étudié Asterionella formosa, une diatomée pennée présente dans de nombreux lacs et cours d’eau à l'aide de données omiques. L’utilisation de la métagénomique a permis de reconstruire 30 génomes bactériens, utilisés pour prédire d'éventuelles interactions avec la diatomée. Le séquençage de la sous-unité 16S de l’ARN ribosomique a montré que les différentes espèces bactériennes avaient une abondance variable au cours des phases de croissance de la diatomée, et que certaines étaient plus souvent au contact de la diatomée que libres dans le milieu. Le génome d'A. formosa a ensuite été séquencé à l'aide de la technologie Pacbio et comparé à ceux d'espèces proches. Enfin, l’impact des bactéries sur les diatomées a été abordé sous l’angle de l’évolution et des transferts horizontaux de gènes, qui ont été prédits à partir des données transcriptomiques d’une centaine de diatomées marines.Ce travail représente une première étape dans l'étude de la communauté bactérienne associée à A. formosa. Des expériences complémentaires incluant l’utilisation de transcriptomique ou métabolomique sont maintenant envisageables. Les données collectées et/ou analysées dans ce travail contribuent d'ores et déjà à l’effort global de caractérisation génomique des diatomées. / Diatoms are ubiquitous microalgae that contribute approximately 25% to the primary production worldwide. Many interactions, either positive, neutral or negative, have been documented between diatoms and bacteria. Diatom genomes also harbor numerous genes of putative bacterial origin.We are studying Asterionella formosa, a freshwater pennate diatom. We characterized the community using a combination of omics and laboratory techniques. We reconstructed of the genome of the diatom as well as 30 individual genomes from co-cultured bacterial species and investigated metabolisms that could support diatom-bacteria interactions. 16S rRNA sequencing revealed that the abundance of some bacterial species was highly variable over the course of A. formosa growth. Some species seemed preferentially attached to the diatom while others were mainly free-living. Then, the reference sequence of the A. formosa genome was improved by additional long-read (Pacbio) sequencing. Last, relationships between diatoms and bacteria were investigated at a broader evolutionary scale, by looking at horizontal gene transfers using transcriptomic data of a hundred marine diatoms.This work is a first step in the study of the dynamic and complex bacterial community associated with the diatom A. formosa. The accurate identification and the reconstruction of the genome of these bacteria will enable further in silico predictions based on metabolic networks and new omics experiments using transcriptomic or metabolomic. This work already contributes to a global effort to study diatoms by the means of genomics.

Nous avons collecté et comparé les microbiotes et les microbiomes intestinaux de plusieurs dizaines de lézards de l’espèce Podarcis sicula, vivant dans des populations continentales et insulaires croates. L’une de ces populations présentait la particularité d’avoir subi un changement de régime alimentaire récent, une transition d’un régime insectivore vers un régime omnivore (à 80% herbivores) sur une période de 46 ans. Les analyses de diversité menées sur la région V4 de l’ARN ribosomique 16S de ces communautés microbiennes ont révélé que la diversité spécifique (diversité alpha) des microbiotes de lézards omnivores (enrichis en archées méthanogènes) excède celle des microbiotes de lézards insectivores. Les communautés microbiennes des lézards apparaissent en outre faiblement structurées : 5 entérotypes peuvent être identifiés au niveau du phylum, et 3 phyla majoraires (les Bactéroidètes, les Firmicutes et les Protéobactéries) sont présents dans cette espèce. Cependant, ni le régime alimentaire, l’origine spatiale ou temporelle, et le sexe des lézards ne se traduisent par des différences significatives et majeures dans les microbiotes. Des analyses linéaires discriminantes avec effet de la taille des OTUs et des reads des microbiomes fonctionnellement annotés indiquent plutôt que le changement de régime alimentaire de Podarcis sicula est associé à des changements ciblés dans l’abondance de certains composants du microbiote et du microbiome de ces lézards, nous conduisant à formuler l’hypothèse de changements ciblés des communautés microbiennes dans cet holobionte non-modèle, par opposition à des transformations plus radicales. Sur un plan plus théorique, cette thèse propose également des modèles de réseaux (réseaux de similarité de reads et graphes bipartis) susceptibles d’aider à approfondir les analyses des microbiomes. / We collected and compared intestinal microbiota and microbiomes from several Podarcis sicula lizards, which live in Croatian continental and insular populations. One of these populations has recently changed its diet over an 46 years timespan, switching from an insectivorous diet to an omnivorous one (up to 80% herbivorous). Diversity analyses of these microbial communities, based on the V4 region of their 16S rRNA, showed that the microbiota taxonomic diversity (or alpha diversity) is higher in omnivorous lizards (enrichment in methanogenic archaea) than in insectivorous ones. Besides, microbial communities seem weakly structured: 5 enterotypes are detected at the phylum level, and 3 major phyla (Bacteroidetes, Firmicutes and Proteobacteria) are present. However, neither diet, spatial or temporal origin, nor lizard gender correlate with significant differences in microbiota. Linear discriminant analyses with size effect, based on OTUs and functionally annotated reads from the microbiomes, suggest that Podarcis sicula diet change is associated to targeted changes of the abundance of some enzymes in the microbiomes. Such a result leads us to propose a hypothesis of targeted changes in the microbial communities of this non-model holobiont, instead of more radical transformations. On a more theoretical level, this thesis also proposes network models (Reads similarity networks and bipartite graphs) that can help improving microbiome analyses.

Le développement des plantes est conditionné par leurs interactions avec le microbiote racinaire, dont le fonctionnement repose sur des fonctions élémentaires partagées par plusieurs taxons, au sein de groupes fonctionnels. Certains de ces groupes incluent des PGPR (Plant Growth-Promoting Rhizobacteria), qui stimulent la croissance des plantes grâce à différentes fonctions phytobénéfiques. L'inoculation d'une PGPR peut avoir un impact sur la physiologie de la plante et sur les autres partenaires microbiens de la racine. D'ailleurs, une PGPR inoculée peut modifier la structure génétique du microbiote racinaire global, sans que l'on sache comment cet impact se concrétise au niveau de groupes fonctionnels particuliers. L'hypothèse de cette thèse est que les PGPR inoculées peuvent modifier la structure de communautés microbiennes fonctionnelles importantes pour le développement de la plante. Ces travaux ont évalué l'impact de l'inoculation de la PGPR Azospirillum lipoferum CRT1 sur la taille et/ou la diversité des diazotrophes, des producteurs d'1-aminocyclopropane-1-carboxylate (ACC) désaminase et des producteurs de 2,4-diacétylphloroglucinol (ainsi que de la communauté bactérienne totale) dans la rhizosphère du maïs cultivé en champ sous différents intrants azotés. Nos travaux ont montré que diazotrophes et producteurs d'ACC désaminase pouvaient être co-sélectionnés dans la rhizosphère du maïs, et que l'inoculation modifiait la composition taxonomique de ces groupes fonctionnels. En conclusion, l'inoculation de PGPR module la sélection rhizosphérique de taxons telluriques portant des fonctions phytobénéfiques, ce qui pourrait contribuer aux effets phytobénéfiques observés / Plant development is influenced by interactions established with root microbiota. Microbiota functioning relies on individual functions carried out by functional groups, which often contain multiple microbial taxa. Some of these groups include plant growth-promoting rhizobacteria (PGPR), which stimulate plant growth thanks to several plant-beneficial functions. PGPR inoculation may impact plant physiology and microbial partners of roots, and inoculated PGPR can modify the genetic structure of the root microbiota. However, it is not known how this impact materializes at the level of particular microbial functional groups. The hypothesis of this thesis is that inoculated PGPR will also modify the structure/composition of microbial functional groups important for plant development. This work assessed the impact of inoculation with the PGPR Azospirillum lipoferum CRT1 on the size and/or diversity of diazotrophs, 1-aminocyclopropane-1-carboxylate (ACC) deaminase producers and 2,4-diacetylphloroglucinol producers (as well as the total bacterial community) colonizing the maize rhizosphere in three fields and under different nitrogen fertilization regimes. Our work showed that diazotrophs and ACC deaminase producers could be co-selected in maize rhizosphere and that PGPR inoculation modified the taxonomic composition of functional groups. To conclude, PGPR inoculation modulates rhizospheric selection of microbial members of functional groups important for plant growth, which may mediate some of the plant-beneficial effects of PGPR inoculants

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