Woody breast (WB) is a meat quality problem that has caused significant economic losses for the poultry industry. Ross × Ross 708 chicks were randomly assigned to a 3 (diet) × 2 (cocci challenge) × 2 (sex) factorial arrangement of treatments. The three diets included the control diet (corn-soybean meal basal diet), antibiotic diet (basal diet + 6.075 mg bacitracin /kg feed), and probiotic diet (basal diet + 2.2 × 108 CFU Bacillus subtilis PB6 /kg feed). Birds in the cocci challenge treatment group received 20 × the live cocci vaccine as an inoculum on d 14. Growth performance and WB score were measured to understand the effects of management factors (diet and coccidiosis) on broiler growth and WB development. Results indicated that dietary bacitracin and Eimeria spp. increased WB incidence, body weight, and growth rate. Bacillus subtilis increased WB incidence in male broilers without affecting body weight and growth rate. The association of the development of the internal organs and skeletal muscle with WB myopathy incidence in broilers were evaluated. The digestion organs (proventriculus and gizzard) and the skeletal muscles (drumsticks, thighs, and wings) developed at lower rates in birds with WB. In addition, the effects of the dietary and challenge interventions on the gut microbiota diversity and composition associated with WB in broilers were investigated. Results showed that cocci challenge altered gut microbiota composition and various biosynthetic pathways. Maintaining a healthy gut ecosystem is critical for the reduction of WB incidence in broilers. Gene expression related to oxidative stress, gut barrier function, and inflammation in jejunal mucus was investigated. Results showed that WB is related to decreased mucin expression (MUC6) in mucus, indicating a correlation between WB incidence and a lessening of the secretion of gel-forming mucin. In conclusion, dietary antibiotic and probiotic and challenge intervention strategies increased WB incidence, and microbiota composition and gut health gene expression differed in broilers exhibiting WB myopathy.

No description available.

Antagonistic interactions between competing species of bacteria are an important driver of bacterial community composition in the human gut microbiota. Of particular significance is the role of the type six secretion system (T6SS), which many species of Gram-negative bacteria use to kill competitor bacteria in a contact-dependent manner. T6SSs are syringe-like nanomachines that function to deliver antibacterial toxins into susceptible competitors. Many bacteria present in the human gut microbiota possess an extremely potent T6SS that is capable of rapidly eradicating nearby bacteria. Remarkably, however, species of beneficial bacteria that coexist in the gut are often resistant to T6SS attack by their neighbours. This resistance is mediated by bacterial immunity proteins that block the activity of the antibacterial toxins delivered by the T6SS. Intriguingly, past studies have shown that the widespread T6SS-mediated competition in the gut has led to the acquisition of repertoires of immunity genes across different bacterial strains. By examining available human gut metagenomes, I identified a putative immunity locus, named I2, in a species of gut bacteria. This locus is located downstream of its cognate T6SS toxin-encoding locus, E2, and I show when co-expressed with E2 in E. coli, it protects against E2 mediated-toxicity. Additionally, I show that four gut-derived I2 homologues bearing sequence identity levels to I2 ranging from 38% to 75% are equally capable of abrogating E2 toxicity. Using quantitative biophysical measurements, I also show that these I2 homologues physically bind E2 equally tightly pointing to the potential molecular mechanism of toxin neutralization. Lastly, through mutagenesis experiments, I found that the E2-I2 interaction is likely mediated by electrostatic forces between a small number of residues found in the interaction interface of the two proteins. Overall, these findings demonstrate that a human gut microbiome encoded type VI secretion system effector can be neutralized by divergent immunity proteins. / Thesis / Master of Science (MSc)

Type II Diabetes Mellitus (T2D) and cardiovascular diseases (CVD) are non-communicable chronic diseases that involves impairments in glucose metabolism and vascular function. Multiple factors may increase the risk for T2D, including but not limited to genetics, obesity and lifestyle, such as physical inactivity and diet. The gut microbiota, the human's largest population of microorganisms, plays an essential role in health and disease. The physiology and function of the gastrointestinal tract can be influenced by the diet. Phosphatidylcholine (PC), a source of choline in the diet, is rich in Western-type diets. Gut microbiota metabolize choline to trimethylamine (TMA) which circulates and is oxidized in the liver to form trimethylamine N-oxide (TMAO). As a result, ingestion of PC or choline could increase levels of TMAO. Preclinical studies indicate a role of TMAO in the development of atherosclerosis. Likewise, multiple observations support a potential role of TMAO in the development of insulin resistance and T2D. Much of the research has been conducted on rodent models, while others are observational human studies. Whether acute and short-term increases in TMAO contribute to impairments in insulin sensitivity in humans remains unknown. To address this, we performed two studies utilizing a double-blind, placebo controlled, crossover design. Eligible participants consumed a 1000mg/day dose of choline bitartrate and placebo (maltodextrin) the night before each testing session (for the acute choline study) or for 4 weeks (for the short-term choline ingestion study). Oral glucose tolerance test, continuous glucose monitoring, flow-mediated dilation, and applanation tonometry was performed the day after the acute choline load and before and after the short-term choline ingestion period. We hypothesized that gut microbiota-generated increase in TMAO will impair insulin sensitivity, glucose tolerance, endothelial function and arterial stiffness in healthy sedentary humans. Following acute choline ingestion, significant increases in plasma TMAO (p = 0.013) and choline (p = 0.003) were evident. There was no statistically significant difference in insulin sensitivity, glucose tolerance or in any of the endothelial function and arterial stiffness measurements. Four weeks of 1000mg choline ingestion per day, significantly increased plasma (p = 0.042) and urine (p = 0.008) TMAO concentrations compared to the placebo. However, no significant differences were observed for any other measurements of insulin sensitivity, glucose tolerance, glycemic variability, endothelial function, and arterial stiffness. More research is needed to elucidate the mechanisms behind the mechanistic observations between elevated TMAO concentrations and T2D and CVD. / Doctor of Philosophy / Type 2 diabetes mellitus (T2D) and cardiovascular diseases (CVD) increase the risk of all-cause mortality. Choline is a nutrient that can be found in foods such as red meat, dairy, fish, and eggs. Choline is metabolized from bacteria in our gut and a metabolite called trimethylamine (TMA) is formed. TMA is then oxidized in the liver and trimethylamine-N-oxide (TMAO) is produced. A Western-type diet is rich in red meat, dairy, fish, and eggs and has been shown to increase production of the compound TMAO. Preclinical studies have suggested a causal role of TMAO in atherosclerosis and T2D and elevated plasma TMAO concentrations have been associated with an increased risk for CVD and T2D in observational studies. However, the causal nature of this relationship in humans is unknown. The studies described herein aimed to investigate the effects of increases in TMAO on insulin sensitivity and vascular function in healthy adults. The first study tested the effect of increasing TMAO on insulin sensitivity, glucose tolerance, and vascular function following an acute choline load (1000mg) and placebo (carbohydrate) the night before each testing session. In the second study, we examined the effect of increasing TMAO on insulin sensitivity, glucose tolerance, and vascular function in healthy adults, following a short-term choline load (1000mg/day) and placebo (carbohydrate) for 4 weeks. Acute and short-term choline ingestion significantly increased plasma TMAO concentrations. No significant differences were observed following acute or short-term choline ingestion for any measurement of insulin sensitivity, glucose tolerance 24-hout glycemic variability, vascular function., and arterial stiffness.

Systemic lupus erythematosus (SLE) is a multi-system autoimmune disease with no known cure. The crosstalk between the gut microbiota and the immune system plays an important role in the tolerance induction to self-antigens both in the intestinal mucosa and at the systemic level. The MRL/lpr mouse model exhibits lupus-like symptoms early in life due to multiple SLE susceptible loci of the MRL background, plus the Faslpr mutation that offers an accelerated model. Recently, we experienced a loss of disease phenotype in our in-house colony compared to the previous published phenotype of MRL/lpr mice. We thus compared mice newly obtained from The Jackson Laboratory (JAX) with our in-house MRL/lpr mice and found that the phenotypic drift, most significantly the attenuation of glomerulonephritis, was present in both colonies. In addition, while JAX mice and mice in our colony are genetically identical, there were minor differences in disease that might be due to differences in splenic microRNAs and the gut microbiota. Once confirming that our MRL/lpr mouse model was as good as that from JAX, we continued our investigation of the role of Lactobacilli in the pathogenesis of lupus-like disease in MRL/lpr mice. We previously published that the mixture of Lactobacillus reuteri (L. reuteri), L. oris, L. johnsonii, L. gasseri, and L. rhamnosus significantly attenuated disease in MRL/lpr mice by restoring the imbalance between regulatory T cells and T helper-17 cells. To further understand the role of Lactobacillus spp., we treated MRL/lpr mice with the combined culture supernatant of the 5 strains containing secreted metabolites, given that the metabolites may induce an immunosuppressive response. The results showed significant attenuation of the inflammation of the spleen and renal lymph nodes similar to the effect of the bacteria themselves. There was also a trending decrease of double-stranded DNA autoantibodies with the combined supernatant. We thus tested the strains individually but none was able to recapitulate the effect of the bacterial mixture. This suggests cell-to-cell contact among different strains of lactobacilli may be required in ameliorating the disease. With these results, we now have a better understanding of the role of probiotic Lactobacillus spp. against SLE. Future investigations will focus on the potential therapeutic effect of Lactobacillus spp. as a combination. Additionally, our group generated a Cx3cr1-deficient MRL/lpr mouse which exhibits a distinct phenotype of exacerbated glomerulonephritis with concurrent change of the gut microbiota composition compared to Cx3cr1+/+ MRL/lpr littermates. Interestingly, upon correction of the gut microbiota with Lactobacillus administration, the phenotype of exacerbated glomerulonephritis was reversed, suggesting that CX3CR1 controls glomerulonephritis in MRL/lpr mice through a gut microbiota-dependent mechanism. In addition, a collaborative project revealed that Cx3cr1 deficiency-mediated pathogenic mechanisms also contributed to SLE-associated cardiovascular disease in MRL/lpr mice. The results of these studies will lead to the identification of new therapeutic targets for the treatment of two severe manifestations, glomerulonephritis and cardiovascular disease, that together account for most of the morbidity and mortality in SLE. / Doctor of Philosophy / Systemic lupus erythematosus (SLE) is an autoimmune disease with no known cure. Commensal microbiota, mostly bacteria living in our gut, and the immune system have a strong relationship in maintaining a healthy state of the gut as well as the whole body. Alterations in the gut microbiota, known as dysbiosis, can facilitate SLE in human and animal models. Current treatments for SLE are primarily focused on using immunosuppressants, but the side effects are still a concern. The use of long-term nonselective immunosuppressant conducts a higher incidence of severe infections in SLE patients. It is thus necessary to develop new approaches and treatments against SLE. My dissertation research is focused on understanding how commensal bacteria influence in the pathogenesis of SLE. My studies have shown that environmental factors can manipulate the gut microbiota leading to different disease outcomes. In addition, following upon previously published studies from our laboratory, I have delineated the mechanism how a mixture of probiotic Lactobacilli can exert a beneficial effect against lupus. Finally, I have revealed a new, CX3CR1-mediated mechanism through which the gut microbiota controls kidney disease in the MRL/lpr lupus-prone mouse model.

The increasing regulation of antimicrobial use in agriculture has driven the search for alternative solutions that support livestock health and production. Essential oils (EO) and prebiotics have recently gained attention as potential alternative supplements due to their antimicrobial properties (benefits for gut health) and ability to improve production parameters in livestock. This study evaluates the impact of a commercially available blend of EO and prebiotics on laying hen production parameters, egg quality, and Gastrointestinal microbiota composition as a possible substitute for antibiotic growth promotors (AGPs). Sixty Hy-Line W-80 laying hens, aged 60 weeks, were divided into four dietary treatment groups: 1) a corn-soybean meal-based basal diet (control), 2) the control diet mixed with 0.5 kg EO (low EO), 3) the control diet mixed with 1.0 kg EO (High EO), 4) the control diet supplemented with 0.5 kg prebiotics (prebiotic). Each diet was administered for 12 weeks, and phased feeding did not occur. Egg production and feed intake were measured weekly, egg quality was measured biweekly, bird body weight was measured monthly, and microbiome samples from both the ileum and ceca were collected at the conclusion of the feeding trial. Repeated measures ANOVA was used to analyze the data for egg production, egg quality, and feed intake using the GLIMMIX function in SAS (9.4). Microbiome samples were processed and analyzed differently. Briefly, 16s rDNA sequencing was conducted on the NovaSeq platform using paired-end reads. Microbiome data underwent quality control and chimera filtering using DADA2. Clean data was then used to construct operational taxonomic units (OTU), and proceed with diversity analysis, species classification annotation, and differential analysis. Taxonomic classification was performed using SILVA (release 138) and NT-16s databases with confidence level set at >0.07. Differential abundance analysis was conducted based on the relative abundance table. Fisher's exact test, Mann-Whitney U, and Kruskal-Wallis tests were used for statistical differences testing. Results showed that prebiotic supplementation negatively affected both body weight (p0.05) on these metrics. Prebiotic-fed hens also exhibited reduced egg production (p = 0.002) compared to control and EO diets. Although egg weight, yolk color, yolk weight, and albumen height remained consistent across treatments (p>0.05), external egg quality assessments revealed significant differences in eggshell thickness and breaking strength between the low and high EO diets (p = 0.01; p = 0.0003, respectively), though these treatments were not significantly different when compared to the control diet. Microbial analysis showed higher microbial diversity in the ceca when compared to the ileum (p < 0.001), with a highly dominant presence of the Lactobacillalesgenus in the ileum. Notably, high EO diets significantly increased Lactobacillus coryniformis (p = 0.009) and Lactobacillus capillatus (p = 0.04) compared to the control diet. Clostridium sensu stricto (mean 0.011) and Salmonella bongori (mean 0.001) were witnessed in control diet birds, while these microorganisms were absent from the high EO and prebiotic diet fed birds. Lastly, this feeding trial observed that the vast majority of potentially pathogenic, anaerobic, biofilm former, and gram-negative microorganisms are found in the ceca. In contrast, aerobic, facultative anaerobic, and mobile microorganisms are found in the ileum. These findings suggest that while EO supplementation alone does not enhance production parameters or egg quality compared to standard diets, it could support beneficial microbiota, offering a promising route to reduce AGP reliance and mitigate antibiotic resistance in livestock production.

Le microbiote intestinal, c'est-à-dire l'ensemble des micro-organismes résidant dans l'intestin, a un impact majeur sur la santé de l'hôte. Certains d'entre eux sont notamment impliqués dans l'apparition et la progression du cancer colorectal (CCR). Le CCR est responsable de 700 000 décès par an dans le monde, ce qui en fait la quatrième cause de mortalité par cancer : un Canadien sur 13 et une Canadienne sur 16 seront touchés par le CCR au cours de leur vie. Il a été démontré que l'apparition du cancer colorectal peut être favorisée par des facteurs alimentaires, en raison de leur influence sur la composition du microbiote intestinal. En outre, l'utilisation fréquente d'antibiotiques est une source majeure de perturbation de l'écosystème intestinal. Le rôle du microbiote intestinal dans l'apparition possible et la promotion du CCR est une question dont les mécanismes ne sont encore que partiellement compris. Il a été démontré que les bactéries pathogènes se développent dans un environnement riche en fer via l’augmentation de leur virulence. Les patients atteints de CCR reçoivent souvent des suppléments de fer par voie orale pour traiter l'anémie liée au CCR, une affection très répandue dans cette population. En outre, lors de l'ablation chirurgicale du CCR, des antibiotiques oraux sont administrés pour réduire le risque d'infection, ce qui entraîne une réduction de la quantité de micro-organismes dans l'intestin. Plus généralement, une proportion importante de la population mondiale reçoit des suppléments de fer et l'utilisation d'antibiotiques est fréquente. Par conséquent, le microbiote intestinal est fréquemment soumis à des perturbations qui peuvent être délétères. L'objectif de ce travail était d'étudier le rôle du fer sur la cancérogénicité du côlon à travers l'hypothèse d'un effet médié par le microbiote intestinal. Le travail présenté démontre dans un modèle de souris, qu'en cas de supplémentation orale en fer après un traitement antibiotique, il y a une augmentation significative de 3 espèces bactériennes et de 4 fonctions microbiennes connues pour favoriser l'inflammation intestinale et/ou le CCR. En outre, il y a eu une diminution de la concentration fécale de butyrate, un produit de la fermentation microbienne, essentiel pour la santé intestinale et pour l'inhibition de la prolifération des cellules du CCR. Dans une deuxième série d'expériences, des souris ApcMin/+, un modèle murin de polypose intestinale, ont été soumises à un régime riche ou pauvre en fer. Il a été démontré que la carcinogenèse colorectale dépendait du microbiote intestinal. Plus précisément, les souris ApcMin/+ précolonisées avec le microbiote intestinal de patients atteints de CCR, mais pas avec des contrôles sains ou murin, ont montré une progression accélérée du CCR dans le groupe recevant un supplément de fer par voie orale. En particulier, les souris précolonisées avec le microbiote intestinal de patients atteints de CCR ont développé davantage de tumeurs coliques de plus grande taille, une prolifération accélérée des cellules épithéliales et des carcinomes invasifs lorsqu'elles étaient supplémentées en fer. Ces effets s'accompagnent d'une diminution unique de l'abondance des bactéries bénéfiques. Ces modifications de la composition du microbiote intestinal en réponse au fer ont entraîné des changements délétères spécifiques dans les fonctions microbiennes intestinales liées à la progression et à l'initiation du CCR, ainsi qu'une diminution de la concentration de butyrate dans les selles. De plus, afin de démontrer un lien de cause à effet entre la promotion du CCR observée lors de la supplémentation orale en fer et l'abondance réduite des espèces bactériennes bénéfiques précédemment identifiées, des souris ApcMin/+précolonisées avec le microbiote intestinal de patients atteints de CCR ont été hebdomadairement supplémentées par voie orale. Ces interventions ont permis de réduire l'effet cancérigène sur le côlon d'une supplémentation orale en fer, par rapport à des souris non supplémentées nourries avec le même régime riche en fer, via l’augmentation de la concentration fécale en acides gras à chaine courte. Enfin, ces travaux ont permis de développer un outil bio-informatique, destiné à tous les chercheurs voulant représenter et analyser les données du microbiote. Il répond au besoin de permettre aux chercheurs, même ceux qui ne sont pas formés à la bio-informatique ou à l'analyse du microbiote, de produire des représentations graphiques de la composition du microbiote. Ces graphiques sont faciles à produire, prêts à être publiés et contiennent des informations utiles pour comprendre la dynamique du microbiote. De plus, un outil statistique spécialisé dans l'analyse des variations de l'abondance des communautés microbiennes est directement inclus, et les différences sont mises en évidence dans le graphique. En résumé, nous avons démontré qu'une supplémentation orale en fer chez des modèles de souris induit un changement délétère, pro-cancérigène, de la composition et de la fonction du microbiote intestinal qui dépendent du microbiote intestinal initial. Ces changements induits par le fer conduisent à une diminution des bactéries protectrices et des métabolites bactériens, induisant une augmentation de la carcinogenèse colorectale dans le modèle de souris ApcMin/+ précolonisées avec le microbiote intestinal CCR. Enfin, des outils d'analyse et de représentation du microbiote intestinal ont été développés et rendus accessibles. / The gut microbiota, i.e. all the microorganisms residing in the gut, have a major impact on host health. In particular, some of them are implicated in the onset and progression of colorectal cancer (CRC). CRC is responsible for 700,000 deaths a year worldwide, making it the 4th leading cause of cancer mortality: one out of 13 Canadian men and one out of 16 Canadian women will be affected by CRC during their lifetime. It has been shown that the onset of CRC can be promoted by dietary factors, through their influences on the composition of the gut microbiota. Furthermore, the frequent use of antibiotics is a major source of disturbance on the intestinal ecosystem. The mechanisms by which the gut microbiota may contribute to the onset and progression of the CRC remain only partially understood. It has been shown that pathogenic bacteria thrive in an iron-rich environment by increasing their virulence. CRC patients are often given oral iron supplementation to treat the CRC-related anemia, a highly prevalent condition in this population. Moreover, when CRC is surgically removed, oral antibiotics are given to reduce the risk of infection, leading to a reduction in the amount of microorganisms within the gut. More generally, a significant proportion of the world's population receives oral iron supplementation, and antibiotic use is frequent. As a result, the gut microbiota is frequently subject to perturbations that may be deleterious. By this work, the aim was to investigate the role of iron on colonic carcinogenicity through the hypothesis of a gut microbiota mediated effect. The presented work demonstrated, in a wild-type (WT) mouse model, that in the occurrence of oral iron supplementation after antibiotic treatment, there was a significant increase in 3 bacterial species and 4 microbial functions known to promote intestinal inflammation and/or CRC. Furthermore, there was a decrease in the fecal concentration of butyrate, a product of microbial fermentation, essential for intestinal health and for the inhibition of the CRC cell proliferation. In a second set of experiments, ApcMin/+ mice, a murine model of intestinal polyposis, were subjected to an iron-rich or iron-sufficient diet. A gut microbiota-dependent response in colonic carcinogenesis was demonstrated. Specifically, ApcMin/+ mice pre-colonized with gut microbiota from CRC patients, but not with healthy controls or murine gut microbiota, showed an accelerated cancer progression among the oral iron supplementation group. In particular, the mice pre-colonized with the CRC gut microbiota developed more colonic tumors of greater size, accelerated epithelial cell proliferation and invasive carcinomas when iron supplemented. These effects were accompanied with a unique decrease in the abundance of beneficial bacteria. These gut microbiota dependant changes in gut microbiota composition in response to iron led to specific deleterious shifts in gut microbial functions related to CRC progression and initiation, as well as a decrease in fecal butyrate concentration. Moreover, in order to demonstrate a causal link between the promotion of CRC observed during oral iron supplementation and the reduced abundance of the beneficial bacterial species previously identified, pre-colonized ApcMin/+ mice with gut microbiota from CRC patients were weekly orally supplemented. These interventions were able to reduce the colonic carcinogenicity effect of oral iron supplementation, comparatively to unsupplemented mice fed the same iron rich diet, through increased fecal short-chain-fatty-acids concentrations. Finally, these works allowed to develop a bioinformatic tool, intended for all researchers looking for representing and analyzing microbiota data. It fills the gap of allowing researchers, even the one not trained on bioinformatics or microbiota analysis, to produce graphical representations of microbiota composition. These graphs are easy to produce, publication-ready, and contain information useful for understanding the dynamics of the microbiota. In addition, a statistical tool specialized in the analysis of variations in microbial community abundance is directly included, and differences are highlighted within the graph. In summary, we have demonstrated that oral iron supplementation in mice models induces a deleterious, pro-carcinogenic, shift of the gut microbiota composition and function that are gut microbiota dependant. These iron-induced changes lead to decreased of protective bacteria and bacterial metabolites, inducing an increase in colorectal carcinogenesis in the ApcMin/+ mouse model pre-colonized with CRC gut microbiota. Finally, tools for analysis and representation of the gut microbiota have been developed and made accessible.

Systemic lupus erythematosus (SLE) is a multi-system autoimmune disease with no known cure. Despite years of study, the etiology of SLE is still unclear. Both genetic and environmental factors have been implicated in the disease mechanisms. Gut microbiota as an environmental factor and the immune system interact to maintain tissue homeostasis, but whether this interaction is involved in the pathogenesis of SLE is unclear. In a classical model of lupus nephritis, MRL/lpr, we found decrease of Lactobacillales but increase of Lachnospiraceae in the gut microbiota. Increasing Lactobacillales in the gut by suppling a mixture of 5 Lactobacillus strains improved renal function of these mice and prolonged their survival. Further studies revealed that MRL/lpr mice possessed a "leaky" gut, which was reversed by increased Lactobacillus colonization. Inside the kidney, oral Lactobacillus treatment also skewed the Treg-Th17 balance towards a Treg phenotype. To remove Lachnospiraceae that was higher in lupus-prone mice than controls, we administered vancomycin orally to MRL/lpr mice after disease onset from 9 to 15 weeks of age. Vancomycin functions by removing Gram-positive bacteria such as Lachnospiraceae but sparing Lactobacillus spp. The treatment during active lupus reshaped the gut microbiota and significantly ameliorated systemic autoimmunity and kidney histopathology at 15 weeks of age. However, when vancomycin treatment was initiated from a very early age, the beneficial effect was not observed. Strikingly, mice given vancomycin only at the young age exhibited an even worse disease outcome. Indeed, regulatory B (Breg) cells were found to be reduced after the vancomycin treatment at young age. Importantly, adoptive transfer of Breg cells at 6-7 weeks of age rescued the beneficial effect, which indicates that Breg cells, inducible by vancomycin-sensitive gut microbiota, plays an important role in suppressing lupus disease initiation and progression. Finally, we demonstrated that bacterial DNA from the gut microbiota might be the inducer of Breg cells, as bacterial DNA administration at young age reproduced the beneficial effect seen in the Breg adoptive transfer experiment. Future studies are required to examine the clinical efficacy of targeting gut microbiota as a novel treatment against SLE. / Ph. D. / Systemic lupus erythematosus (SLE) is a multi-system autoimmune disease with no known cure. SLE affects over 5 million people worldwide, especially women of childbearing age. Lupus nephritis is a manifestation of SLE occurring in the kidney which affects more than 50% of SLE patients and is a major cause of morbidity and mortality in SLE. Current treatments for lupus nephritis are primarily nonselective immunosuppressants, which can cause a higher incidence of severe infections. There is an imperative need for the development of new therapeutic strategies against SLE. Our research team was the first to describe the dynamics of gut microbiota in a mouse model of SLE. My dissertation research studying the role of gut microbiota in the pathogenesis of lupus-like disease in mice showed that there were both pathogenic and beneficial bacteria co-existing in the gut microbiota of lupus-prone mice. My studies revealed not only the effects of different bacteria on lupus pathogenesis, but also the immunological mechanisms by which they exert the effects. The results suggest that modulation of the gut microbiota through diet, probiotics, and/or prebiotics to selectively enhance the abundance and activity of beneficial bacteria may be an attractive strategy for disease prevention and treatment of SLE patients. Nevertheless, studies on human samples and clinical trials are required to confirm the translational application of this strategy.

No / Inflammatory bowel diseases are associated with increased risk of developing colitis-associated colorectal cancer (CAC). Epidemiological data show that the consumption of ω-3 polyunsaturated fatty acids (ω-3 PUFAs) decreases the risk of sporadic colorectal cancer (CRC). Importantly, recent data have shown that eicosapentaenoic acid-free fatty acid (EPA-FFA) reduces polyp formation and growth in models of familial adenomatous polyposis. However, the effects of dietary EPA-FFA are unknown in CAC. We tested the effectiveness of substituting EPA-FFA, for other dietary fats, in preventing inflammation and cancer in the AOM-DSS model of CAC. The AOM-DSS protocols were designed to evaluate the effect of EPA-FFA on both initiation and promotion of carcinogenesis. We found that EPA-FFA diet strongly decreased tumor multiplicity, incidence and maximum tumor size in the promotion and initiation arms. Moreover EPA–FFA, in particular in the initiation arm, led to reduced cell proliferation and nuclear β-catenin expression, whilst it increased apoptosis. In both arms, EPA-FFA treatment led to increased membrane switch from ω-6 to ω-3 PUFAs and a concomitant reduction in PGE2 production. We observed no significant changes in intestinal inflammation between EPA-FFA treated arms and AOM-DSS controls. Importantly, we found that EPA-FFA treatment restored the loss of Notch signaling found in the AOM-DSS control and resulted in the enrichment of Lactobacillus species in the gut microbiota. Taken together, our data suggest that EPA-FFA is an excellent candidate for CRC chemoprevention in CAC.

L'avènement des méthodes de séquençage moléculaire à large échelle a permis l'identification d'altérations du microbiote digestif spécifiquement associés à l'obésité notamment un ratio Bacteroidetes/Firmicutes diminué chez les obèses. Depuis, de nombreux travaux ont décrit de nouvelles altérations associées à l'obésité, notamment une augmentation des représentants du genre Lactobacillus mais l'ensemble de ces résultats sont souvent l'objet de controverses. Afin de clarifier si le genre Lactobacillus était associé à l'obésité, nous avons réalisé deux études cas témoins (la deuxième étant le prolongement de la première avec un effectif de 263 individus) qui nous ont permis d'identifier que les altérations du microbiote digestif sont plus reproductibles au niveau de l'espèce. A ce titre nous avons retrouvé une plus grande concentration de Lactobacillus reuteri dans le microbiote digestif de sujets obèses alors que les concentrations de Bifidobacterium animalis, Methanobrevibacter smithii et Escherichia coli étaient diminuées. Nous avons pu établir une relation dose-dépendante entre la concentration de Lactobacillus reuteri et l'indice de masse corporelle. Par ailleurs, nous avons réalisé une méta-analyse sur les résultats des études publiées et avons retrouvé une association entre les genres Bifidobacterium (6 études, 348 individus) et Methanobrevibacter (3 études, 195 individus) avec l'absence d'obésité (…) / The revolution of large scale molecular sequencing methods allowed the identification of specific alterations in the gut microbiota associated with obesity such as a decreased Bacteroidetes / Firmicutes ratio in obese individuals. Since then, many studies have described different alterations associated with obesity, including an increase in members of the Lactobacillus genus, but results are often controversial. To clarify whether the genus Lactobacillus was associated with obesity, we conducted two case-control studies (the second being the follow-up of the first study with a total of 263 individuals) allowing us to understand that gut microbiota alterations are more reproducible at the species level. We found a greater concentration of Lactobacillus reuteri in the gut microbiota of obese while concentrations of Bifidobacterium animalis, Methanobrevibacter smithii and Escherichia coli were reduced. We were able to establish a dose-dependent relationship between the concentration of Lactobacillus reuteri and body mass index. In addition, we performed a meta-analysis on the results of published studies and we found an association between the Bifidobacterium (6 studies, 348 individuals) and Methanobrevibacter (3 studies, 195 individuals) with absence of obesity. (…)