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.

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.

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.

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. (…)

O diabetes tipo 1 (DM1) é uma doença autoimune caracterizada pela destruição das células ? presentes nas ilhotas pancreáticas por linfócitos T autorreativos, especialmente Th1 e Th17, levando o indivíduo a um estado de hiperglicemia. Embora existam diversos estudos que abordam a resposta imune adaptativa no contexto do DM1, poucos trabalhos tentaram elucidar o papel da resposta imune inata no desenvolvimento da doença. Neste contexto, observamos que camundongos WT pré-diabéticos possuem um aumento significativo na expressão gênica e proteica do receptor AIM2 e de moléculas relacionadas à sua via de ativação e sinalização (Caspase-1, IL-1? e IL-18) nos linfonodos pancreáticos (LNPs) e no íleo. Posteriormente, foi verificado que camundongos deficientes do receptor AIM2 tornaram-se mais suscetíveis ao DM1, comprovado por elevados níveis de glicose sanguínea e menor produção de insulina em relação aos animais selvagens (WT) após a administração com estreptozotocina (STZ). Tal suscetibilidade está relacionada a um processo de disbiose e aumento da translocação de bactérias da microbiota intestinal para os LNPs de camundongos AIM2-/-. De maneira interessante, o inflamassoma AIM2 foi ativado apenas na presença de DNA fecal de animais diabéticos, que possui uma microbiota em disbiose, uma vez que resultou na produção significativa da citocina IL-1?. Também foi constatado que a ativação do receptor AIM2 na mucosa intestinal regulou a expressão gênica e proteica de proteínas de junção celular, peptídeos antimicrobianos e mucinas, como forma de minimizar a translocação de bactérias da microbiota para os LNPs. Adicionalmente, foi visto que a ativação do receptor AIM2 contribui para a indução de células Th17 intestinais, para a migração de neutrófilos no intestino, assim como para a expressão das citocinas IL-23, IL-17 e IL-22 no íleo. Por fim, mostramos que o receptor AIM2 modulou negativamente a ativação de células dendríticas expressando TLR4 e TLR9, que correlacionou com o aumento de células Tc1 patogênicas nos LNPs. De forma geral, nossos resultados demonstram que a ativação do receptor AIM2 na mucosa intestinal desempenha um importante papel em controlar a homeostase da microbiota intestinal, manter a integridade da barreira intestinal, e consequentemente. / Type 1 diabetes (T1D) is an autoimmune disease characterized by the destruction of ? cells present in the pancreatic islets by autoreactive T lymphocytes, especially Th1 and Th17, leading to a state of hyperglycemia. There are many studies that address the role of adaptive immune response, so only some studies have attempted to elucidate the role of the innate immune response in the context of T1D. In this regard, we observed that pre-diabetic WT mice have a significant increase in the gene and protein expression of the AIM2 receptor and in molecules related to its activation and signaling pathways (Caspase-1, IL- 1? and IL-18) in the pancreatic lymph nodes (PLNs) and in the ileum. Subsequently, it was verified that AIM2 receptor deficient mice became more susceptible to T1D, as proved by blood glucose levels and lower insulin production compared to wild-type mice (WT) after administration of streptozotocin (STZ). This susceptibility was related to a process of dysbiosis and increased translocation of bacteria from gut microbiota to PLNs in AIM2-/- mice. Interestingly, the AIM2 inflammasome was activated in the presence of fecal DNA from diabetic mice, which has a gut microbiota in dysbiosis, since resulted in significant production of IL-1?. It was found that activation of the AIM2 receptor in the intestinal mucosa regulated the gene and protein expression of tightjunction proteins, antimicrobial peptides and mucins in order to minimizing a bacterial translocation of the microbiota to the PLNs. In addition, it was seen that activation of the AIM2 receptor contributes to induction of intestinal Th17 cells, to neutrophil migration in the intestine, as well as for expression of IL-23, IL-17 and IL-22 cytokines in the ileum. Finally, we show that the AIM2 receptor negatively modulated the activation of dendritic cells expressing TLR4 and TLR9, which correlated with the increase of pathogenic Tc1 cells in the PLNs. In general, the results demonstrate that activation of the AIM2 receptor in the intestinal mucosa plays an important role in controlling the composition of gut microbiota homeostasis, maintaining the intestinal barrier function, and consequently reducing the bacterial translocation to the PLNs, conferring a protective effect to the immunopathogeny against to DM1.

Tidigare forskning har visat ett samband mellan vår tarmflora och vår fysiska hälsa, och idag görs även mycket forskning på om den även kan påverka vår mentala hälsa. Idag lider över fyra procent av världens befolkning av depression, och den här litteraturstudien har, genom att analysera sju studier och deras resultat, försökt få svar på frågan om probiotika kan lindra depression. Antingen som primär behandling eller som komplement till annan behandling. Den här litteraturstudien gav inga konkreta svar på den frågan, annat än att alla inblandade forskare är överens om att det behövs göra fler, längre och större studier innan man kan dra några slutsatser. / Previous research has shown a connection between our microbiota and physical health, and today a lot of research is also being done on whether it also can affect our mental health. Today, over four percent of the world's population suffers from depression, and this literature study has, by analysing seven studies and their results, attempted to answer the question of whether probiotics can alleviate depression. Either as primary treatment or as a supplement to other treatment. This literature study did not provide any definite answers to that question, other than that all the researchers involved in the studies analysed agree that more, longer and larger studies are needed before one can draw any conclusions.