O diabetes tipo 1 (DM1) é uma doença autoimune caracterizada pela destruição das células b presentes nas ilhotas pancreáticas por linfócitos T auto-reativos, 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, avaliamos o perfil de expressão e o papel do receptor NLRP1 na patogênese do DM1 experimental e em humanos. Nossos dados apontam que no modelo de DM1 induzido por STZ, NLRP1 possui um papel protetor no desenvolvimento da doença de forma independente da ativação do inflamassoma, através da inibição da translocação de bactérias para os linfonodos pancreáticos (LNPs), além de reduzir a diferenciação de células Th17 e Tc17 nos LNPs, o que foi correlacionado à diminuição de IL-17 no pâncreas. Posteriormente, analisamos o papel de NLRP1 em outro modelo experimental, o NOD (nonobese diabetic), onde descrevemos que NLRP1 também é expresso no desenvolvimento da doença. Por fim, avaliamos o papel de NLRP1 em pacientes com DM1, através da genotipagem desses pacientes para um polimorfismo com ganho de função em NLRP1, o rs12150220. Ao contrário do que acontece em camundongos, NLRP1 em humanos parece ter um papel patogênico, uma vez que detectamos mais células T produtoras de IL-17 em células mononucleares do sangue periférico de indivíduos com o polimorfismo, além de níveis elevados da citocina no soro. Em suma, nossos dados apontam para papéis distintos de NLRP1 em camundongos e humanos com DM1, sugerindo cautela ao tentarmos transpor os achados sobre o receptor em camundongos para a clínica. / Type 1 diabetes (T1D) is an autoimmune disease that is caused by the destruction of the pancreatic b cells by autoreactive T cells, especially Th1 and Th17, leading to a state of hyperglycemia. Even though there are several studies on the role of the adaptive immune response in T1D, little is known about the role of an innate immune response in the development of the disease. Thus, we investigated the role of NLRP1 in the pathogenesis of mouse and human T1D. Our data indicate that in STZ-induced T1D, NLRP1 exerts a protective role in the development of the disease in an inflammasome-independent pathway, through the inhibition of bacterial translocation to the pancreatic lymph nodes (PLNs), and inhibition of the differentiation of Th17 and Tc17 cells in the PLNs, which correlated with decreased levels of IL-17 in the pancreas. Then, we analyzed the role of NLRP1 in nonobese diabetic (NOD) mice. We demonstrate that NLRP1 is also expressed in the development of T1D in this murine model. Lastly, we evaluated the role of NLRP1 in T1D patients, by genotyping these individuals for a polymorphism with a gain-of-function in NLRP1, the rs12150220. Unlike murine NLRP1, NLRP1 in humans appears to be pathogenic, considering that we detected more IL-17-producing T cells in peripheral blood mononuclear cells in patients carrying the polymorphism, besides elevated levels of this cytokine in the serum. Overall, our data suggest distinct roles for murine and human NLRP1 in the context of T1D, suggesting carefulness when translating the findings from murine NLRP1 to the clinic.

A sequência de eventos bacterianos que ocorre durante a colonização do trato gastrointestinal pode afetar o futuro da saúde do hospedeiro, particularmente no que diz respeito à regulação do sistema imunológico. Um entendimento claro do processo de colonização do intestino humano neonatal nos países em desenvolvimento está faltando, porque os poucos estudos disponíveis foram, em sua maioria, realizados utilizando técnicas de cultura. O objetivo deste estudo foi detectar e quantificar as bactérias dos gêneros Bifidobacterium, Lactobacillus, Eubacterium e Lactococcus, importantes componentes anaeróbios da microbiota intestinal usando PCR em tempo real. O grupo de estudo foi composto por 10 crianças, acompanhadas durante o primeiro ano de vida, vivendo em baixas condições sócio-econômicas em São Paulo, Brasil. Amostras de fezes foram avaliadas em períodos de 24 horas, 7 dias, 30 dias, 3 meses, 6 meses e 1 ano. Durante o primeiro ano de vida, há um aumento da quantidade de Bifidobacterium spp., quando comparada com as outras bactérias anaeróbias estudadas, com médias variando de 8,27x1010 a 2,51x1012 número de cópias de DNA/g de fezes. Lactobacillus spp. também foi encontrado em todos os pontos de tempo estudado, com médias variando de 4,03x108 a 1,46x1010 número de cópias de DNA/g de fezes. Lactococcus spp. foi o gênero bacteriano encontrado em quantidades menores. As contagens máximas desses gêneros foram encontradas entre o terceiro e sexto mês de vida. Embora o gênero Eubacterium seja descrito como um dos principais membros da microbiota intestinal, este foi encontrado em amostras de apenas duas crianças. A inclusão de dieta sólida e a mudança do tipo de amamentação influenciam a composição da microbiota. No entanto, não se pode estabelecer um padrão para a presença destes micro-organismos ao longo dos meses, mostrando que a microbiota é única e está sujeita a interferências ambientais. / The sequence of bacterial events that occurs during the colonization of the gastrointestinal tract may affect the future health of the host, particularly with respect to the regulation of the naive immune system. A clear understanding of the colonization process of the human neonatal gut in developing countries is lacking because the few available studies were mostly performed using culture techniques. The aim of this study was to detect and quantify the bacterial genera Bifidobacterium, Eubacterium, Lactobacillus and Lactococcus, important anaerobic components of the intestinal microbiota using real-time PCR. The study group comprised 10 children followed during the first year of life, living in low socio-economic conditions in São Paulo, Brazil. Fecal samples were evaluated at times of 24 hours, 7 days, 30 days, 3 months, 6 months and 1 year. During the first year of life, there is an increased amount of Bifidobacterium spp. compared to others studied anaerobic bacteria, with averages ranging from 8,27x1010 to 2,51x1012 DNA copy number/g of feces. Lacotbacillus was also found in all studied time point, with averages ranging from 4,03x108 to 1,46x1010 DNA copy number/g of feces. Bacterial genus Lactococcus is found in smaller quantities. The maximum counts of these genera were found between the third to sixth month of life. Although the genus Eubacterium is described as one of the leading members of the intestinal microbiota, this was found in samples of only 2 children. The inclusion of solid diet and change of type of feeding influences the composition of the microbiota, however, could not set a standard for the presence of these micro-organisms over the months, showing that the microbiota is unique and is subject to environmental interference.

Orientador: Gláucia Maria Pastore / Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Engenharia de Alimentos / Made available in DSpace on 2018-08-21T02:44:12Z (GMT). No. of bitstreams: 1 Lemos_AdrianeCristinaGarcia_D.pdf: 1535863 bytes, checksum: be0f41cf63bbd79b46b680df59cba450 (MD5) Previous issue date: 2012 / Resumo: Galacto-oligosacarídeos (GOS) são prebióticos obtidos via transgalactosilação enzimática da lactose. Dentre os vários benefícios associados ao consumo de GOS destaca-se a capacidade de estimular o crescimento e atividade de bactérias benéficas no cólon. O objetivo deste estudo foi avaliar as propriedades prebióticas dos GOS sintetizados, a partir da lactose, por ß-galactosidase de Scopulariopsis sp. A digestibilidade e a fermentabilidade foram avaliadas in vitro, enquanto os efeitos prebióticos foram avaliados in vivo em um conjunto de experimentos com ratos Wistar. Os resultados observados in vitro demonstraram que os GOS produzidos neste estudo são indigeríveis, altamente fermentáveis e convertidos em ácidos graxos de cadeia curta (acetato, propionato e butirato). Estudos in vivo demonstraram que o consumo de diferentes doses de GOS por 42 dias não produziu efeitos tóxicos nos animais, evidenciado a partir de avaliações clínicas, exames hematológicos, bioquímicos, necroscópicos e histológicos. Os ratos suplementados com GOS apresentaram maior (p<0.05) população cecal de bifidobactérias (log10 10,05 ± 0,27 UFC/g) e lactobacilos (log10 8,92 ± 0,16 UFC/g). Para os ratos não suplementados com GOS estas proporções foram de log10 8,22 ± 0,33 e 7,2 ± 0,15 UFC/g, para bifidobacterias e lactobacilos,respectivamente. Por outro lado, a população de Escherichia coli foi significativamente reduzida (p<0.05), sendo 24,75% menor, quando comparada ao grupo controle sem GOS. Além disso, a fermentação dos GOS pelas bactérias intestinais resultou em um aumento na produção de ácidos graxos de cadeia curta de 2,73 vezes, em relação aos animais sem acréscimo de GOS na dieta.Observou-se, ainda, que o grupo suplementado com GOS apresentou maiores valores de espessura total da mucosa, altura dos vilos e profundidade das criptas,evidenciado pela maior relação altura de vilosidades:profundidade de cripta em relação ao grupo controle / Abstract: Galacto-oligosaccharides (GOS) are prebiotics obtained via transgalactosylation enzymatic of lactose. Among the many benefits associated with consumption of GOS stands the ability to stimulate growth and activity of beneficial bacteria in the colon. The objective of this study was to evaluate the properties of prebiotic GOS synthesized from lactose by ß-galactosidase from Scopulariopsis sp. The digestibility and fermentability were evaluated in vitro, while the prebiotic effects were evaluated in vivo in a series of experiments with Wistar rats. The results observed in vitro showed that the GOS produced by this study are indigestible highly fermentable and converted into short-chain fatty acids (acetate,propionate and butyrate). In vivo studies have showed that consumption of different doses of GOS for 42 days produced no toxic effects in animals, as evidenced from clinical, hematological, biochemical, and histological necropsy. The rats supplemented with GOS had higher (p<0.05) cecal populations of bifidobacteria (log10 10.05 ± 0.27 UFC/g) and lactobacillus (log10 8.92 ± 0.16 UFC/g). For rats not supplemented with GOS these proportions were log10 8.22 ± 0.33 and 7.2 ± 0.15 UFC/g, for bifidobacteria and lactobacillus, respectively.Furthermore, the population of Escherichia coli was significantly reduced (p<0.05) and 24.75% less when compared to controls without GOS. Furthermore, the GOS fermentation by intestinal bacteria resulted in an increase in the production of short chain fatty acids from 2.73 times in compared with those without the addition of GOS diet.It was observed also the supplemented group with GOS showed higher values of total mucosal thickness, villous height and crypt depth, evidenced by the higher ratio of villus height: crypt depth in the control group / Doutorado / Ciência de Alimentos / Doutora em Ciência de Alimentos

Three investigations were conducted in order to investigate the effect of dietary probiotics on tilapia (Oreochromis niloticus) growth performance, intestinal morphology, intestinal microbiology and immunity. The first experiment demonstrated that Bacillus subtilis, Lactobacillus reuteri and Pediococcus acidilactici supplemented individually and as a mixed probiotic (in addition to Enterococcus faecium; AquaStar® Growout) were capable of modulating intestinal microbial populations as determined by culture dependent methods and DGGE. Furthermore, high-throughput sequencing reported that >99% of 16S rRNA reads in the mixed probiotic group belonged to the probiotic genera, predominantly assigned to Enterococcus (52.50%) and Bacillus (45.94%). Tilapia in the mixed probiotic group displayed significantly higher intraepithelial leucocyte (IEL) populations in the mid intestine when compared to the control and L. reuteri treatment. The mixed probiotic also improved microvilli density and had a higher absorptive surface area when compared to the control. In the second trial, after six weeks of supplementing tilapia diets with AquaStar® Growout at 3g kg-1, fish demonstrated significantly higher final weight, weight gain and SGR when compared to that of the control (void of probiotic) treatment or an initial probiotic feed (lasting two weeks) followed by control feeding. Probiotic supplementation at 3g kg-1 also caused an increase in the abundance of intestinal IELs and goblet cells and an up-regulation in the gene expression of intestinal caspase-3, PCNA and HSP70 and immunity genes TLR2, TNFα, IL-1β, TGFβ and IL-10 when compared with the expression of control replicates. These changes were not observed when supplementing tilapia diets with a lower dose (1.5g kg-1), nor when supplementing the probiotic in either a pulsed manner or as an initial feed (two weeks) followed by control feeding. Trial three revealed that the probiotic had a more discrete effect on the intestinal allochthonous microbiota as 16S rRNA reads assigned to probiotic genera only accounted for 5-10% of total reads. Nevertheless, the supplementation of dietary AquaStar® Growout at 3g kg-1 improved the localised immune response in tilapia, through the regulation of immunity genes TLR2, MYD88, NFκB, TNFα, IL-1β, TGFβ and IL-10, larger populations of goblet cells and a higher recruitment of IELs. Furthermore, the probiotic also improved the systemic immune response through the regulation of immunity genes (mentioned above) in the head kidney and significantly higher circulating leucocyte levels in whole blood. The extent of these changes were dependent on the probiotic treatment (i.e. continuously supplemented in feed or alternating weekly between probiotic at 3 g kg-1 and control feeding), the duration of feeding and the parameter investigated. This research demonstrates that B. subtilis, L. reuteri, P. acidilactici and AquaStar® Growout can modulate the intestinal microbiota. In addition, AquaStar® Growout can improve intestinal morphology, growth performance and modulate both the localised and systemic immune responses of tilapia when supplemented through the feed at the appropriate dosage and feeding regime.

A l`heure où le cancer a supplanté les maladies cardiovasculaires en tant que première cause de mortalité en France, le CCR représente la deuxième cause de mortalité par cancer. Longtemps dominé par la génétique, le paradigme du cancer colorectal a récemment évolué laissant une place prépondérante aux facteurs environnementaux. Il est néanmoins difficile d’étudier l’impact de l’environnement sur la carcinogénèse colorectale de façon exhaustive compte tenu de la multiplicité de ces facteurs environnementaux. Dans la présente étude, nous avons essayé d’appréhender la contribution de la composition du microbiote intestinal, de la composition métabolomique des eaux fécales et des altérations épigénétiques de l’hôte comme témoin de ces facteurs environnementaux au cours de la carcinogénèse colorectale et d’en évaluer le bénéfice en tant que marqueur diagnostique non invasif. Nous avons ainsi pu montrer au sein d’une population de patients à risque moyen de cancer colorectal qu’il existait une signature microbiologique, métabolomique et épigénétique spécifique du cancer colorectal. Nous avons également pu montrer que ces marqueurs présentaient des performances diagnostiques supérieures au test colorimétrique au guaiac utilisé dans le dépistage organisé du cancer colorectal. / Colorectal cancer (CRC) is a significant cause of morbidity and mortality in developed countries. The majority of CRC are called sporadic, meaning they are due to environmental factors rather than constitutional genetic alterations. Indeed, the role of environment, i.e. western lifestyle, is also underlined by dramatic geographic variations in CRC incidence in both sexes. However, it is difficult to take into account the totality of human environmental exposures for a better understanding of the colorectal cancer pathogenesis. In the present work, we tried to highlight the contribution of the environment in the development of colorectal cancer by studying the role of the intestinal microbiota together with the role of the fecal metabolites and the presence of epigenetic alterations of the host. We also investigated the performance accuracy of the latter changes for colorectal cancer diagnosis as compared to the guaiac fecal occult blood test which is widely used as a non-invasive test in several screening program. We demonstrated a specific signature associated with advanced colorectal neoplasia for the intestinal microbiota and the fecal metabolite profile for colorectal cancer as well as a link between colorectal cancer and Wif-1 gene methylation in urine and/or fecal samples. Those specific signatures disclosed higher diagnostic accuracy compared to guaiac fecal occult blood test as colorectal cancer screening test.

Les hépatopathies métaboliques regroupent les maladies non alcooliques du foie (NAFLD) et les maladies alcooliques du foie (MAF) causées respectivement par l’obésité ou une consommation excessive d’alcool. Ces pathologies vont de la simple stéatose à des formes aggravées pouvant aller jusqu’au carcinome hépatocellulaire. D’autres facteurs que le surpoids ou l’abus d’alcool jouent un rôle dans la susceptibilité des patients à développer une NAFLD ou une MAF. Cette thèse a pour objectif de clarifier et d'étudier les mécanismes et les facteurs participant à l’installation de l’inflammation dans ces deux pathologies. Mes travaux ont porté d’une part sur le rôle de la cellule de Kupffer dans les étapes précoces de la NAFLD et d’autre part sur l’étude du microbiote intestinal comme cofacteur déclenchant de la MAF. La cellule de Kupffer lors de la stéatose, étape précoce de la NAFLD, présente une dérégulation de son homéostasie lipidique qui participe à son phénotype pro-inflammatoire et favorise l’inflammation hépatique. L’impact du fructose, largement utilisé dans notre alimentation actuelle, a été étudié et aggrave l’inflammation hépatique lors d’un régime hyperlipidique et ceci est associé à une dysbiose spécifique. Dans la MAF, une dysbiose intestinale, une diminution des Bacteroides, a été associée aux lésions hépatiques dans un modèle murin d’alcoolisation. L‘utilisation de traitements permettant de maintenir cette population à des taux élevés a corrigé cette dysbiose et protégé les animaux face aux lésions hépatiques. Ces travaux permettent d‘envisager le MI comme une cible prometteuse permettant de contrôler l’évolution des hépatopathies métaboliques vers des formes sévères. / Metabolic hepatopathies is including Non Alcoholic Fatty Liver Disease (NAFLD) and Alcoholic Liver Disease (ALD) due to an excessive consumption of alimentation or alcohol. The pathologies range from simple steatosis to aggravated forms until hepatocellular carcinoma. Other factors than overweight or alcohol abuse play a role in sensitivity of patients to develop NAFLD or ALD. The aim of this thesis is to clarify and study the mechanisms and factors that lead to the installation of inflammation in those pathologies. My work covered in part on the role of Kupffer cell in the early stages of NAFLD and secondly on the study of intestinal microbiota as a cofactor triggering the MAF.The Kupffer cell role in steatosis, the early stages of NAFLD, showed a deregulation of its lipid homeostasis involved in the pro-inflammatory phenotype and promotes liver inflammation. The impact of fructose, widely used in our current diet, was studied and worsening liver inflammation during high fat diet. This is associated with a specific dysbiosis. In ALD, intestinal dysbiosis, a decrease of Bacteroides, leading to liver damage has been established. The use of treatments to maintain this population with high levels corrected the dysbiosis and has protected animals against liver damages. Both works on the NAFLD and ALD establish MI is a promising target to control the evolution of metabolic liver diseases toward aggravated forms.

La réduction du taux de cholestérol (CH) sanguin est un point clé dans la lutte contre les maladies cardiovasculaires. L’efficacité contrastée des médicaments disponibles actuellement ainsi que l’intérêt porté autour du microbiote intestinal dans la régulation de la physiologie de l’hôte nous amènent à envisager cette voie comme alternative thérapeutique. La production de coprostanol (CO), dérivé très peu absorbé du CH, par des bactéries de ce microbiote a été corrélée positivement à une faible cholestérolémie. Les objectifs de cette thèse sont i) d’isoler et d’identifier de nouvelles souches bactériennes ayant cette activité, ii) d’identifier les gènes bactériens responsables de cette transformation et iii) de détereminer l’impact de ce métabolisme sur la physiologie de l’hôte. Nous avons isolé 22 nouvelles souches productrices de CO à partir des selles d’un individu en produisant beaucoup. Nous avons choisi les souches Bacteroides sp. D8 et Bacteroides sp. BV pour la construction de deux banques génomiques et huit autres pour des essais d’implantation in vivo dans le tractus gastro-intestinal (TGI) de souris axéniques. Nous avons identifié 55 clones potentiellement positifs par le criblage fonctionnel des banques génomiques. Leurs analyses supplémentaires devraient nous apporter des informations sur les gènes impliqués dans cette activité. Toutes les bactéries sélectionnées sont capables de coloniser le TGI de la souris axénique. La souche Parabacteroides distasonis est la meilleure souche productrice de CO in vivo. Nous avons testé son effet sur la cholestéolémie chez des souris axéniques soumises à un régime riche en CH sur 11 semaines en comparaison avec une souche non productrice in vitro, B. dorei, et avec des souris conventionnalisées comme contrôle. La souche B. dorei produit du CO in vivo, soulignant l’importance de l’environnement dans l’activité de production de CO déjà supposée d’après la littérature et nos résultats in vitro. Des gènes impliqués dans l’excrétion du CH de l’organisme vers les selles sont surexprimés chez ces souris et celles colonisées avec P. distasonis. Cependant seules ces dernières présentent une cholestérolémie plus faible que les souris conventionnalisées. Le mécanisme impliqué semble indépendant de la production de CO et de l’excrétion de CH car les mêmes quantités de ces composés sont retrouvées dans les selles indépendamment du statut bactérien. Les concentrations en acides biliaires totaux dans la bile et dans les selles sont supérieures pour les souris monocolonisées comparées au conventionnalisées. Les selles des souris colonisées avec P. distasonis présentent plus d’acides urso- et chénodésoxycholiques que les souris conventionnalisées et plus d’acide cholique que les souris colonisées avec B. dorei. En conclusion, nous avons isolé de nouvelles souches et identifier des clones potentiellement positifs. Les études in vivo tendent à montrer que l’activité de production de coprostanol n’a pas d’effet sur la cholestérolémie. En revanche, la souche P. distasonis semble diminuer la cholestérolémie par un mécanisme encore inconnu. / Cholesterol (CH) level management is a keystone to limit cardiovascular diseases. The contrasted efficiency of the drugs currently available as well as the interest around the intestinal microbiota in regulating the host physiology lead us to consider this pathway as a therapeutic alternative. The production of coprostanol (CO), a very poorly absorbed CH derivative, by bacteria of this microbiota has been positively correlated with low CH plasma level. The aims of this thesis are (i) isolate and identify new bacterial strains possessing this activity, (ii) identify the bacterial genes responsible for this transformation and (iii) determine the impact of this metabolism on host physiology. We isolated 22 new strains producing CO from the stools of a high-coprostanol producing individual. We chose Bacteroides sp. D8 and Bacteroides sp. BV for the construction of two genomic libraries and eight others for in vivo implantation tests in the gastrointestinal tract (GIT) of germ-free mice. We identified 55 potentially positive clones by functional screening of these genomic libraries. Their additional analyzes should provide us with information about the genes involved in this activity. All selected bacteria are capable of colonizing the GIT of germ-free mice. Parabacteroides distasonis is the best strain producing CO in vivo. We tested its effect on blood cholesterol level in germ-free mice subjected to an 11-week CH-rich diet compared to an in vitro non-producing strain, B. dorei, and with conventionalized mice as control. The B. dorei strain produces CO in vivo, emphasizing the importance of the environment in the CO production activity already assumed from the literature and our results in vitro. Genes involved in the excretion of CH from body to feces are overexpressed in these mice and those colonized with P. distasonis. However, only the latter have lower cholesterolemia than conventional mice. The mechanism involved appears to be independent of CO production and CH excretion because the same amounts of these compounds are found in feces independently of bacterial status. Total biliary acids concentrations in bile and feces are higher for monocolonized mice compared to conventionalized mice. The feces of mice colonized with P. distasonis exhibited more urso- and chenodeoxycholic acids than conventionalized mice and more cholic acid than mice colonized with B. dorei. In conclusion, we have isolated new strains and identified potentially positive clones. In vivo studies tend to show that coprostanol production activity has no effect on plasma cholesterol. In contrast, P. distasonis seems to decrease plasma cholesterol by a still unknown mechanism.

<p>Stress is known to play an important role in the natural history of gastrointestinal diseases, and functional disorders in particular. In health, activation of the stress response serves to maintain homeostasis in response to harmful stimuli. However, prolonged activation of the stress response can become maladaptive and contribute to the initiation and maintenance of symptoms in disorders such as irritable bowel syndrome (IBS). The mechanisms underlying this detrimental effect are unclear. This thesis investigates this relationship by examining the influence of 10 days of water avoidance stress on a murine model of acute bacterial gastroenteritis; a known trigger in a subset of IBS patients. Results indicate that stress can increase the level of the stress hormone norepinephrine in the gut. However, the overall influence of host stress during infection proves to be beneficial in this model, with decreased colonic inflammation and earlier clearance of the pathogen. Next, we utilized the olfactory bulbectomy (OBx) model of depression comorbid anxiety, which shows a heightened stress response, to examine mechanism underlying stress-mediated susceptibility in a more chronic setting. OBx resulted in increased neural activity and motility in the gut, and a change in composition of gut microbiota. These responses were not accompanied by changes in gut permeability or immune activation. Thus stress alters the habitat of commensal bacteria via a neurally mediated change in colonic motility. These results have bearing on the ability of stress to alter the microbiota: a feature of functional GI disorders.</p> / Doctor of Philosophy (Medical Science)

The development of molecular tools for detection and typing of unicellular intestinal parasites has revealed genetic diversities in species that were previously considered as distinct entities. Of great importance is the genetic distinction found between the pathogenic Entamoeba histolytica and the non-pathogenic Entamoeba dispar, two morphologically indistinguishable species. Blastocystis sp. is a ubiquitous intestinal parasite with unsettled pathogenicity. Molecular studies of Blastocystis sp. have identified 17 genetic subtypes, named ST1-17. Genetically, these subtypes could be considered as different species, but it is largely unknown what phenotypic or pathogenic differences exist between them. This thesis explores molecular methods for detection and genetic subtyping of unicellular intestinal parasites, with special focus on Blastocystis. We found that PCR-based methods were highly sensitive for detection of unicellular intestinal parasites, but could be partially or completely inhibited by substances present in faeces. A sample transport medium containing guanidinium thiocyanate was shown to limit the occurrence of PCR inhibition. The prevalence of Blastocystis in Swedish university students was over 40%, which is markedly higher than what was previously estimated. Blastocystis ST3 and ST4 were the two most commonly found Blastocystis subtypes in Sweden, which is similar to results from other European countries. Blastocystis sp. and Giardia intestinalis were both commonly detected in Zanzibar, Tanzania, each with a prevalence exceeding 50%. Blastocystis ST1, ST2, and ST3 were common, but ST4 was absent. While G. intestinalis was most common in the ages 2-5 years, the prevalence of Blastocystis increased with increasing age, at least up to young adulthood. We found no statistical association between diarrhoea and Blastocystis sp., specific Blastocystis subtype or G. intestinalis. Metagenomic sequencing of faecal samples from Swedes revealed that Blastocystis was associated with high intestinal bacterial genus richness, possibly signifying gastrointestinal health. Blastocystis was also positively associated with the bacterial genera Sporolactobacillus and Candidatus Carsonella, and negatively associated with the genus Bacteroides. Blastocystis ST4 was shown to have limited intra-subtype genetic diversity and limited geographic spread. ST4 was also found to be the major driver behind the positive association between Blastocystis and bacterial genus richness and the negative association with Bacteroides.

Le tube digestif héberge une communauté microbienne complexe, le microbiote intestinal, dont les capacités métaboliques sont plus riches et diversifiées que celles codées par le génome de l'hôte. L'implication du microbiote intestinal dans divers aspects de la physiologie de l'hôte, comme le métabolisme nutritionnel et l'immunité, est depuis longtemps étudiée. En revanche, l'action potentielle du microbiote sur le développement et le fonctionnement du cerveau constitue une nouvelle piste de recherche, encore peu explorée. Dans ce contexte, nous avons réalisé une première étude générale de l'action du microbiote intestinal sur le cerveau en comparant les fonctions sensori-motrices, le comportement de type anxieux, l'état d'activation de l'axe hypothalamo-hypophyso-surrénalien et le profil cérébral des monoamines de rats F344 axéniques et conventionnels. Les résultats révèlent que, chez cette lignée particulièrement sensible au stress, l'absence de microbiote intestinal exacerbe le comportement de type anxieux et la réponse hormonale au stress, et atténue le métabolisme dopaminergique cérébral. Afin d'étudier par quel moyen le microbiote peut agir sur le cerveau, une seconde étude a été menée, ciblant un métabolite bactérien spécifique, l’indole, dont certains dérivés oxydés par le foie sont connus pour avoir des propriétés neuroactives. L'indole est un métabolite naturel du microbiote intestinal, dont la surproduction pourrait survenir lors d'une dysbiose du microbiote. Deux cas de surproduction ont été modélisés : chronique et aiguë. Dans les deux cas, des modifications importantes du comportement de l'hôte ont été observées. En situation de surproduction chronique, l'indole favorise des comportements de type anxieux et dépressif, tandis qu'une surproduction aiguë a un effet sédatif marqué. D'un point de vue mécanistique, nous confirmons que l’indole peut agir sur le système nerveux central par la voie sanguine impliquant les dérivés oxydés et montrons pour la première fois qu'il peut aussi agir en activant les noyaux cérébraux du nerf vague. / The gastro-intestinal tract hosts a complex microbial community, the gut microbiota, whose collective genome coding capacity vastly exceeds that of the host genome. The involvement of the gut microbiota in various aspects of the host physiology, such as the nutritional metabolism and the immunity, has long been studied. In contrast, the possible action of the gut microbiota on brain development and functioning is a new line of research, still poorly explored. In this context, we performed a first general study of the effect of gut microbiota on the brain by comparing the sensory-motor functions, the anxiety-like behaviour, the activation of the hypothalamic-pituitary-adrenal axis and the brain monoamine profile in germ-free and conventional F344 rats. The results show that, in this particularly stress-sensitive strain, absence of gut microbiota exacerbates the anxiety-like behaviour and neuroendocrine response to stress, and reduces brain dopamine metabolism. To investigate the means by which the microbiota can affect the brain, a second study was conducted, targeting a specific bacterial metabolite, indole, whose oxidative derivatives, produced by the liver, are known to have neuroactive properties. Indole is a natural metabolite of the gut microbiota, whoseoverproduction could occur during a microbiota dysbiosis. Two conditions of overproduction, namely chronic and acute, were modelled. In both cases, significant changes in the behaviour of the host were observed. In chronic overproduction, indole promotes anxiety- and depressive-like behaviours, while acute overproduction has a marked sedative effect. From a mechanistic point of view, we confirm that indole can act on the central nervous system through its oxidized derivatives and show for the first time that it can also act by activating the brain nuclei of the vagus nerve.