Background: Age is an important risk factor for rheumatoid arthritis (RA), which often develops in middle age. However, how age-associated changes in immunity impact RA is poorly understood. Gut microbiota are known to be involved in the pathogenesis of RA, but the effects of microbiota in older subjects remain mostly unknown. Methods: We used segmented filamentous bacteria (SFB), a gut commensal species with immunomodulatory effects, and K/BxN mice, a T cell receptor (TCR) transgenic model, to study the effect of age and microbiota on autoimmune arthritis. Comparing young and middle-aged K/BxN T cells of the same TCR specificity allows us to study T cells with an age focus eliminating a key variable: TCR repertoire alteration with age. In addition to joints, we also studied pathological changes in the lung, an important extra-articular RA manifestation. We used flow cytometry to evaluate T follicular helper (Tfh) and T helper 17 (Th17) cells, as they both contribute to autoantibody production, a key disease index in both RA and K/BxN arthritis. Results: Middle-aged K/BxN mice had aggravated arthritis and pathological changes in the lung compared to young mice. Middle-aged mice displayed a strong accumulation of Tfh but not Th17 cells, and had defective Th17 differentiation and low expression of interleukin-23, a critical cytokine for Th17 maintenance. Although a soaring Tfh cell population accompanied by robust germinal center B cell responses were found in middle-aged mice, there was decreased cycling of Tfh cells, and SFB only induced the non-Tfh cells to upregulate Bcl-6, the Tfh master transcription factor, in the young but not the middle-aged group. Finally, the accumulated Tfh cells in middle-aged mice had an effector phenotype (CD62LloCD44hi). Conclusion: Age-dependent Tfh cell accumulation may play a crucial role in the increased autoimmune disease phenotype in middle-age. SFB, a potent stimulus for inducing Tfh differentiation, fails to promote Tfh differentiation in middle-aged K/BxN mice, suggesting that most of the middle-aged Tfh cells with an effector phenotype are Tfh effector memory cells induced at an earlier age. Our results also indicate that exposure to immunomodulatory commensals may allow the young host to develop an overactive immune system reminiscent of that found in the middle-aged host.

Les eaux florales sont des matières premières aromatiques issues de la distillation, contenant généralement moins de 1 g/L de composés volatils leur conférant leurs propriétés organoleptiques. Elles sont utilisées principalement en industrie agroalimentaire et cosmétique. Elles sont sujettes à des problèmes d’instabilité microbienne incompatibles avec leurs applications. Ces microorganismes, leurs dynamiques, ainsi que les nutriments disponibles nécessaires à leur croissance restent mal connus. Les eaux florales sont actuellement stabilisées par ajout de conservateurs dont certains sont controversés et visent à être retirés du marché. De plus, leur efficacité dans les eaux florales n’a pas été évaluée.L’objectif de cette thèse est d’apporter une meilleure connaissance de la composition des eaux florales et de ses contaminants afin de proposer une méthode de stabilisation adaptée.La composition en huile essentielle et le microbiote de 22 échantillons d’eau de fleur d’oranger (Citrus aurantium L. ssp. amara L.) et de rose (Rosa damascena Miller et Rosa centifolia L.), provenant de différents producteurs autour du bassin méditerranéen, ont été analysés afin de déterminer les facteurs responsables de leur altération. Bien que les composés volatils soient connus pour leurs propriétés antimicrobiennes, leurs concentrations dans les hydrolats ne sont pas suffisantes pour assurer la stabilité microbiologique. En plus des composés volatils, les hydrolats contiennent des composés non-volatils tels que des sucres, entraînés vers le distillat par effet de primage ou de moussage pendant la distillation, et pouvant être utilisés comme substrat de croissance par les microorganismes. La population microbienne peut atteindre 106 à 107 UFC/mL en quelques jours à température ambiante et jusqu’à 3 mois à 5°C. Des bactéries environnementales, oligotrophes, et acido-tolérantes, appartenant principalement aux genres Pseudomonas sp. et Burkholderia sp. ont été isolées et identifiées. Parmi ces bactéries, B. vietnamiensis et Novosphingobium capsulatum ont été capables de métaboliser des composés volatiles tels que le géraniol ou l’acétate de 2-phényléthyle pour produire la 6-méthyl-5-heptèn-2-one ou le 2-phényléthanol, et modifier ainsi les propriétés organoleptiques des hydrolats. Enfin, la capacité de croissance de bactéries pathogènes et d’altération dans les hydrolats a été évaluée, et différents conservateurs ont été testés sur les souches capables de se multiplier dans les hydrolats.Une distillation aseptique et un conditionnement stérile permettrait d’assurer la stabilité des hydrolats sans ajout de conservateurs. En l’absence de conditions aseptiques, l’ajout de conservateurs est nécessaire pour assurer la stabilité des hydrolats. / Hydrosols are hydrodistillation products mainly used as food flavoring agents or ingredient in cosmetics. They contain less than 1 g/L of dispersed essential oils giving the organoleptic properties. These are subjected to microbial proliferation that can prevent use due to non-compliance to professional microbiological standards. The microorganisms, their growth dynamics, and the available nutrients in hydrosols remain unknown. Hydrosols can contain few preservatives, but there is no data about their efficiency in hydrosols.The aim of this study was to have a better knowledge on hydrosols composition, their microbiota, and spoilage conditions, in order to propose an adapted stabilization method.The composition in volatile compounds and the microbiota of 22 hydrosol samples of Citrus aurantium L. ssp. amara L. (orange blossom), Rosa damascena Miller (rose D.), and Rosa centifolia L. (rose C.) flowers were analyzed to determine factors responsible for decay. Some non-volatile compounds were likely carried over during distillation by a priming and foaming effect, and could be used as nutrients by microorganisms. Concentrations of volatile compounds in hydrosols are not high enough to prevent microbial proliferation, and bacteria concentrations can reach up to 106 CFU/mL in both hydrosols. The isolated microbial population was composed of oligotrophic Gram-negative bacteria, arranged in four major genera: Pseudomonas sp., Burkholderia cepacia complex, and presumably two new genera belonging to Acetobacteraceae and Rhodospirillaceae. Among those bacteria, Burkholderia vietnamiensis and Novosphingobium capsulatum were able to metabolize volatile compounds, such as geraniol to produce 6-methyl-5-hepten-2-one or geranic acid, or 2-phenylethyl acetate to produce 2-phenylethanol. Finally, the growth potential of a range of bacteria isolated from hydrosols and of pathogenic micro-organisms was evaluated, then the anti-microbial activity in nutrient broth and/or in hydrosols of a range of chemical preservatives authorized for food and cosmetic applications was tested.Additional hurdles such as chemical preservatives or aseptic packaging will be necessary to insure microbial stability.

Doctor of Philosophy / Division of Biology / Brett K. Sandercock / Gastrointestinal microbiota play a vital role in maintaining organismal health, through facilitating nutrient uptake, detoxification and interactions with the immune system. Shorebirds vary widely in life-history characteristics, such as habitat, migration and breeding system, but the dynamics of their gut microbial communities are unknown. In my dissertation, I investigated composition and dynamics of gut microbiota in migratory shorebirds from embryos to 10 day old chicks, and determined environment and host-related factors affecting gut microbial communities of adults. First, I tested whether precocial chicks from three species of arctic-breeding shorebirds acquire gut microbiota before or after hatching using next-generation sequencing. In addition, I documented the dynamics of gut microbial establishment. I showed that gut microbiota were absent in shorebird embryos before hatching, but that stable gut communities established within the first three days after hatching. In addition, gut microbiota of young shorebird chicks were more similar to the environmental microbiome than later in life, suggesting that the environment is a likely source for microbial recruitment. After reaching adulthood, shorebirds migrate long distances, potentially exposing them to a wide range of microorganisms. Host phylogeny and environmental factors have both been identified as drivers of gut microbiota composition in birds in previous studies. The second part of my project aimed to compare the relative importance of host and environmental factors that underlie variation in gut microbiota composition in eight species of migratory shorebirds sampled across the North American Arctic. I found that sampling site was the main driver of variation in gut microbiota of Arctic-breeding shorebirds, and that site-related variation in gut microbiota of shorebirds was a result of differences in core bacterial taxa that occurred in more than half of the analyzed samples. A relatively large influence of local environment on gut microbiota composition of chicks and adults lead to the question: how does site affect pathogen prevalence in shorebirds? Migratory behavior has been hypothesized to have evolved as a response to variation in climatic conditions and food availability, to avoid predation, and to reduce risk of exposure to pathogens. The migratory escape hypothesis predicts avoidance of high disease prevalence areas through migration, and has been proposed as one of the main reasons that many bird species migrate to the Arctic for breeding. To test the migratory escape hypothesis in shorebirds, I screened for prevalence of seven known avian pathogens in shorebirds at different stages of migration. I did not detect the majority of pathogens we tested for, with the exception of Campylobacter jejuni and C. coli. Prevalence of C. jejuni in shorebirds was linked to sampling sites but not shorebird species. My dissertation is the first comprehensive study to broadly characterize the gut microbiota in shorebirds. Overall, local environment emerged as an important factor in shaping microbiota composition in Arctic-breeding shorebirds throughout my dissertation research. The role of local environment in shaping gut microbiota invites future investigations of the interactions among shorebirds and the microorganisms present in their environment, as well as the functions gut microbiota perform within their shorebird hosts.

La forte prévalence des problèmes digestifs chez les lapins en croissance autour du sevrage, et le taux élevé de mortalité chez les lapines associé à une forte prévalence de femelles ayant un état corporel dégradé pourrait être le témoin d’une discordance entre les apports nutritionnels des animaux et leurs besoins. Nous avons visé, dans le cadre d’une alimentation séparée entre les lapines et leurs lapereaux avant le sevrage, de répondre à deux objectifs complémentaires : i) de mieux comprendre les relations entre les apports nutritionnels, la mise en place de l’ingestion d’aliment, la maturation de l’écosystème caecal, la santé et la croissance des jeunes lapereaux, et ii) d’explorer le lien entre la nature des nutriments apportés au cours du cycle de reproduction et les performances chez les lapines reproductrices. Nous avons observé que dans le cadre d’une stratégie de restriction alimentaire après le sevrage, la distribution, de 18 à 70 jours d’âge, d’un aliment plus riche en énergie (+7% ED), mais contenant un niveau de fibres suffisant, permet d’optimiser la croissance des lapereaux avant et après sevrage,sans pénaliser la santé des lapereaux(1,49% de mortalité). Nous avons aussi montré, que lors de l’application d’une restriction alimentaire après le sevrage, la distribution d’un aliment riche soit en amidon (166 vs 72 g/kg),soit en fibres (173 vs 220 g/kg d’ADF),avant le sevrage conditionne le poids des lapereaux non seulement au moment du sevrage (+7,7%) mais également jusqu’au moment de la vente (2522 vs 2584 g). Enfin, nous avons constaté que le niveau d’ingestion de l’aliment chez les lapereaux au moment de la mise en place de l’ingestion d’aliment solide influence la maturation de l’écosystème caecal. Chez les lapines, notre étude a apporté des résultats mitigés. Nous avons observé peu d’effet sur les performances de reproduction chez les lapines, mais nous avons observé des conséquences importantes sur le bilan énergétique des femelles (-4,94 vs -2,05 MJ), la quantité (3911 vs 3415 g)et la qualité du lait produit. Ce dernier élément a des effets sur la croissance des lapereaux et leur ingestion précoce d’aliment solide (7 vs 9 g/j entre 18 à 25 jours d’âge), ce qui en conséquence affecte leur santé après le sevrage (5,8 vs 1,7 % de mortalité).Cela a été le cas avec l’utilisation d’un aliment riche en lipides (49 g/kg de lipides brute) au début de la lactation.Toutefois, nous avons aussi montré que les coefficients d’utilisation digestive des nutriments sont très différents chez les lapereaux et chez les femelles à différents stades physiologiques. Par conséquent, en l’absence de mesures réelles de la valeur nutritionnelle des aliments sur les femelles elles-mêmes et au stade physiologique considéré, nos estimations des apports nutritionnels et donc l’estimation des bilans peuvent être erronés. Au final, nos résultats suggèrent que la stratégie qui consisterait à valoriser le système d’alimentation séparée pour n’utiliser qu’un seul aliment pour les lapines pendant toute leur vie reproductive pourrait être le meilleur compromis entre simplicité, efficacité et rentabilité. Celui-ci devrait être riche en énergie sous forme d’amidon pour favoriser le maintien de la fertilité et des réserves corporelles sur le long terme. Ce système d’alimentation séparée permettrait aussi chez les lapereaux de limiter les conséquences néfastes d’un changement d’aliment et d’optimiser le compromis entre performances de croissance et de santé par l’introduction d’un aliment plus riches en énergie et en protéine mais avec un niveau de fibres suffisant dans le cadre d’une restriction alimentaire après le sevrage. Mieux comprendre l’adaptation digestive et la gestion des priorités métaboliques au cours du cycle de reproduction chez la femelle ainsi que la relation entre ingestion précoce et maturation de l’écosystème caecal chez le jeune lapereau sont des perspectives de recherche intéressante à nos travaux. / The high prevalence of digestive problems in growing rabbits around weaning and the high rate of mortality in rabbit does associated with a high prevalence of does having a degraded body condition can contest to a mismatch between the nutritional intake of animals and their needs. This thesis aimed, through the use of a separate feeding system between rabbits does and their kits before weaning, to respond to two complementary objectives: i) to better understand the relationship between nutrient intake, the establishment of solid feed intake, the maturation of the cecal ecosystem, and the health and growth of young rabbits, and ii) to explore the relationship between the nature of nutrients provided throughout the reproduction cycle and performance in breeding does. We observed that in the context of a feed restriction strategy after weaning, the distribution, from 18 to 70 days of age, of a more energy-rich feed (+7% DE), but containing sufficient level of fiber, optimizes young rabbit growth before and after weaning, without compromising their health (1.49% mortality). We also showed that when a feed restriction plan is implemented after weaning, the nutritional strategy used before weaning, the distribution of a feed either rich in starch (166 vs 72 g/kg) or in fiber (173 vs 220 g/kg ADF), conditions the weight of growing rabbits not only at weaning (+7.7%) but also at the time of sale (2522 vs 2584 g). Finally, we found that the solid feed intake level of rabbit kits at the establishment of solid feed intake influences the maturation of the cecal ecosystem. In reproductive does, our study has produced mixed results. We observed little effect on reproductive performances in does, but observed a significant impact on their energy balance (-4.94 vs -2.05 MJ), and the quantity (3911 vs 3415 g) and quality of the milk produced. The latter had an effect on the growth of young rabbits and early ingestion of solid food (7 vs 9 g/day from 18 to 25 days of age), which consequently affects their health after weaning (5.8 vs 1.7% mortality).This was the case with the introduction of a feed rich in fat (49 g/kg crude fat) during early lactation. However, our latest work revealed that, in the absence of actual measurements of the nutritional value of feed using the females themselves and taking into consideration their physiological state, our estimation of nutrient intake, and therefore the estimation of the energy balance may be wrong. Finally, our results suggest that the strategy which introduces the separate feeding system in order to distribute only one type of feed for the rabbit does throughout their reproductive life might be the best compromise between simplicity, efficiency and profitability. The feed used should be rich in energy, in the form of starch, to help maintain fertility and body reserves of the does in the long term. This separate feeding system would also allow the rabbits to limit the negative consequences of a diet change and optimize the trade off between growth performance and health by introducing a richer food energy and protein but with a sufficient level of fiber as part of a feed restriction strategy after weaning. A better understanding of the digestive adaptation and management of metabolic priorities during the reproductive cycle in the female and the relationship between early maturation and ingestion of cecal ecosystem in young rabbit are interesting research perspectives to our work.

En faisant le parallèle avec les selles modernes, les coprolithes peuvent être appropriés à l'étude des habitudes alimentaires, de la flore intestinale et des maladies, des animaux et des hommes ayant vécu il y a des siècles. Dans le travail de thèse ici présenté, un coprolithe datant des 14-15ième siècles, provenant de Namur en Belgique, a été étudié. Dans un premier temps l'ensemble de la communauté microbienne associée au coprolithe été characteriser. Les résultats ont montré qu'une partie du microbiote est similaire à l'environnement et l’autre la flore intestinale, des parasites intestinaux et des pathogènes systémiques ont été aussi trouvés. Un second projet a visé à la purification de particules virales à partir du coprolithe et leur analyse par microscopie électronique et métagénomique virale. Des particules virales sphériques, ainsi que des bactériophages, ont ainsi été observés. Les virus associés au coprolithe correspondent à des virus d'eucaryotes, de procaryotes et d'archaea. La communauté virale était dominée par des bactériophages détectés dans le sol et les selles. Parmi les fonctions métaboliques détectées, une correspond d'ailleurs à des résistances aux antibiotiques. Dans un troisième projet, des cultures et des identifications moléculaires ont été réalisées sur des kystes d'amibes observés dans le coprolithe. Les amibes isolées appartiennent au genre Acanthamoeba et pourraient avoir été conservées sous forme de kystes pendant des siècles dans le coprolithe. Les co-cultures d'amibes ont mené à l'isolement d'une nouvelle bactérie bi-flagellée résistante aux amibes, proche des Rickettsiales. / By drawing parallels to modern stools, coprolites can be suitable specimen to study diet habits, gut microbiota and diseases of animals and humans that have lived centuries ago. During this thesis work, a 14-15th century coprolite specimen from Namur, Belgium was analyzed. At the initiation of this thesis work, it was aimed to characterize the entire microbial communities associated to the coprolite and to identify ancient pathogens. Results indicated that parts of the microbiota are similar to those coming from environment and the gut microbiota inhabitants. Further intestinal parasites and systemic pathogens – still relevant nowadays – were also found. In a second work, viral particles were purified from the Namur coprolite and analyzed by electron microscopic and viral metagenomic. Viral particles associated to spherical virions and bacteriophages were observable. Viruses infecting eukaryotes, bacteria and archaea were associated to the specimen. The viral community was dominated by bacteriophages commonly found in soil and in modern stools and antibiotic resistance was one of the metabolic functions detected. In a third project, culture and molecular identification were performed on amoebal cysts observed within the coprolite. The amoebas isolated belong to the genus Acanthamoeba and might have been conserved in form of cysts inside the Namur coprolite for centuries. Amoeba-co culturing leaded to the isolation and identification of a new bi-flagellar amoeba-resistant bacterium closely related to Rickettsiales.

La consommation d'aliments riches en ellagitannins (ETs) pourrait être associée principalement à la prévention des maladies cardiovasculaires et la régulation des cancers hormono-dépendants. Néanmoins, les ETs ne sont pas biodisponibles en tant que tel et, après avoir été partiellement transformés en acide ellagique (EA) dans le tractus gastro-intestinal (GI) supérieur, ils sont métabolisés dans le côlon par la flore intestinale en urolithines, un groupe de molécules plus biodisponibles et bioactives qui peuvent persister jusqu'à 4 jours à des concentrations relativement élevées dans le plasma et l'urine. La variabilité de l'excrétion des urolithines dans l'urine est importante et à partir d'un échantillon de population de 26 volontaires sains, trois groupes principaux d'individus ont pu être distingués : "faible ou non-excréteur d'urolithin », « Excréteur prédominant d'UA et dérivés» et « Excréteur prédominant d'UB et dérivés»". Ces groupes ont également été observés en considérant la cinétique totale d'excrétion sur une période de 4 jours après ingestion du jus et à des périodes différentes tout au long d'une année. Bien que les variabilités inter-et intra-individuelles soient relativement élevées, les individus conservent leur statut au cours des différentes périodes d'intervention même en modifiant les quantités d'ETs ingérées. L'analyse par UPLC-PDA/ESI-Q-TOF/MS2 a permis d'attribuer hypothétiquement une identité à 15 autres métabolites d'ETs dans l'urine, mais le profilage métabolomique n'a pas permis de discriminer d'autres composés exceptés les dérivés d'UA ou d'UB. La fermentation in-vitro des ETs et EA, par les matières fécales a montré une voie métabolique spécifique qui débouche sur la production d'UA. Néanmoins, les métabolites excrétés in vivo sont beaucoup plus complexes ce qui met en évidence de fortes interactions entre le système excréteur de l'hôte et la composition du microbiote intestinal. La recirculation hépatique suivie par une re-conversion des métabolites de phase II dans le côlon permettrait d'expliquer l'excrétion d'UB chez certains volontaires. L'écologie spécifique de la flore intestinale évaluée par la méthode des empreintes PCR-DGGE a permis d'identifier quelques microorganismes associés à une plus grande capacité de bioconversion des ETs en urolithins / Consumption of dietary ellagitannins (ETs) could be associated mainly with prevention of cardiovascular diseases and regulation of hormone-dependent cancers. Nonetheless, ETs are not bioavailable as such; therefore, after being partially converted into ellagic acid (EA) in the upper gastrointestinal (GI) tract, they undergo sequential bioconversion in the colon by gut microbiota into urolithins, a more bioavailable and bioactive group of molecules that persist up to 4 days at relatively high concentrations in urine. Variability of urolithin excretion in urine is high and three main groups, “no or low urolithin excreters,” “predominantly UA derivatives excreters” and “predominantly UB derivatives excreters,” were observed on a cohort of 26 healthy volunteers. These categories were also unambiguously observed following the total excretion of main ETs' metabolites over a 4 day period after ingesting one shot of juice, and at different periods of time along one year. Although relatively high inter- and intra-individual variabilities were observed, individuals preserved their status during various intervention periods with different amounts of ETs ingested. UPLC-PDA and ESI-Q-TOF/MS1 and MS2 allowed the tentative assignment of an identity to 15 other ETs metabolites in urine, but this profiling did not allow the discrimination of any other compounds aside from UA or UB derivatives. In-vitro fermentation of ETs and EA with fecal stools showed a specific metabolic pathway ending in the production of UA. Nonetheless, metabolites excreted in-vivo are much more complex, highlighting strong interactions between host excretory system and composition of gut microbiota. Hepatic recirculation and additional bioconversion of Phase II metabolites in the colon may explain predominant excretion of UB in some volunteers. Microbiota ecology assessed by PCR-Denaturing Gradient Gel Electrophoresis (DGGE) fingerprint method allowed the association of some microorganism species to higher capacity of bioconversion of dietary ETs into urolithins.Key words: Ellagitannins, blackberry, urolithin, colonic metabolites, ETs degradation patterns, gut microbiota, gastrointestinal tract,

La réduction des émissions de méthane (CH 4) des ruminants permet de limiter les impacts environnementaux négatifs de leur élevage et d’améliorer leur efficacité digestive. Dans le rumen, le CH 4 est majoritairement produit par les méthanogènes à partir de l’hydrogène (H 2). La disponibilité de l’H 2 pour ces micro-organismes est réduite en limitant sa production par les protozoaires (via un apport de lipides ou extraits de plantes dans la ration) ou en stimulant des voies utilisatrices d’H 2 compétitives à la méthanogenèse (via un apport alimentaire de nitrate). Aucune étude n’a porté sur l’association de stratégies alimentaires jouant à la fois sur la production et l’utilisation d’H 2 pour diminuer les émissions de CH 4 . Notre objectif était de comprendre l’importance des différentes voies métaboliques de l’H 2 dans le rumen. Nous avons émis l’hypothèse que manipuler simultanément la production et l’utilisation de l’H 2 permet une diminution plus importante des émissions de CH 4 plutôt que d’agir sur un seul niveau. Nos résultats expérimentaux ont montré l’additivité de l’association lipides du lin-nitrate sur la méthanogenèse des bovins. Cet effet était persistant mais non bénéfique pour les performances digestives et laitières des animaux. L’association saponine de thé-nitrate n’a pas été efficace pour réduire les émissions de CH 4 car l’effet dépressif de la saponine sur les protozoaires n’a pas été observé. Cette thèse ouvre la possibilité d’étudier le potentiel anti-méthanogène de nouvelles associations de stratégies alimentaires ayant des mécanismes d’action différents dans le rumen. Les conditions d’utilisation de ces stratégies en élevage devront être délimitées, et leur rentabilité prouvée, pour être acceptées par l’éleveur. / Reduction of methane (CH 4) emissions from ruminants may limit the negative environmental impacts of their breeding and may improve their digestive efficiency. In the rumen, CH 4 is mainly produced by methanogens from hydrogen (H 2). Hydrogen availability for these micro-organisms is reduced by limiting its production by protozoa (via lipids or plants extracts supplementation in diets) or by stimulating pathways competing with methanogenesis for H 2 consumption (via nitrate supplementation in diets). No study tested association of dietary strategies acting on both H 2 production and consumption to reduce CH 4 emissions. Our objective was to understand the importance of the different H 2 metabolic pathways in the rumen. We assumed that simultaneous manipulation of H 2 production and consumption reduces CH 4 emissions to a higher extent than acting on a single pathway. Our experimental results showed the additive CH 4 -mitigating effect of the association lipids from linseed-nitrate supplemented to bovine. This effect was persistent but not beneficial for digestive and lactating performances of animals. The association tea saponin-nitrate was not efficient to reduce CH 4 emissions, as the depressive effect of saponin towards protozoa has not been observed. This PhD thesis opens the possibility to study the anti-methanogenic potential of new association of dietary strategies having different mechanisms of action in the rumen. Conditions of use of these strategies at the breeding scale will have to be delineated, and their cost effectiveness proved to be accepted by farmers.

Dans le contexte de l'antibiorésistance, l'objet de ce doctorat vise à évaluer l'impact d'antibiotiques sur le microbiote intestinal de porcelets. La colistine et le ceftiofur, pour lesquels les résistances incluent essentiellement et respectivement mutations chromosomiques et gènes plasmidiques, ont été utilisés. La colistine a significativement réduit la population des entérobactéries, mais aucun E. coli résistant n'a été détecté. L'administration de ceftiofur a eu un impact limité sur les populations bactériennes composant l'écosystème digestif mais a conduit à une forte sélection et à la diffusion d'un gène plasmidique codant pour une bêta-lactamase à spectre étendu. Puis, dans le cadre de la réglementation visant à diminuer l'expérimentation animale, un modèle in vitro colique porcin, nommé PigutIVM, a été mis au point afin de simuler l'environnement digestif du porcelet et a permis de confirmer, in vitro, l'effet observé in vivo de la colistine sur le microbiote. Cet outil a ensuite été utilisé pour évaluer l'impact d'un probiotique, Saccharomyces cerevisiae, comme alternative aux antibiotiques. Le modèle PigutIVM devrait se positionner comme un outil de prédiction pertinent dans les domaines d'investigation aussi bien nutritionnels que pharmacologiques. / In the context of antibiotic resistance, the aim of the current PhD work is to assess the impact of antibiotics on intestinal microbiota of piglets. Two antibiotics i.e. colistin and ceftiofur, for which the main resistances include respectively chromosomal mutations and plasmid genes have been used. Colistin significantly reduced the population of Enterobacteriaceae, but there was no selection of resistant E. coli. The administration of ceftiofur had a limited impact on the bacterial populations that make up the digestive ecosystem but it led to strong selection and dissemination of a plasmid gene encoding an extended-spectrum beta-lactamase. Then, in the framework of regulations to reduce animal testing, an in vitro model of colonic pig named PigutIVM was developed in order to simulate the digestive environment of the piglet and then check the effect of colistin on the microbiota simulated in PigutIVM in vitro. Therefore both the approaches i.e. in vivo and in vitro were compared in order to check the effect of colistin on intestinal microbiota of piglets. This tool was then used to evaluate the impact of a probiotic i.e. Saccharomyces cerevisiae, as alternative to antibiotics. Therefore we assume that this PigutIVM model should be positioned as a relevant predictive tool in the fields of nutritional and pharmacological investigations.

Orientadores: Jaime Amaya-Farfan, Fernanda de Pace / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Engenharia de Alimentos / Made available in DSpace on 2018-08-27T12:05:55Z (GMT). No. of bitstreams: 1 Roquetto_AlineRissetti_M.pdf: 2148135 bytes, checksum: 6a59bf58e9dbc6285574497bb9558141 (MD5) Previous issue date: 2015 / Resumo: A obesidade é um dos maiores problemas de saúde pública no mundo, sendo associada a diversas doenças metabólicas como inflamação, resistência insulínica, dislipidemia, esteatose hepática, entre outras. Recentemente, tem sido demonstrado que alterações nas proporções dos filos que compõem a microbiota intestinal repercutem negativamente sobre o metabolismo e processos fisiológicos do hospedeiro. A dieta moderna é apontada como um dos fatores capazes de modular as bactérias intestinais e desencadear respostas inflamatórias. Diante deste cenário e tendo conhecimento de que a própolis, resina produzida por abelhas que possui ação anti-inflamatória e antimicrobiana, a presente pesquisa teve como objetivo avaliar o efeito da suplementação da própolis em camundongos tratados com dieta hiperlipídica sobre a microbiota intestinal e biomarcadores inflamatórios. Quarenta camundongos da linhagem C57BL/6 foram divididos em 4 grupos (n=10) aleatoriamente: grupo controle ¿ dieta baseada na AIN-93G; grupo hiperlipídico (HF) ¿ dieta com 37% de gordura; e grupos HFP2 e HFP5 tratados com dieta hiperlipídica, seguida de suplementação com própolis 0,2% nas duas e cinco semanas que antecederam ao sacrifício respectivamente. Foram coletadas amostras de sangue e músculo para determinações bioquímicas e indicadores de inflamação, o conteúdo cecal foi extraído para sequenciamento do DNA da microbiota intestinal. Os resultados não mostraram diferenças no ganho de peso entre os grupos experimentais, mas o tratamento com própolis por 5 semanas foi efetivo em reverter a disbiose causada pela dieta HF, com relação aos filos Firmicutes, e Proteobacteria. Os níveis de lipopolissacarídeos (LPS) no soro, bem como a expressão de toll-like receptor-4 (TLR4) e de citocinas pró-inflamatórias no músculo foram reduzidos pelo tratamento prolongado com própolis. Além disso, esta intervenção melhorou os níveis séricos de glicose e triacilgliceróis. Estes resultados sugerem a possibilidade de que a própolis exerça ação benéfica modificando o microbioma que limita a permeabilização da parede intestinal, regulando a translocação de componentes bacterianos para a corrente sanguínea e, consequentemente, conduzindo a uma menor expressão de citocinas inflamatórias / Abstract: Obesity is a major world-wide public health problem and is associated with metabolic disorders as generalized inflammation, insulin resistance, dyslipidemia, hepatic steatosis, among others. Recently, it has been demonstrated that changes in the proportions of phyla that make up the gut microbiota have a profound effect on the metabolism and physiology of the host. The modern diet has been identified as one of the factors that modulate the intestinal bacteria and trigger inflammatory responses. Considering this state of affairs and knowing that propolis, a resin present in bee honey, has anti-inflammatory and anti-microbial action, the present study was designed to evaluate the effect of propolis supplementation on the intestinal microbiome and inflammatory biomarkers of mice pre-conditioned with a high-fat diet. Forty mice of the C57BL/6 strain were randomly divided into four groups (n = 10): control group ¿ diet based on the AIN 93-G; high-fat group ¿ diet with 37% fat; and two other groups treated with high-fat, HFP2 and HFP5, that were supplemented with 0.2% propolis during two and five weeks preceding sacrifice, respectively. Blood and muscle samples were collected for biochemical analyses and inflammation markers, the cecal contents were extracted for DNA sequencing of the intestinal microbiota¿s genome. The results showed no differences in weight gain among the experimental groups, but treatment with propolis for 5 weeks effectively reverted the dysbiosis caused by the HF diet with respect to the Firmicutes and Proteobacteria phyla. The levels of serum lipopolysaccharide (LPS), and Toll-like receptor-4 (TLR4) expression, and proinflammatory cytokines in muscle were reduced by the longer propolis treatment. In addition, this intervention improved serum glucose and serum triacylglycerol levels. The present results suggest that ingested propolis exerts its beneficial action, first modifying the intestinal microbiota, which limits intestinal wall permeability and controls the translocation of bacterial components into the bloodstream and thus averting inflammatory cytokine overexpression / Mestrado / Nutrição Experimental e de Alimentos / Mestra em Alimentos e Nutrição

A utilização de técnicas moleculares têm facilitado o estudo de comunidades bacterianas complexas no ambiente. O presente trabalho teve como objetivo utilizar a técnica DGGE para avaliação dos efeitos do aumento da temperatura, causado pela queima de um canavial, na estrutura da comunidade bacteriana de solo, com ênfase ao grupo dos actinomicetos. Foram coletadas amostras de solo em diferentes profundidades, antes e depois da queima, e dados físico-químicos e climáticos associados. O DNA da comunidade bacteriana foi amplificado utilizando conjunto de primers específicos para o Domínio Bacteria e para o grupo de actinomicetos, e os produtos de amplificação analisados por DGGE. Resultados obtidos para as populações de actinomicetos não foram conclusivos. Apesar da variação dos parâmetros físico-químicos do solo provocadas pela queima, os padrões de bandas obtidos com os primers para o Domínio Bacteria, apresentaram-se uniformes. Sendo assim, nas condições de estudo deste trabalho, os resultados obtidos não revelaram alterações na estrutura da comunidade bacteriana do solo de canavial depois da queima. / The utilization of molecular techniques has facilitated the study of complex bacterial communities in the environment. The present study aimed at using DGGE technique to evaluate the effect of temperature variation, caused by sugar-cane plantation burn, in the soil bacterial community structure emphasizing the actinomycete group. Soil samples from different depths, were collected before and after the bum, as well as physical-chemical and climatic associated data. The bacterial community DNA was amplified using a specific primer set and the amplification products analyzed by DGGE. The results obtained for the actinomycete populations were not conclusive. Despite the variation of the soil parameters caused by the burn, the band patterns obtained used in this study were uniform. Therefore, under the conditions used in this study, the results obtained did not show any alteration in the structure of soil bacterial community associated with sugar-cane plantation after the burn.