Förekomsten av övervikt och fetma har ökat kraftigt de senaste åren över hela världen och i fetmans fotspår ökar även fetmarelaterade sjukdomar. Utvecklingen anses bero på en kombination av faktorer som större tillgång på energirik kost, miljömässiga, livsstilsrelaterade, genetiska och patologiska faktorer. Ny forskning har gett en ökad kuskap om tarmflorans betydelse för hälsa och studier på både obesa människor och djur visar att deras sammansättning i tarmfloran skiljer sig jämfört med normalviktiga individer. Detta har lett till ett ökat intresse hos forskare att titta närmare på kostens relation tilltarmfloran och dess sammansättning för att få klarhet i dess koppling till fetma och kunna använda denna kunskap för att förebygga och utveckla behandlingsmetoder mot fetma. Syftet med denna litteraturstudie var att analysera vetenskapliga artiklar och titta närmare på relationen mellan tarmfloran, kost och fetma. Resultaten visade att tarmflorans sammansättning är olika hos normalviktiga och obesa individer och att sammansättningen påverkar fermentationen av ej nedbrytningsbara kolhydrater i kolon. Studierna visade också att det finns en koppling mellan tarmfloran och inflammation som i sin tur också är en faktor relaterad till fetma. Ytterligare studier krävs för att besvara frågan ifall sammansättningen av tarmfloran är en orsakande faktor till utveckling av fetma, eller ett resultat av sjukdomen, samt vilka bakterier och grupper i den som genom bland annat kost går att påverka på ett positivt sätt mot fetma. / Obesity has increased dramatically during the past decades over the whole world, and has resulted in an increase of obesity-related diseases. The potential contributing factors to obesity are a combination of increase in the availability of energy-rich foods, environmental, lifestyle-related, genetic and pathological factors. New research has led to more knowledge about the gut microbiota and its role in health and studies show a difference in the microbial communities of lean vs. obese humans and animals. These findings have created an interest in research to understand gut microbiota composition and its relation to obesity so that the knowledge can be used in the prevention and treatment of obesity. The aim of this project was to analyse scentific articles and investigate the relation between the gut microbiota, diet and obesity. The studies showed differences in gut microbiota composition between lean vs. obese individuals, and that the composition affects the microbiotas ability to ferment non-digestible carbonhydrates in the colon. The studies also showed that the gut microbiota is related to inflammation, and inflammation is another factor that´s also related to obesity. There is a need for further studies to answer the question if the composition of the gut microbiota is the cause or the consequence of obesity, and which bacteria that for example through dietary modulation, can have a positive effect on obesity.

Improved life expectancy is a triumph of modern medicine. However, today’s senior citizens are predicted to soon consume 75% of the available health-care resources. Identifying new strategies to promote a healthy ageing process has thus become a priority. In contribution to the research field of healthy ageing this thesis is focused on the health and gut function of older adults. Paper I explored ‘optimal functionality’; a new approach to put the older adult’s own perspectives on health in focus. According to the results a plethora of factors related to the body, the self and the external environment needs to be considered in order to create a comprehensive understanding of the health experience in old age. Paper II characterised senior orienteering athletes as a new model of healthy ageing, due to their significantly better percived health as compared to other free-living older adults; in particular they report better gut health. As the gut is important to health maintenance and immune function paper III explored inflammation and oxidative stress in senior orienteering athletes, and older adults with gut problems, generally finding low levels in both groups. Subsequently, Paper IV investigated the health status of free-living older adults in Örebro County and also reports the results from a randomised controlled trial evaluating the effect of a probiotic supplement on self-reported health and gut symptoms. Two-thirds of the included older adults reported gut problems, however, the probiotic intervention failed to show any effects. This thesis provides additional perspectives on older adults health and gut function, by concluding that 1) optimal functionality may be a useful concept to map areas of importance to the older adult’s health experience, 2) senior orienteers may be regarded as a suitable model to study healthy ageing, 3) the prevalence of gut problems among the general population of Swedish older adults is high, but was not improved by probiotic supplementation with Lactobacillus reuteri.

As we age, the risk for gut issues, such as smooth muscle tone, may be an underlying indirect or direct cause or risk factor for many age-related issues, such as frailty. Consequences of decreased motility and depleted epithelial barrier may result in nutrient deficiencies that may increase the risk for malnutrition (Brownie, 2006). Further, there is increasing evidence that there is a gut-brain-axis relationship that may influence cognition and mental health issues, such as depression and anxiety. While there are relationships established, the interconnections of these factors have yet to be fully understood. This dissertation examined several relationships specific to nutrient intake, physical function, and depression in older adults while probing for a moderating effect of gut health. Looking further at this theory of the gut-brain bi-directional relationship, an additional gut health assessment was further examined to investigate the relationship with cognitive performance. Participants were from two separate but complementary data sets. The first data set from the National Health and Nutritional Examination study included a depression outcome analytic sample and a physical function analytic sample who had valid data on nutrient intake, bowel measures, demographic characteristics, depression scores, physical function measurements, and total BMI. The depression analytic sample had a total of 1918 participants with a mean age of 73.76 years, and 1864 participants with a mean age of 73.28 years in the physical function analytic sample. The available nutrients within the data set were further broken down into several different components by a component factor analysis and each component used as a predictor. Two separate bowel measures were examined with one as a fecal incontinence measure and the other, the Bristol Stool Form Scale, as categorical (normal, constipation, or diarrhea). The second data set, the Nutraceutical Blueberry Study, had a total of 108 participants with a mean age of 73.42 years who had valid data on cognitive measures and a complete gut assessment. Among the depression analytic sample, there were significant moderating effects of fecal incontinence between several nutrient components and depression after accounting for the control variables. An additional moderated multivariate regression with only the significant components was carried out and resulted in only Component 9 (carbohydrates, sugar, beta-cryptoxanthin, and vitamin C) and Component 12 (alcohol) having the fecal incontinence measure as a significant moderator with depression as the outcome. Within the physical function analytical sample, the Bristol Stool Form Scale categorical measure was a significant moderator among Component 6 (MFA22_1, PFA18_4, PFA20_5, PFA22_5, and PFA 22_6) and physical function. Both the constipation and diarrhea categories were related to worse physical function, while in all groups, increase in nutrients from Component 6 resulted in better physical function. Within the second data set, AVLT and AVLT Delay had a significant quadratic relationship with bowel function. Within the four different groups in the bowel measure (gastric function, gastrointestinal inflammation, small intestine and pancreas, and colon), gastrointestinal inflammation with a negative association and the colon category with a positive association were significant. Among the AVLT Delay, gastrointestinal inflammation was also negatively associated significant predictor. Outcomes from the current study suggest that fecal incontinence was indicative as a moderator among the first data set, as well as significant predictor for AVLT and AVLT Delayed in relation to cognition in older adults. Although there were many relationships not found with bowel function as a moderator, the current findings suggest that more thorough measures in additional to microbiota measures could further provide possible directions for new therapeutics in psychological and cognitive therapy, as well as improving physical function in older adults.

Master of Science / Department of Diagnostic Medicine/Pathobiology / Tiruvoor G. Nagaraja / Escherichia coli O157:H7 is a food-borne pathogen that causes hemorrhagic enteritis in humans. Cattle are asymptomatic carriers and their feces are the major source of infection. The objective of the first study was to determine the prevalence of E. coli O157:H7 in the gut of cattle at slaughter. Gut contents (rumen, cecum, colon and rectum) were collected from slaughtered cattle (n=815) at a packing plant and prevalence of E. coli O157:H7 was determined. The overall prevalence of E. coli O157:H7 in cattle was 20.6%. The prevalence (%) in the rumen, cecum, colon, and rectum was 4.9, 9.1, 7.7, and 10.3, respectively. Prevalence in rectal content was positively associated (P < 0.01) with that of the rumen or colon and not of the cecum. Pulsed-field gel electrophoresis typing showed that the majority of isolates obtained within the same animal shared a clonal similarity. There was no significant difference in the acid tolerance of ruminal compared to hindgut isolates. It was concluded that hindgut was the major site of prevalence of E. coli O157:H7 in cattle at slaughter. Neomycin, an aminoglycoside, is approved as a feed additive and for use in water to cattle. The objective of the second study was to determine the efficacy of feeding neomycin on fecal shedding of E. coli O157:H7 in cattle. Cattle were randomly assigned to control (n=14) or neomycin (n=10) supplemented group and orally inoculated with nalidixic acid-resistant (NalR) E. coli O157:H7. Neomycin was fed at 10 mg/0.45 Kg body weight for 15 days. Fecal samples and rectoanal mucosal swab (RAMS) samples were collected day before (d -1), on days 1, 3, 5, 10, 13, 17, 20, 24, 27, 31, 34, 38, 41, 44, and 48, and then approximately weekly through day 111. Fecal shedding of NalR E. coli O157:H7 was quantified and prevalence in RAMS was determined. Neomycin significantly reduced prevalence and concentration of E. coli O157:H7 compared to the control. Following two weeks of neomycin feeding, concentration and prevalence were similar between the two groups. Short term neomycin feeding before slaughter may reduce the E. coli O157:H7 load in cattle.

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.

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.

Au début de ce doctorat, plusieurs études avaient identifié l'intestin grêle, siège de l'absorption du glucose, en tant que premier organe impliqué dans le contrôle de l'homéostasie glucidique lors d'un repas. En particulier, il a été démontré que la détection entérique de glucose permettait d'impacter son utilisation par le muscle et le foie, via un relai central impliquant une libération hypothalamique de monoxyde d'azote (NO). De plus, notre groupe a également démontré qu'une altération de la détection entérique du glucose, associée à une réponse neuronale hypothalamique anormale, participait à la mise en place d'un Diabète de Type 2 (DT2). En plus de ces problèmes de détection de nutriments, les patients obèses et diabétiques souffrent de troubles de la motilité intestinale (en particulier d'une hypercontractilité intestinale), liés à une atteinte du Système Nerveux Entérique (SNE). En effet, ce dernier est constitué d'environ 600 millions de neurones interconnectés chez l'Homme, contrôlant les contractions des muscles lisses intestinaux. D'un point de vue régulation, le SNE communique en permanence avec le Système Nerveux Central (SNC) via des voies nerveuses afférentes et efférentes. L'équipe s'intéresse au rôle de l'apeline en tant que nouvelle cible thérapeutique potentielle pour traiter le DT2. En particulier, notre équipe a récemment montré que l'apeline était libérée par les entérocytes dans la partie proximale de l'intestin, et qu'à ce niveau elle contrôlait l'absorption intestinale du glucose. Cependant, le fait que l'apeline puisse également cibler les neurones du SNE, et donc moduler la contractilité intestinale, n'était pas encore démontré. Lors de ce travail de thèse, nous avons ainsi pu montrer qu'en fonction de sa concentration, l'apeline activait des populations neuronales entériques différentes provoquant une stimulation ou, au contraire, une inhibition des contractions duodénales. La stimulation de cette contractilité duodénale par de faibles concentrations d'apeline entraîne une augmentation de l'absorption intestinale de glucose, mais également une diminution de la libération de NO hypothalamique, aboutissant à une moindre utilisation de ce dernier par le muscle squelettique. A l'inverse, de fortes concentrations d'apeline sont associées à une diminution de cette activité duodénale, entraînant un retour de l'ensemble de ces paramètres à des niveaux contrôles. Dans un second temps, nous avons voulu tester si cette motilité duodénale pouvait être considérée comme une cible thérapeutique pour traiter le DT2. Pour cela, nous avons effectué un traitement oral quotidien, pendant une semaine, avec la concentration d'apeline capable de diminuer l'activité duodénale, chez des souris obèses-diabétiques. Cette stimulation chronique par l'apeline permet de restaurer la contractilité duodénale de ces souris diabétiques au même niveau que celle de souris saines. De plus, cet effet est associé à une amélioration de leur tolérance au glucose ainsi que leur index de résistance à l'insuline. Ainsi, ce doctorat a permis de décrire un nouveau mode de communication entre l'intestin et le cerveau dans le contrôle de l'homéostasie glucidique. En effet, moduler les contractions duodénales en modifiant l'activité du SNE permettrait non seulement d'impacter l'absorption intestinale de glucose, mais également d'activer un axe duodénum-hypothalamus aboutissant au contrôle de l'utilisation périphérique de glucose. Dès lors, ce couplage " SNE-contraction duodénale " représenterait une cible thérapeutique prometteuse dans le traitement de maladies métaboliques telles que le DT2. / Prior to this PhD, several studies had determined that the small intestine, the site of glucose absorption, is the first organ involved in the control of glucose homeostasis during food intake. In particular, enteric glucose detection has been demonstrated to impact its utilization by muscles and liver, via a central relay involving hypothalamic nitric oxide (NO) release. Moreover, our group has also demonstrated that an alteration of enteric glucose detection, associated with an abnormal hypothalamic neuronal response, participates in type 2 diabetes (T2D) development. In addition to these defaults of nutrients detection, obese and diabetic patients suffer from intestinal motility disorders (in particular intestinal hypercontractility), linked to an alteration of the Enteric Nervous System (ENS). The ENS is composed of 600 million interconnected neurons in humans, known to control intestinal smooth muscles. The ENS permanently communicates with the Central Nervous System (CNS) via afferent and efferent nervous messages. Our team studies the role of apelin as a new potential therapeutic target to treat T2D. In this context, our group has recently demonstrated that apelin is released by the enterocytes in the proximal part of the intestine. At this site, apelin controls intestinal absorption of glucose. However, it hadn't been addressed yet whether apelin is also able to target enteric neurons, and consequently modulate intestinal contractility. During this PhD, we have highlighted that, depending of its concentration, apelin activates different enteric neuronal populations, leading to stimulation or, on the contrary, inhibition of duodenal contractions. Stimulation of this duodenal contractility by low concentrations of apelin causes an increase in intestinal glucose absorption, but also a decrease in hypothalamic NO release, leading to a reduced utilization of glucose by skeletal muscle. Conversely, high concentrations of apelin are associated with a decrease in the duodenal activity, leading to the restoration of all these parameters at basal levels. Then, we wanted to test whether duodenal motility could be considered as a therapeutic target to treat T2D. We performed a daily oral treatment, during one week, with the concentration of apelin able to decrease duodenal activity in obese and diabetic mice. We have shown that this chronic apelin treatment restores duodenal contractility in diabetic mice, at a similar level to that observed in normal mice. Moreover, this effect is associated with an improved glucose tolerance and insulin resistance index. Thus, this PhD describes a new mode of communication between the intestine and the brain, in the control of glucose homeostasis. Indeed, the modulation of duodenal contraction by targeting ENS activity could not only impact intestinal glucose absorption, but also activate a duodenum-hypothalamus axis, leading to the control of peripheral glucose utilization. Consequently, the "ENS-duodenal contraction" coupling could represent a promising therapeutic target to treat metabolic diseases such as T2D.

Clostridium difficile infection (CDI) is a major healthcare-associated disease with high recurrence rates. Host colonization is critical for the infectious process, both in first episodes and in recurrent disease, with biofilm formation playing a key role. The ability of C. difficile to form a biofilm on abiotic surfaces is established, but has not yet been confirmed in the intestinal tract. Here, four different isolates of C. difficile, which are in vitro biofilm producers, were studied for their ability to colonize germ-free mice. The level of colonization achieved was similar for all isolates in the different parts of the murine gastrointestinal tract, but pathogen burden was higher in the cecum and colon. Confocal laser scanning microscopy revealed that C. difficile bacteria were distributed heterogeneously over the intestinal tissue, without contact with epithelial cells. The R20291 strain, which belongs to the Ribotype 027 lineage, displayed a unique behavior compared to the other strains by forming numerous aggregates. By immunochemistry analyses, we showed that bacteria were localized inside and outside the mucus layer, irrespective of the strains tested. Most bacteria were entrapped in 3-D structures overlaying the mucus layer. For the R20291 strain, the cell-wall associated polysaccharide PS-II was detected in large amounts in the 3-D structure. As this component has been detected in the extrapolymeric matrix of in vitro C. difficile biofilms, our data suggest strongly that at least the R20291 strain is organized in the mono-associated mouse model in glycan-rich biofilm architecture, which sustainably maintains bacteria outside the mucus layer.

Natural killer (NK) cells represent a crucial component of the innate immune system and are primarily regulated by the interactions of their activation and inhibitory receptors with ligands available on target cells. The genetically linked Ly49 and NKR-P1 family of receptors constitute two of the major regulatory receptor systems used by NK cells and have been shown to bind different ligands. Whereas the Ly49 receptors survey MHC-I ligands on target cells, the NKR-Pl receptor family members bind to various members of the C-type lectin-related (Clr) family. Interestingly, NKR-P1 and Clr haplotypes possess a stable genomic polymorphism across multiple mouse strains, suggesting that this inhibitory receptor:ligand relationship has an important role in the maintenance of host cellular cognate specificities. The NKR-P1 and Clr receptor-ligand pairs identified in mice include the NKR-P1B:Clr-b and the NKR-P1G:Clr-f interacting pairs. Previous RT-PCR and in situ RNA hybridization data generated by our laboratory determined that kidney tubular epithelium as well as the small and large intestinal epithelial cells specifically and highly expresses the Clr-f transcripts. Contrarily, the Clr-b transcripts were only detected on hematopoietic cells of various lymphoid organs and kidneys. Moreover, foregoing studies revealed that the loss of Clr-b following viral or chemical induced stress mediates NK cell killing of the target cell, suggesting a tissue-specific immune-surveillance mechanism in parallel with the global MHC-I-dependent missing-self model. However, the role of the NKR-P1B:Clr-b recognition-system have never been examined in the intestine. Additionally, the role of Clr-f in the kidney and intestines, where they are highly expressed, has not been investigated. For these reasons, I aimed in my thesis to provide a better understanding of the functional aspect of the NKR-P1B:Clr-b and NKR-P1G:Clr-f recognition systems in mediating gut mucosal and renal homeostasis, respectively. First, in order to determine the role of NKR-P1B and Clrb receptor:ligand pair as a “missing-self” immunosurveillance system in the gut, I started by identifying the expression pattern of both the receptor and ligand on various intestinal cells. My results demonstrate that NK cells do not represent the major NKR-P1B-expressing cells in the gut lamina propria. Instead, ILC3 subsets constituted the predominant cell population expressing the receptor, whereas γδT cells composed a small fraction of NKR-P1B+ lymphocytes. In addition, the NKR-P1B expression on myeloid cells was exclusive to colon macrophages and DC subsets. Interestingly, the highest percentage of NKR-P1B+ immune cells was found in the gut, which suggests the dominant role of NKR-P1B in regulating immune functions at the level of intestinal mucosa. As expected, the expression of the NKR-P1B ligand, Clr-b, appeared on all innate immune cell types in the gut. Next, using oral infection models of Salmonela typhimurium and Citrobacter rodentium, I showed that NKR-P1B-deficient NK cells, ILC3 and γδ T cells are hyporesponsive compared to their WT counterparts. In particular, gut NKR-P1B-deficient NK cells and γδT cells secreted low levels of IFNγ cytokine while infected with S.typhimurium. Importantly, the decreased IFNγ secretion by NK and γδT cells was associated with an increased dissemination of the bacterium into the knockout spleens at day 5 post-infection. Likewise, I detected a significant decrease in IL-22 cytokine production by NKR-P1B-deficient ILC3 compared to their WT counterparts at both steady state and following C.rodentium infection. Next, I address the potential role of Clr-f in the kidney. Renal tubular epithelial cells have been shown to express high levels of Clr-f transcripts. Epithelial cells constitute the major cellular component of kidney tubules and are well known to mediate metabolic waste excretion, reabsorption of essential molecules as well as other physiological functions, such as ions exchange and water retention. To determine the role of Clr-f in renal epithelial cells, I generated a Clr-f-deficient mouse with the help of two of my previous lab colleagues. Importantly, chemical analysis on urine and serum samples from knockout and WT littermates indicated that Clr-f-deficient kidneys display a decreased filtration capacity. In particular, higher creatinine levels were detected in the Clr-f deficient serum. In addition, Clr-f-deficient mice appeared to have a lower fractional excretion of sodium (FENa) in their urine filtrates in comparison to WT excreted urine. Blood pressure measurements on the same mice at 12 and 24 weeks of age revealed a hypotensive phenotype in the Clr-f-deficient mice. Furthermore, pathological assessment of Clr-f-deficient kidneys exhibited moderate and aggravated lesions of the tubular epithelium along with marked glomerular mesangiolysis. Lastly, flow cytometry analysis on isolated lymphocytes from Clr-f-deficient and WT mice demonstrated comparable immune infiltrates between the two mouse genotypes. Altogether, our data shows that the absence of Clr-f results in the development of glomerular and tubular lesions in an immune-independent manner leading to an abnormal kidney function. Additionally, the disruption of NKR-P1B:Clr-b recognition system results in abnormal innate immune cell number and function in the mouse intestine. These novel findings sheds light on the important role of Clr-f in maintaining healthy kidney morphology and function, as well as the crucial role for NKR-P1B:Clr-b interactions in mediating intestinal homeostasis at steady and infected states.

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.