No description available.

No description available.

Le microbiote humain est défini par l’ensemble des microbes habitant un site corporel en particulier. Les différents microbiotes de l’Homme, notamment le microbiote intestinal qui est le plus étudié, peuvent moduler de nombreux mécanismes biologiques dont le métabolisme et la réponse immunitaire. Un débalancement du microbiote au niveau des espèces qui le composent, ou dysbiose, a été associé à plusieurs maladies inflammatoires comme le diabète, l’obésité, mais aussi divers types de cancer. De plus, il a été démontré que les bactéries pouvaient avoir un impact sur la réponse des patients aux thérapies contre le cancer. Le cancer du sein est le cancer le plus mortel chez la femme. Or, l’étiologie de la maladie reste incertaine. Récemment, il a été montré que des bactéries pouvaient infiltrer les tissus plus profonds comme le tissu mammaire, formant un microbiote local. Considérant l’impact que la dysbiose peut avoir sur la réponse immunitaire antitumorale et la réponse aux traitements, nous avons émis comme hypothèse qu’une présence bactérienne intratumorale similaire, en composition et en quantité, à celle du tissu normal non-cancéreux affecte la progression du cancer du sein ainsi que le devenir clinique des patientes. La présence du microbiote intratumoral du sein a donc été validée par la détection de plusieurs composants bactériens sur des coupes tumorales à l’aide de marquages moléculaires. Puis, nous avons évalué le rôle potentiel de ce microbiote en quantifiant et identifiant les espèces bactériennes présentes dans les tumeurs et les tissus normaux adjacents des patientes de notre cohorte du cancer du sein. Nos résultats montrent une abondance moins élevée de l’ADN bactérien dans les tumeurs du sein comparativement aux tissus normaux adjacents appariés, suggérant qu’une altération du microbiote mammaire est associée au cancer. De plus, les patientes ayant un signal bactérien très faible dans leur tumeur avaient un nombre de récidives plus élevé. Cette influence de la quantité apparente de bactéries sur le devenir clinique a été observée principalement chez les patientes ayant une tumeur avancée, soit un grade ou un stade élevé, et de sous-types moléculaires Luminal HER2+, HER2+ (non-luminal) et Luminal B. Aucune relation n’a été observée entre la composition bactérienne du microbiote intratumoral mammaire et la récidive. Nos travaux suggèrent une implication pronostique et thérapeutique de la charge bactérienne du microbiote associé aux tumeurs mammaires. / The human microbiota is defined by all the microbes inhabiting a specific body site. The different human microbiota, and in particular the intestinal microbiota which is the most studied, can modulate many biological mechanisms, including metabolism and the immune response. An imbalance in the bacterial species that compose the microbiota, or dysbiosis, has been associated with several inflammatory diseases such as diabetes, obesity, but also various types of cancer. Additionally, bacteria have been shown to impact the response of patients to cancer therapy. Breast cancer is the deadliest cancer in women. However, the etiology of the disease remains uncertain. Recently, it has been shown that bacteria can infiltrate deeper tissues like breast tissue, forming a local microbiota. Considering the impact that dysbiosis can have on the anti-tumor immune response and the response to treatments, we hypothesized that an intratumoral bacterial presence similar in composition and quantity to that of normal non-cancerous tissue affects the progression of breast cancer, as well as the clinical outcomes of patients. The presence of the intratumoral breast microbiota was therefore validated by the detection of several bacterial components on whole tumor sections using molecular staining. Then, we evaluated the potential role of this microbiota by quantifying and identifying the bacterial species present in tumors and adjacent normal tissues of patients in our breast cancer cohort. Our results show a lower abundance of bacterial DNA in breast tumors compared to adjacent paired normal tissues, suggesting that an alteration of the mammary microbiota is associated with breast cancer. In addition, patients with a very low bacterial signal in their tumor had a higher number of recurrences. This influence of the apparent quantity of bacteria on the clinical outcomes has been observed mainly in patients with an advanced tumor, either a high grade or a high stage, and of the Luminal HER2+, HER2+ (non-luminal) and Luminal B molecular subtype. No relationship has been observed between the bacterial composition of the breast intratumoral microbiota and the recurrence. Our work suggests a prognostic and therapeutic implication of the bacterial load of the microbiota associated with breast tumors.

Culicoides (Diptera: Ceratopogonidae) are small (<3mm) blood feeding flies. These flies are biological vectors of viruses, protozoa and filarial nematodes affecting birds, humans, and other animals. Among the viruses transmitted those causing bluetongue (BT), African horse sickness (AHS) and epizootic haemorrhagic disease (EHD) are of major veterinary significance. Culicoides (Avaritia) imicola Kieffer, a proven vector of both AHS and BT viruses, is the most abundant and wide spread livestock-associated Culicoides species in South Africa. Field isolations of virus and oral susceptibility studies, however, indicated that a second Avaritia species, C. bolitinos Meiswinkel may be a potential vector of both BT virus (BTV) and AHS virus (AHSV). Differences in oral susceptibility, which are under genetic control, of populations from different geographical areas to viruses may be an indication of genetic differences between these populations, which may be the result of limited contact between these populations. A good knowledge of the distribution, spread and genetic structure of the insect vector is essential in understanding AHS or BT disease epidemiology. In the present study, an effort was made to gather field specimens of both C. imicola and C. bolitinos from different areas within their natural distribution in South Africa. The aim was to partially sequence two mitochondrial genes from these specimens and to analyse the sequence data making use of phylogenetic trees to clarify the genetic relationships between individuals or groups collected from geographically distinct sites. The two species were collected from four geographically separated areas in South Africa viz. Gauteng Province, Eastern Cape Province, Western Cape Province as well as the Free State Province. DNA was extracted from a total of 120 individual midges of the two Culicoides species using DNA extraction kits. Extracted DNA was analysed using PCR, sequencing as well as phylogenetic methods. A total of 117 mitochondrial DNA COI and 104 mitochondrial 16S ribosomal RNA Culidoides</i. sequences were analysed. DNA sequence polymorphism and phylogenetic relationships of various groups of C. imicola and C. bolitinos midges were determined. The results of the phylogenetic analysis of Culicoides populations using mitochondrial COI gene fragment showed that, at least one subpopulation of C. imicola and two distinct genotypes of C. bolitinos species do exist in South Africa, and further analysis is necessary. This study showed that COI has the potential to separate Culicoides midges based on their geography / Dissertation (MSc)--University of Pretoria, 2010. / Veterinary Tropical Diseases / unrestricted

The cell wall provides a complex and rigid structure to the plant for support, protection from environmental factors, and transport. It is mainly composed of polysaccharides, proteins, and lignin. Arabinoxylan (AX), pectin (P), and cellulose (C) are the main components of cereal cell walls and are particularly concentrated in the bran portion of the grain. Cereal arabinoxylans create networks in plant cell walls in which other cell wall polysaccharides are imbedded forming complex matrices. These networks give an insolubility profile to plant cell wall. A previous study in our lab showed that soluble crosslinked arabinoxylan with relatively high residual ferulic acid from corn bran provided advantageous <i>in vitro </i>human fecal fermentation products and promoted butyrogenic gut bacteria. In the present work, arabinoxylan was isolated from corn bran with a mild sodium hydroxide concentration to keep most of its ferulic acid content. Highly ferulated corn bran arabinoxylan was crosslinked to create an insoluble network to mimic the cereal grain cell wall matrices. Firstly, arabinoxylan film (Cax-F), pectin film (P-F), the film produced by embedding pectin into arabinoxylan networks (CaxP-F), and cellulose embedding arabinoxylan matrices (CaxC-F), and embedding the mixture of cellulose and pectin into arabinoxylan networks (CaxCP-F) were fabricated into simulated plant cell wall materials. Water solubility of films in terms of monosaccharide content was examined and revealed that Cax-F was insoluble, and P-F was partially insoluble, and nanosized pectin and cellulose were partially entrapped inside the crosslinked-arabinoxylan matrices. In a further study, these films were used in an <i>in vitro </i>human fecal fermentation assay to understand how gut microbiota access and utilize the different simulated plant cell walls to highlight the role of each plant cell wall component during colonic fermentation. <i>In vitro </i>fecal samples, obtained from three healthy donors were used to ferment the films (Cax-F, P-F, CaxP-F, CaxC-F, and CaxCP-F) and controls (free form of cell wall components -Cax, P and C). The fabricated films that were compositionally similar to cell walls were fermented more slowly than the free polysaccharides (Cax and P). Besides, CaxP-F produced the highest short chain fatty acids (SCFA) amount among the films after 24 hour <i>in vitro </i>fecal fermentation. Regarding specific SCFA, butyrate molar ratio of all films was significantly higher than the free, soluble Cax and P. 16S rRNA gene sequencing explained the differences of the butyrate proportion derived from specific butyrogenic bacteria. Particularly, some bacteria, especially in a butyrogenic genera from Clostridium cluster XIVa, were increased in arabinoxylan films forms compared to the native free arabinoxylan polysaccharide. However, no changes were observed between P and P-F in terms of both end products (SCFA) and microbiota compositions. Moreover, CaxP-F promoted the butyrogenic bacteria in fecal samples compared with pectin alone, arabinoxylan alone, and the arabinoxylan film. Differences in matrix insolubility of the film, which was high for the covalently linked arabinoxylan films, but low for the non-covalent ionic-linked pectin film, appears to play an important role in targeting Clostridial bacterial groups. Overall, the cell wall-like films were useful to understand which bacteria degrade them related to their physical form and location of the fiber polymers. This study showed how fabricated model plant cell wall films influence specificity and competitiveness of some gut bacteria and suggest that fabricated materials using natural fibers might be used for targeted support of certain gut bacteria and bacterial groups.

No description available.

No description available.

Il y a actuellement une pression mondiale pour revoir les pratiques d'utilisation des antimicrobiens (UAM) en production animale afin de limiter la propagation de bactéries résistantes aux antibiotiques. Conséquemment, les Producteurs de Poulet du Canada examinent la possibilité de réduire leur UAM en supprimant les antibiotiques médicalement importants en médecine humaine (AIM) des programmes préventifs avec la mise en place de leur stratégie de réduction de l’UAM. Cependant, les informations sont rares sur les conséquences de telles approches dans un contexte canadien. L'objectif de cette thèse était d'étudier les impacts sur les performances zootechniques, le contrôle des maladies intestinales et le microbiote cécal de deux stratégies de réduction de l'UAM dans des troupeaux commerciaux de poulets de chair par rapport à une UAM conventionnelle. Sur sept fermes commerciales de poulets de chair, un poulailler a été attribué aux traitements de réduction des antibiotiques pour six troupeaux consécutifs, tandis qu'un poulailler similaire sur le même site a été alloué à l'UAM conventionnelle (CONV) pour six troupeaux consécutifs (n = 84). Les stratégies de réduction des antibiotiques consistaient en l'utilisation continue d'ionophores dans l'alimentation sans (TX1) ou avec de l'acide butyrique (TX2). Aucune différence statistique (p > 0.05) n’a été notée entre TX1, TX2 et CONV sur les performances zootechniques et la santé intestinale. Les comptes d’oocystes d’Eimeria spp. étaient significativement (p < 0.05) inférieurs entre 22 et 34 jours d'âge dans les troupeaux CONV comparé aux TX1 et TX2. Le type de programme antibiotique a eu un impact relativement mineur (valeur R = 0.039), mais statistiquement significatif (p = 0.002), sur le microbiote cécal, tandis que les facteurs environnementaux ont montré les corrélations significatives (p = 0.001) les plus fortes avec le microbiote. Parmi les composantes du microbiote cécal associées à la croissance, le gain quotidien moyen (GMQ) était significativement associé à la Richesse bactérienne (p < 0.05). L’abondance relative de la famille bactérienne Lachnospiraceae fut la mesure la plus fortement corrélée à un GMQ augmenté, tandis que l’abondance relative de nombreuses familles bactériennes, incluant les Porphyromonadaceae, les Planococcaceae et les Veillonellaceae, fut corrélée à un faible GMQ. Ces taxons défavorables formaient un vaste réseau de corrélations positives entre elles, et négativement corrélées aux Lachnospiraceae. En conclusion, ces travaux ont contribué à améliorer la résilience de l'industrie avicole en fournissant des stratégies alternatives aux AIM pour prévenir les maladies intestinales. Des connaissances importantes sur le microbiote cécal des poulets de chair furent générées et pourront considérablement influencer les directions futures de la manipulation du microbiote pour favoriser la croissance. Par exemple, un paradigme important a été remis en question en illustrant que les additifs médicamenteux dans l'alimentation n’influencent que marginalement le microbiote cécal et que ce sont plutôt des facteurs environnementaux qui sont fortement impliqués dans la formation des communautés bactériennes cécales. La clé pour développer un microbiote cécal idéal chez les poulets de chair pourrait résider dans la capacité d'influencer ces facteurs, plus particulièrement l'exposition précoce à des communautés bactériennes bénéfiques et le contrôle de la flore résidente spécifique à la ferme. / There is a global pressure to review current antimicrobial use (AMU) practices in animal production and limit large-scale propagation of antibiotic resistant microorganisms. Consequently, the Chicken Farmers of Canada are examining the possibility to responsibly reduce AMU by discontinuing medically important antibiotics (MIAs) for humans from disease prevention programs of broiler chicken flocks through the implementation of their Antimicrobial Use Reduction Strategy. However, information is sparse on the consequences of such approaches in a Canadian commercial poultry production context. The general objective of this thesis was to investigate the impacts of two strategies reducing AMU in commercial broiler chicken flocks on zootechnical performance, control of intestinal diseases and the cecal microbiota compared to conventional AMU. On seven commercial broiler chicken farms, a house was allocated to the antibiotic reduction treatments for six consecutive flocks, while a similar house on the same premises was assigned to the conventional AMU (CONV) for six consecutive flocks (n = 84). The antibiotic reduction strategies consisted of continuous in-feed ionophores without (TX1) or with butyric acid (TX2). There were no statistical differences (p > 0.05) between TX1, TX2 and CONV for zootechnical performance and intestinal health. Predicted Eimeria spp. oocysts were significantly lower (p < 0.05) between 22 to 34 days of age in CONV flocks compared to TX1 and TX2. The type of antibiotic program had a relatively minor impact (R-value = 0.039), but statistically significant (p = 0.002), on the cecal microbiota composition, while environmental factors such as the farm and flock cycle showed the strongest statistically significant (p = 0.001) correlations with the microbiota composition (R-values of 0.239 and 0.374, respectively). Amongst the cecal microbiota components associated with weight gain, the average daily gain (ADG) was significantly associated with bacterial Richness (p < 0.05). The relative abundance of the bacterial family Lachnospiraceae was the most important measure correlated with ADG, while the relative abundance of numerous bacterial families, including Porphyromonadaceae, Planococcaceae and Veillonellaceae, were correlated with decreased growth rate. These unfavourable taxa formed a large network of positive correlations, indicating potential co-occurring synergies between these undesirable taxa. This network was also negatively correlated to Lachnospiraceae. In conclusion, the findings in this work contributed to improve the sustainability of the modern poultry industry by providing feasible alternatives to the practice of using MIAs for the prevention of intestinal diseases in broiler chickens. This project also generated important knowledge on the cecal microbiota of broiler chickens that could considerably influence future directions of microbiota manipulation in a perspective of improving zootechnical performance. For instance, an important paradigm was challenged by the indication that in-feed antibiotics and prebiotics may only influence marginally the microbiota during grow-out. Rather, this work suggests environmental factors are strongly involved in shaping the bacterial communities residing in the ceca of broiler chickens. Hence, the key to successfully develop an ideal cecal microbiota in broiler chickens may reside in the ability to influence such factors, more specifically the early exposure to beneficial bacterial communities and the control of farm-specific resident flora.

<p dir="ltr">ABSTRACT</p><p dir="ltr">Bovine Respiratory Disease (BRD) poses a significant challenge in the dairy and beef industry, contributing to high mortality, morbidity, and economic costs. Extensive research has aimed to enhance BRD diagnosis, focusing on various factors such as predisposition, environment, and epidemiology. While diverse methods have been developed for BRD detection, including clinical signs, behavioral changes, lung consolidation assessment via ultrasonography, and molecular techniques for microbiome analysis, accurate diagnosis remain inconsistent. Notably, many studies lack exploration of microbial interactions (fungi, viruses, and bacteria) within BRD-affected animals compared to healthy ones. Moreover, the impact of age, disease, and antibiotic treatment on the microbiome community remains understudied. Thus, additional analysis is crucial to understand the relationships between these factors and BRD development. This dissertation is divided into two parts, each addressing specific conditions. The first part focuses on characterizing the nasopharyngeal (NP) microbiome of dairy calves, pre-weaned and post-transported, and those diagnosed with BRD within the first two weeks of life. The objective is to identify NP microbiome changes as indicators of disease development, considering antibiotic treatment effects on NP alpha and beta diversity. The second part delves into characterizing the fungal and bacterial nasal cavity among BRD-affected and healthy cattle within the same pen. This section, presented in three chapters, explores the bovine nasal mycobiome in beef cattle, as well as the nasal microbiome in both dairy and beef cattle. The overarching goals of these studies are to evaluate differences in the nasal mycobiome or microbiome community between BRD-affected and healthy cattle, focusing on alpha, beta, and community compositions as potential disease indicators. Additionally, the aim is to determine if BRD-affected cattle exhibit higher abundance of BRD-pathobionts (fungi and bacteria) in the nasal cavity compared to healthy pen-mates. In conclusion, findings from this research emphasize the importance of incorporating both mycobiome and microbiome analyses in understanding BRD development. Future studies should consider geographical influences on nasal microbiome structure, highlighting the need for separate investigations in dairy and beef calves due to breed variations. Ultimately, studying mycobiome and microbiome ecology offers insights into microbial transitions from commensal to pathogenic farms in the bovine upper respiratory tract, supporting advancements in BRD prevention or mitigation strategies.</p>

Des études ont récemment mis en évidence le rôle des lipopolysaccharides (LPS) des bactéries à Gram négatif de la flore intestinale dans le processus de l’inflammation conduisant à l’obésité et au diabète de type 2.Le présent travail est réalisé dans le cadre d’une collaboration entre les équipes du Dr. Caroff (U. Paris-Sud, Orsay) et du Pr. Zhao (U. Jiao Tong, Shanghai). Les expériences présentées ont été réalisées lors de séjours dans les deux laboratoires.Il a été démontré en Chine que des bactéries Sulfato-réductrices (SRB) à Gram négatif étaient présentes en plus forte proportion dans la flore intestinale chez les souris suivant un régime gras. Les mêmes résultats ont été observés chez l'homme. L’hypothèse selon laquelle des SRB seraient à l’origine de grandes quantités d’endotoxines chez les obèses et les patients diabétiques a été émise. Plusieurs souches de SRB isolées de la flore intestinale humaine d’un sujet sain et d’un sujet diabétique ont été cultivées en Chine. Des études de relation structure/activité des LPS isolés de ces bactéries ont été réalisées dans le laboratoire Français pour déterminer leur rôle dans le développement des maladies métaboliques. Les souches isolées des deux sujets ont pu être classées dans le genre Desulfovibrio. Les LPS correspondants ont été extraits et purifiés par des méthodes mises au point dans l’équipe d’Orsay. La structure chimique a été élucidée par les méthodes suivantes : Electrophorèse, Chromatographie sur couche mince, Chromatographie en phase gazeuse et Spectrométrie de masse MALDI. C’est ainsi que des spectres de masse ont été obtenus et que la structure des lipides A, principes actifs des LPS, isolés de SRB a été décrite pour la première fois. Les activités biologiques testées (TNFα, IL-6) varient en fonction du nombre d’acides gras présents. Les LPS de SRB du patient sain ont une structure variable (Smooth versus Rough) en fonction de la quantité de fer présent dans le milieu, et ceux isolés du patient diabétique présentent des structures atypiques qui ne sont pas toutes inflamogènes. Une molécule membranaire inconnue, que nous avons nommée « Glycosyl’X » était co-extraite avec les LPS. Elle joue apparemment un rôle important dans la croissance des SRB et a été étudiée après des étapes de purification complexes. Les structures et le pouvoir inflammatoire de ces molécules dont la structure varie avec les souches, et qui chélatent le fer, ont été étudiées. Elles sont de nature principalement osidique et fixées à la membrane. La proportion de ces molécules par rapport aux LPS varie avec la quantité de fer disponible dans le milieu. Un milieu riche en fer favorise la croissance des Desulfovibrio portant les Glycosyl’X qui n’ont pas de pouvoir inflammatoire eux-mêmes, mais entrent en compétition avec les LPS, modulant ainsi indirectement l’activité de ces derniers. L’augmentation du nombre de Desulfovibrio conduisant à l’augmentation des molécules Glycosyl’X pourrait aussi moduler positivement (par présentation) ou négativement (par élimination des bactéries) l’adsorption du fer dans les intestins dont l’équilibre est essentiel pour l’homéostasie métabolique.Par ailleurs, la croissance des Desulfovibrio augmente la production d’Hydrogène Sulfuré connu pour son action délétère sur les cellules. Nous favorisons l’hypothèse selon laquelle son action sur la disjonction des cellules épithéliales permettrait le passage des différents LPS relargués par la flore Gram-négative intestinale, et même des bactéries entières, vers la circulation sanguine. / Recent studies have highlighted the role of lipopolysaccharide (LPS) in the intestinal flora (gut microbiota) which could contribute to the inflammation process leading to obesity and type 2 diabetes. This thesis is part of a collaborative project between the laboratories of Dr. Caroff (U. Paris -Sud, Orsay, France) and Prof. Zhao (U. Jiao Tong , Shanghai, China). It has been shown by Pr.Zhao’s team in 2010 that the Sulfate -Reducing Bacteria (SRB) were presented in greater proportion in the intestinal mice flora following a fat diet compared to mice following a normal diet. The same results were observed in humans. The starting hypothesis was that SRB could produce a large amount of endotoxin in obese and diabetic patients and play a role in the development of metabolic diseases. Several SRB strains isolated from the human intestinal flora of a healthy subject and of a diabetic subject were grown in the Chinese laboratory. Studies of their LPS structure / activity relationships were carried out in the French laboratory. The aim of this study was to determine their roles in the development of metabolic diseases.Strains isolated from the two subjects could be classified in the Desulfovibrio genus. The corresponding LPS were extracted and purified by the methods developed in the French laboratory. The chemical structure was elucidated by the following methods: Electrophoresis, Thin layer chromatography, Gas chromatography and MALDI mass spectrometry. The mass spectra were obtained and the structure of lipid A, the active part of LPS isolated from SRB was described here for the first time. The biological activities test (TNFα, IL-6) vary depending on the number of fatty acids present in their lipid A structure. The LPS of SRB isolated from the healthy patient had a variable structure (Smooth versus Rough) depending on the amount of iron present in the medium, and those isolated from diabetic patients had atypical structures are not all inflamogenic .An unknown membrane molecule, which we named "Glycosyl'X" was co-extracted with the LPS. It apparently plays an important role in the growth of SRB was investigated after complex purification steps. The structures and the inflammatory power of these molecules variying with strains chelating iron were studied. They are mainly of glycosidic nature and linked to the bacterial membrane.The proportion of these molecules relatively to LPS varies with the amount of iron in the medium. An environment rich in iron promotes the growth of Desulfovibrio Glycosyl'X, molecules but competes with LPS and indirectly modulates the activity of the latter. The increase number of Desulfovibrio leading to increased Glycosyl'X molecules may also modulate positively (by presentation) or negatively (by killing bacteria) the absorption of iron in the intestines which balance is essential for metabolic homeostasis.Furthermore, the growth of Desulfovibrio increasing the production of Hydrogen Sulfide is known for its deleterious effects on the cells. We favor the hypothesis that its action on the separation of epithelial cells favors the passage of different LPS released by the Gram- negative of intestinal flora and even whole cell bacteria into the bloodstream.