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Summary Heterogeneity of infection and extreme shedding patterns are common features of animal infectious diseases. Individual hosts that are super‐shedders are key targets for control strategies. Nevertheless, the mechanisms associated with the emergence of super‐shedders remain largely unknown. During chicken salmonellosis, a high heterogeneity of infection is observed when animal‐to‐animal cross‐contaminations and reinfections are reduced. We hypothesized that unlike super‐shedders, low‐shedders would be able to block the first Salmonella colonization thanks to a different gut microbiota. The present study demonstrates that (i) axenic and antibiotic‐treated chicks are more prone to become super‐shedders; (ii) super or low‐shedder phenotypes can be acquired through microbiota transfer; (iii) specific gut microbiota taxonomic features determine whether the chicks develop a low‐ and super‐shedder phenotype after Salmonella infection in isolator; (iv) partial protection can be conferred by inoculation of four commensal bacteria prior to Salmonella infection. This study demonstrates the key role plays by gut microbiota composition in the heterogeneity of infection and pave the way for developing predictive biomarkers and protective probiotics., The present study demonstrates that (i) axenic and antibiotic‐treated chicks are more prone to become super‐shedders; (ii) super or low‐shedder phenotypes can be acquired through microbiota transfer; (iii) specific gut microbiota taxonomic features determine whether the chicks develop a low‐ and super‐shedder phenotype after Salmonella infection in isolator; (iv) partial protection can be conferred by inoculation of four commensal bacteria prior to Salmonella infection. This study demonstrates the key role plays by gut microbiota composition in the heterogeneity of infection and pave the way for developing predictive biomarkers and protective probiotics.

The postnatal period is critical for early development. Due to the great plasticity of the digestive tract, this period constitutes a unique window to orient the digestive phenotypes. Xylo-oligosaccharides (XOS) produced from the hydrolysis of non-starch polysaccharides (NSPs) by xylanase are prebiotics acting on the caecal microbiota. In this work, we compared the effects on metabolome and caecal microbiota composition of early (starter) or late (grower) supplementation with a mixture of xylanase and XOS (Xyl.XOS) with an E. tenella challenge. Chicks fed a basal diet rich in NSPs were divided into four groups: without additive (D0-D22), with a supplementation of Xyl.XOS during the start-up period (D0-D9), the growth period (D10-D22), or during theentire period (D0-D22). Based on this full factorial design, effects on performance as well as on the metabolome and caecal microbiome were assessed (D9 and D22). During the start-up period, the addition of Xyl.XOS has a positive effect on growth. At D9, a decrease in Short Chain Fatty Acids (SCFAs) and Lachnospiraceae, producers of SCFAs observed in the caeca of supplemented animals with Xyl.XOS. In contrast, supplementation in the starter diet alone increased SCFA production until D22. We are actually evaluating the effect of this early supplementation on the microbiota at D22. Finally, animals inoculated with E. tenella, the supplementation with Xyl.XOS in grower reduced significantly the deleterious effects of infection on growth while early supplementation had no detectable effect. In conclusion, early supplementation with Xyl.XOS has a short and medium term effect on the metabolites and growth of the animals., La période postnatale est une période de forte plasticité permettant une orientation précoce des fonctionnalités digestives. Les xylo-oligosaccharides (XOS), produits de l’hydrolyse des polysaccharides non amylacés (NSPs) par la xylanase (Xyl), sont des prébiotiques agissant sur le microbiote caecal. Dans ce travail, nous avons comparé les effets sur le métabolome et le microbiote caecal d’une supplémentation précoce (démarrage) ou tardive (croissance) d’un mélange de xylanase et XOS (Xyl.XOS) en présence d’un challenge infectieux à E. tenella. Des poussins recevant un régime basal riche en NSP ont été répartis en quatre groupes : sans additif (J0-J22), avec ajout de Xyl.XOS en démarrage (J0-J9) ou en croissance (J10-J22) ou pendant toute la période (J0-J22). A partir de ce plan factoriel complet, les effets sur les performances ainsi que sur le métabolome et le microbiome caecal ont été évalués (J9 et J22). Lors de la période de démarrage, l’ajout du mélange Xyl.XOS a un effet positif sur la croissance. A J9, une diminution des acides gras à chaînes courtes (SCFAs) et des bactéries de la famille des Lachnospiraceae, productrices des SCFAs, a été observée dans les caeca des animaux supplémentés. A l’inverse, la supplémentation dans l’aliment démarrage seul augmente la production de SCFAs jusqu’à J22. Nous évaluons actuellement l’effet différé de cette supplémentation précoce sur le microbiote à J22. Enfin chez les animaux inoculés, la supplémentation tardive en Xyl.XOS réduit significativement les effets délétères de l’infection sur la croissance alors que la supplémentation précoce n'a pas eu d'effet détectable. En conclusion, la supplémentation précoce en Xyl.XOS a un effet à court et moyen terme sur les métabolites et la croissance des animaux.

International audience; Coccidiosis is a widespread intestinal disease of poultry caused by a parasite of the genus Eimeria. Eimeria tenella, is one of the most virulent species that specifically colonizes the caeca, an organ which harbors a rich and complex microbiota. Our objective was to study the impact of the intestinal microbiota on parasite infection and development using an original model of germ-free broilers. We observed that germ-free chickens presented significantly much lower load of oocysts in caecal contents than conventional chickens. This decrease in parasite load was measurable in caecal tissue by RT-qPCR at early time points. Histological analysis revealed the presence of much less first (day 2pi) and second generation schizonts (day 3.5pi) in germ-free chickens than conventional chickens. Indeed, at day 3.5pi, second generation schizonts were respectively immature only in germ-free chickens suggesting a lengthening of the asexual phase of the parasite in the absence of microbiota. Accordingly to the consequence of this lengthening, a delay in specific gamete gene expressions, and a reduction of gamete detection by histological analysis in caeca of germ-free chickens were observed. These differences in parasite load might result from an initial reduction of the excystation efficiency of the parasite in the gut of germ-free chickens. However, as bile salts involved in the excystation step led to an even higher excystation efficiency in germ-free compared to conventional chickens, this result could not explain the difference in parasite load. Interestingly, when we shunted the excystation step in vivo by infecting chickens with sporozoites using the cloacal route of inoculation, parasite invasion was similar in germ-free and in conventional chickens but still resulted in significantly lower parasite load in germ-free chickens at day 7pi. Overall, these data highlighted that the absence of intestinal microbiota alters E. tenella replication. Strategies to modulate the microbiota and/or its metabolites could therefore be an alternative approach to limit the negative impact of coccidiosis in poultry.

International audience; Deux défensines aviaires nommées AvBD2 et AvBD7, peptides antimicrobiens naturels de l’immunité innée des oiseaux, sont extraites et purifiées à partir de la moelle osseuse du poulet [1]. Elles sont actives contre des bactéries pathogènes Gram- et Gram+ et sont remarquablement résistantes à la protéolyse [2]. L’efficacité antimicrobienne de l’AvBD7 a été démontrée dans un modèle murin de salmonellose systémique [3]. Ces propriétés particulières font de l’AvBD2 et de l’AvBD7 des candidats thérapeutiques prometteurs en alternative aux antibiotiques. La production de ces molécules à grande échelle est nécessaire à leur développement industriel, c’est pourquoi un projet visant à faire la preuve de concept de production recombinante d’AvBD2 et d’AvBD7 fortement antimicrobiennes a été réalisé. Des systèmes d’expression, (i) chez la levure Yarrowia lipolytica qui bénéficie d’outils performants (promoteurs inductibles, nouvelles séquences de sécrétion) pour la production de protéines hétérologues [4] et (ii) chez la cellule S2 d’insecte qui a fait ses preuves pour produire des molécules structuralement très proches des défensines [5], ont été développés. La montée en échelle de production des défensines aviaires a été évaluée afin d’envisager une application pharmaceutique, avec une demande importante en santé publique et vétérinaire.

International audience; The autonomy for Protein-Rich resources of poultry feed in France is around 40%, due in particular to massive imports of soybean meals, which are economically and nutritionally competitive. The study ofnew French Protein-Rich Feedstuffs (FPRF) within the framework of VOCALIM has shown that technological processes make it possible to better exploit fiber-rich resources (rapeseed and sunflower meals), without affecting the performance or health of the animals. The genetic selection of animals could be a lever to further improve the valuation of these resources. Simulations up to 2023 showed a gain of 17 protein autonomy points in broilers production and a reduction in food costs of 2.8% thanks to these FPRF. Their use allows, according to the scenarios studied, to gain in protein efficiency and to reduce overall environmental impacts.; L’autonomie protéique de l’alimentation des volailles est en France d’environ 40%, en raison notamment d’importations massives de tourteau de soja, très concurrentiel sur le plan économique et nutritionnel. L’étude de nouvelles Matières Premières Riches en Protéines françaises (MPRP) dans le cadre du projet VOCALIM a permis de montrer que des procédés technologiques permettent de mieux valoriser des ressources riches en fibres (tourteaux de colza et tournesol), sans altérer les performances ou la santé des animaux. La sélection génétique des animaux pourrait être un levier pour encore améliorer la valorisation de ces ressources. Des simulations à l’horizon 2023 montrent un gain de 17 points d’autonomie protéique dans la filière poulet de chair et une réduction du coût alimentaire de 2,8% grâce à ces MPRP. Leur utilisation permet, selon les scénarios étudiés, de gagner en efficience protéique et de réduire globalement tous les impacts environnementaux.

International audience; Studies of the gut microbiota contribution to the host physiology and immunocompetence are facilitated by the availability of germ-free animal models, which are considered the gold standard. Nesting birds are ideal models for the production of germ-free animals since there is no need to raise their relatives under sterile conditions. Germ-free chickens are mainly generated from specific-pathogen-free (SPF) experimental lines, which are poorly representative of commercial chicken lines. The method proposed here allowed the production of germ-free chickens from the fast growing broiler line Ross PM3, commonly used by the poultry industry. Eggs were quickly collected after laying at a broiler breeder farm. They underwent a strict decontamination process from the collection to the introduction in a sterile egg hatching isolator. The chicks have been hatched and kept in these sterile isolators during the period necessary to control their sterility. Originally developed for an experimental SPF white leghorn line, the present protocol has been adapted not only to the Ross PM3 broiler line but also to quails. It therefore represents a robust and readily adaptable procedure to other poultry species and nesting birds of economic, biological or ecological relevance.

International audience; Eimeria tenella infection leads to a severe intestinal disease leading to high economic impact in poultry industry. Coccidiosis is frequently associated with a high prevalence of opportunistic infections. Our objective was to study during E. tenella infection the importance of immune cells and mediators of the inflammatory response on the severity of caecal lesions and on the potential dissemination of commensal bacteria. An original model of germ-free and conventional broilers chickens was developed to study the impact of the caecal microbiota on the physiopathology of the infection. Our results show that, at the same parasite load, lesions caused by E. tenella are dependent on the microbiota. Seven days post-infection, an increase of inflammatory mediators (interferon-g, colony stimulating factor, CSF-1, 2) are detected at the caecal tissue level in conventional chickens and germ-free chickens whereas interleukin-17A (IL-17A) is increased only in conventional chickens. Moreover, administration of microbiota to germ-free chickens 4 days post-E. tenella infection restored the caecal lesions and the expression of IL-17A to a similar level to conventional chickens suggesting that inflammatory cells producing IL-17A could play a role in the physiopathology of the infection. The lesions represent a rupture of the intestinal barrier, which, at homeostasis, protects the chicken against invasion of commensal bacteria. Our hypothesis is that intestinal lesions caused by the infection would lead to commensal bacterial translocation. This was confirmed with a non-pathogenic E. coli strain administered by oral route that presented a dissemination in the spleen during E. tenella infection. In conclusion, during infection, the microbiota is responsible for the inflammatory response via IL-17A and the formation of lesions. The loss of the intestinal integrity leads to commensal bacterial translocation that could contribute to the development of opportunistic diseases.

International audience; Coccidiosis is caused by the parasite Eimeria, the first parasite in poultry farms. E. tenella, the most virulent specie colonize the caeca rich in bacteria. Our objective was to study the impact of intestinal microbiota on E. tenella infection. An original model of germ-free and conventional broilers was developed. While using the same dose of E. tenella inoculum, germ-free chickens excrete 4000 fold less oocysts than conventional chickens 6 days post-infection. This lower parasite load in caecal tissues is measurable as soon as 2 days post infection. Several biological processes in the parasite cycle may explain this result (excystation, invasion, development, …). As the excystation is the first step of the parasite cycle, in vitro capacity of excystation of the parasite using intestinal contents and biles of chickens was studied. When using duodenal contents and biles from germ-free chickens, the excystation rate of sporozoites was higher in contrast to those from conventional chickens. To shunt the excystation step in vivo, chickens were infected with sporozoites by cloacal inoculation. Parasite invasion after 24h infection was similar between germ-free and conventional chickens. However, after 7 days of infection, there was still less parasite excretion and parasite tissue load in germ-free chicken compared to conventional chicken (500 fold) suggesting that the microbiota and its metabolites may play an important role on parasite replication. We also studied the development stages of the parasite by using specific gene of different parasite stages. A delay of schizonte and gamete specific gene expression was observed in caeca of germ-free chicken compared to conventional chickens. Overall, these data suggest that the microbiota and its metabolites may play an indirect role on bile content and subsequently on the excystation rate and, also on the parasite development. Consequently, modulation of microbiota composition could influence coccidiosis severity.

National audience

National audience

National audience

National audience; Colibacillosis, caused by some strains of Escherichia coli, a common host of the intestinal tract of poultry, is a multifactorial disease often occurring under deficient rearing conditions. The objectives of the COLISEE study are to prevent the disease by identifying field conditions associated with colibacillosis and by developing tools to characterize E. coli virulent strains. The UMT Sanivol conducts a study in 80 broiler farms. This article presents the intermediate results of the data collected in the first 40 farms. During the first visit, before the arrival of the chicks, swabs were collected in the houses. At the chicks’arrival, a swab on delivery box and ten chicks were sampled. These samples were analyzed for E. coli isolation. A notation of chick quality and behavior, and of ambient parameters were also collected. During the second visit at three weeks of age, ambient parameters and welfare indicators were noted. In case of colibacillosis suspicion, chickens were examined in laboratory for bacteriological diagnosis. The results of the first 40 flocks showed that E. coli was identified in 20 houses prior to the chicks’arrival (swab on litter in 11 houses, on walls in 9 houses, on wall subbases in 5 houses, on air inlet and equipment in 3 houses). E. coli was also identified from swabbing delivery boxes in 37 flocks and from chicks in 29 flocks (yolk and/or liver). Clinical colibacillosis cases were reported in 15 farms. These first results showed a detection of E. coli in half of the houses prior to the arrival of the chicks and a carriage of E. coli by the chicks at arrival in most of the flocks. The study of the rearing conditions and of the virulence of the E. coli strains will provide means of action for a better control of the disease; La colibacillose, provoquée par certaines souches d’Escherichia coli, un hôte commun du tube digestif des volailles, est une maladie multifactorielle qui peut se déclencher principalement suite à des conditions d’élevage défavorables. Les objectifs de l’étude COLISEE visent à prévenir la maladie par l’identification des facteurs déclenchants en élevage et à développer des outils de caractérisation des souches d’E. coli virulentes. Pour cela, une étude est conduite par l’UMT Sanivol dans 80 élevages de poulets de chair. Ce travail présente les résultats intermédiaires des données collectées dans les 40 premiers élevages. Lors de la première visite, avant l’arrivée des poussins, des chiffonnettes sont réalisées dans le bâtiment puis lors de leur mise en place, une chiffonnette de fonds de boite et dix poussins sont prélevés. Ces prélèvements sont analysés en bactériologie pour recherche d’E. coli. Une notation de la qualité des poussins, de leur comportement et des mesures d’ambiance sont également réalisées. Lors de la seconde visite à trois semaines d’âge, des mesures d’ambiance et des indicateurs de bien-être sont relevés. En cas de suspicion d’une colibacillose par l’éleveur, des poulets sont examinés au laboratoire pour diagnostic bactériologique. Les résultats des 40 premiers lots montrent qu’E. coli a été identifié dans 20 bâtiments avant l’arrivée des poussins (chiffonnettes de litière dans 11 bâtiments, de parois dans 9 bâtiments, de soubassements dans 5 bâtiments, des entrées d’air et du matériel dans 3 bâtiments). E. coli a également été identifié à partir des chiffonnettes de fonds de boites dans 37 lots et des poussins dans 29 lots (sur vitellus et/ou foie). Des colibacilloses cliniques ont été signalées dans 15 élevages. Ces résultats intermédiaires montrent une détection d’E. coli dans la moitié des bâtiments avant l’arrivée des poussins et un portage d’E. coli par les poussins à leur arrivée pour la plupart des lots. L’étude des facteurs déclenchants en élevage et de la virulence des souches d’E. coli permettra de fournir des moyens d’action pour une meilleure maitrise de la maladie.