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International audience; Intestinal organoids are increasingly being used to study the gut epithelium for digestive disease modeling, or to investigate interactions with drugs, nutrients, metabolites, pathogens, and the microbiota. Methods to culture intestinal organoids are now available for multiple species, including pigs, which is a species of major interest both as a farm animal and as a translational model for humans, for example, to study zoonotic diseases. Here, we give an in-depth description of a procedure used to culture pig intestinal 3D organoids from frozen epithelial crypts. The protocol describes how to cryopreserve epithelial crypts from the pig intestine and the subsequent procedures to culture 3D intestinal organoids. The main advantages of this method are (i) the temporal dissociation of the isolation of crypts from the culture of 3D organoids, (ii) the preparation of large stocks of cryopreserved crypts derived from multiple intestinal segments and from several animals at once, and thus (iii) the reduction in the need to sample fresh tissues from living animals. We also detail a protocol to establish cell monolayers derived from 3D organoids to allow access to the apical side of epithelial cells, which is the site of interactions with nutrients, microbes, or drugs. Overall, the protocols described here is a useful resource for studying the pig intestinal epithelium in veterinary and biomedical research.

Pigs subjected to heat stress (HS) decrease their feed intake and growth. The objectives of the experiment were to determine the effects of live yeast (LY) supplementation (Saccharomyces cerevisiae var boulardii CNCM I-1079) on feeding behaviour, energy metabolism and faecal microbiota composition of finishing boars (n 10) housed in a respiration chamber at thermoneutrality (7 d at 22°C) or during HS (seven plus six days at 28°C). Dietary LY supplementation increased DM intake (P = 0·01) whatever the ambient temperature, whereas HS decreased feed intake whatever the dietary supplementation (P = 0·01). Dietary LY supplementation increased the number of meals (P = 0·02). Energy retention was higher with dietary LY supplementation (P < 0·01) but decreased during HS (P < 0·01). The skin temperature of the supplemented pigs was lower at thermoneutrality and increased during HS to a lesser extent than that of non-supplemented pigs (P < 0·01). Faecal microbiota composition was determined using 16S rRNA gene sequencing. Treponema, Christensenellaceae R-7, Ruminococcaceae UCG-002, Rikenellaceae RC9, Clostridium sensu stricto 1 and Romboutsia genera and some bacteria belonging to Alloprevotella, Oxalobacter and Anaeroplasma genera were more abundant under HS. LY supplementation attenuated HS effects on Romboutsia abundance, while decreasing the abundance of some bacteria from Ruminoccocus, Coprococcus, Peptococcus and Oxalobacter genera and increasing the abundance of beneficial bacteria from Lactococcus and Subdoligranulum genera. Our results suggest that higher level of the keystone species Ruminococcus bromii at thermoneutrality may be one of the causes for higher energy retention observed under subsequent HS.

International audience; In suckling mammals, the onset of solid food ingestion is coincident with the maturation of the gut barrier. This ontogenic process is driven by the colonization of the intestine by the microbiota. However, the mechanisms underlying the microbial regulation of the intestinal development in early life are not fully understood. Here, we studied the co-maturation of the microbiota (composition and metabolic activity) and of the gut barrier at the suckling-to-weaning transition by using a combination of experiments in vivo (suckling rabbit model), ex vivo (Ussing chambers) and in vitro (epithelial cell lines and organoids). The microbiota composition, its metabolic activity, para-cellular epithelial permeability and the gene expression of key components of the gut barrier shifted sharply at the onset of solid food ingestion in vivo, despite milk was still predominant in the diet at that time. We found that cecal content sterile supernatant (i.e. containing a mixture of metabolites) obtained after the onset of solid food ingestion accelerated the formation of the epithelial barrier in Caco-2 cells in vitro and our results suggested that these effects were driven by the bacterial metabolite butyrate. Moreover, the treatment of organoids with cecal content sterile supernatant partially replicated in vitro the effects of solid food ingestion on the epithelial barrier in vivo. Altogether, our results show that the metabolites produced by the microbiota at the onset of solid food ingestion contribute to the maturation of the gut barrier at the suckling-to-weaning transition. Targeting the gut microbiota metabolic activity during this key developmental window might therefore be a promising strategy to promote intestinal homeostasis.

Heating oils and oilseeds results in oxidized fatty acids with potential antimicrobial properties, that could affect digestive microbiota and therefore health. A long-term in vitro study was conducted to check the effects of one hydroperoxide, 13OOH cis-9,trans-11-C18:2 (13HPOD), and two aldehydes, hexanal and trans-2,trans-4-decadienal (T2T4D), on rumen bacteria and superoxide dismutase (SOD) activity. Rumen fluid was incubated with one of the three oxidation products for 54 h or 102 h. Controls without oxidation products were also incubated. Increasing incubation duration changed the bacterial community and caused acidification and probably oxidative stress, resulting in increased SOD activity. The bacterial community was highly affected by T2T4D, in particular the Bacteroidetes/Firmicutes ratio and the relative abundance of the Bacteroidales S24-7 group family, leading to an alteration of fermentation responsible for a higher final pH than those in control cultures and a diminution of SOD activity. Other oxidative products did not affect SOD activity, and hexanal did not modify the bacterial community compared to that of the control. The modification of the bacterial community by T2T4D represents a potential risk for the health of its host. Oxidative stress needs to be investigated in digestive ecosystems.

International audience; Postweaning feed restriction preserves rabbit digestive health after weaning, but the underlying physiological mechanisms are not yet understood. To elucidate whether the feeding intake pattern modification related to feed restriction might be involved, we studied the effects of both feed intake quantity and intake frequency. Animals were allotted at weaning (28 d old) in a 2 × 2 factorial design: feed intake quantity (AL = ad libitum vs R = 75% of AL) and fragmented feed distribution (FFD) (1 vs 13 distributions), thus forming four groups (AL1, AL13, R1 and R13). New Zealand White growing rabbits were used from weaning to slaughter (70 d old), to analyse mortality, morbidity, performance, intake behaviour, digestion and microbial activity. Seven days after starting feed restriction (35 d old, group R1), rabbits consumed 44% of the feed within 2 h, 65% in 4 h and in 7 h over 95%. Over the 28-70 d period, mortality was low (5.3%) while morbidity averaged 18.5% and neither was affected by treatment. However, FFD tended to decrease the morbidity rate during the first 14 days after weaning (P = 0.06). Feed conversion (28-70 d) was improved by restriction (+15%, P

International audience; The gut microbiota plays a key role in intestinal development at the suckling-to-weaning transition. The objective of this study was to analyze the production of metabolites by the gut microbiota in suckling and weaned piglets. We studied piglets raised in two separate maternity farms and weaned at postnatal day 21 in the same farm. The fecal metabolome (1H nuclear magnetic resonance) and the microbiota composition (16S rRNA gene amplicon sequencing) and its predicted functions (PICRUSt2) were analyzed in the same piglets during the suckling period (postnatal day 13) and 2 days after weaning (postnatal day 23). The relative concentrations of the bacterial metabolites methylamine, dimethylamine, cadaverine, tyramine, putrescine, 5-aminovalerate, succinate, and 3-(4-hydroxyphenylpropionate) were higher during the suckling period than after weaning. In contrast, the relative concentrations of the short-chain fatty acids acetate and propionate were higher after weaning than during the suckling period. The maternity of origin of piglets also influenced the level of some bacterial metabolites (propionate and isobutyrate). The fecal metabolome signatures observed in suckling and weaned piglets were associated with specific microbiota-predicted functionalities, structure, and diversity. Gut microbiota-derived metabolites, which are differentially abundant between suckling and weaned piglets (e.g., short-chain fatty acids and biogenic amines), are known to regulate gut health. Thus, identification of metabolome signatures in suckling and weaned piglets paves the way for the development of health-promoting nutritional strategies, targeting the production of bacterial metabolites in early life.

Intestinal organoids are self-organized 3-dimensional (3D) structures formed by a single layer of polarized epithelial cells. This innovative in vitro model is highly relevant to study physiology of the intestinal epithelium and its role in nutrition and barrier function. However, this model has never been developed in rabbits, while it would have potential applications for biomedical and veterinary research. Here, we cultured rabbit caecum organoids with either pharmacological inhibitors (2Ki medium) or L-WRN cells conditioned medium (L-WRN CM) to reconstitute the intestinal stem cell niche in vitro. Large spherical organoids were obtained with the 2Ki medium and this morphology was associated with a high level of proliferation and stem cells markers gene expression. In contrast, organoids cultured with L-WRN CM had a smaller diameter; a greater cell height and part of them were not spherical. When the L-WRN CM was used at low concentration (5%) for two days, the gene expression of stem cells and proliferation markers were very low, while absorptive and secretory cells markers and antimicrobial peptides were elevated. Epithelial cells within organoids were polarized in 3D cultures with 2Ki medium or L-WRN CM (apical side towards the lumen). We cultured dissociated organoid cells in 2D monolayers, which allowed accessibility to the apical compartment. Under these conditions, actin stress fibers were observed with the 2Ki medium, while perijonctionnal localization of actin was observed with the L-WRN CM suggesting, in 2D cultures as well, a higher differentiation level in the presence of L-WRN CM. In conclusion, rabbit caecum organoids cultured with the 2Ki medium were more proliferative and less differentiated than organoids cultured with L-WRN CM. We propose that organoids cultured with the 2Ki medium could be used to rapidly generate in vitro a large number of rabbit intestinal epithelial stem cells while organoids cultured with the L-WRN CM used at low concentration represent a suitable model to study differentiated rabbit epithelium.

SUMMARYThe objective of this study was to analyze in piglets the impact of weaning on the production of metabolites by gut bacteria and to determine whether early life environment influences the functional maturation of the gut microbiota. Fecal metabolome and microbiome were analyzed in piglets raised in two separate maternity farms and mixed at weaning. In piglets from both maternity farms, the relative abundance ofLactobacillusand of the predicted function “Fucose degradation” decreased after weaning while the relative abundance ofRuminococcus 2and of the predicted function “Starch degradation” increased. In piglets from the first maternity farm, the relative concentration of biogenic amines and the relative abundance ofEscherichi-Shigelladecreased after weaning while the relative concentration of short chain fatty acids and the relative abundance ofChristensenellaceae R-7 groupandRuminococcaceae UCG-002increased. These changes were not observed at weaning in piglets from the second maternity farm probably because they already had high relative concentration of short chain fatty acids and higher relative abundance ofChristensenellaceae R-7 groupandRuminococcaceae UCG-002during the suckling period. In conclusion, the functional maturation of the microbiota at weaning is highly dependent on the maternal environment in piglets.ORIGINALITY - SIGNIFICANCE STATEMENTBacterial metabolites are key molecular intermediates between the gut microbiota and host cells. Our study in piglets reveals that the metabolic activity of the gut microbiota shifts at weaning, a key developmental period for intestinal and immune health. We also show that this functional maturation of the gut microbiota is strongly influenced by maternal environment. Thus, targeting early life environmental factors is a promising strategy to program health trough the production of beneficial bacterial metabolites at the suckling-to-weaning transition.

Intestinal organoids are self-organized 3-dimensional (3D) structures formed by a single layer of polarized epithelial cells. This innovative in vitro model is highly relevant to study physiology of the intestinal epithelium and its role in nutrition and barrier function. However, this model has never been developed in rabbits, while it would have potential applications for biomedical and veterinary research. Here, we cultured rabbit caecum organoids with either pharmacological inhibitors (2Ki medium) or L-WRN cells conditioned medium (L-WRN CM) to reconstitute the intestinal stem cell niche in vitro. Large spherical organoids were obtained with the 2Ki medium and this morphology was associated with a high level of proliferation and stem cells markers gene expression. In contrast, organoids cultured with L-WRN CM had a smaller diameter; a greater cell height and part of them were not spherical. When the L-WRN CM was used at low concentration (5%) for two days, the gene expression of stem cells and proliferation markers were very low, while absorptive and secretory cells markers and antimicrobial peptides were elevated. Epithelial cells within organoids were polarized in 3D cultures with 2Ki medium or L-WRN CM (apical side towards the lumen). We cultured dissociated organoid cells in 2D monolayers, which allowed accessibility to the apical compartment. Under these conditions, actin stress fibers were observed with the 2Ki medium, while perijonctionnal localization of actin was observed with the L-WRN CM suggesting, in 2D cultures as well, a higher differentiation level in the presence of L-WRN CM. In conclusion, rabbit caecum organoids cultured with the 2Ki medium were more proliferative and less differentiated than organoids cultured with L-WRN CM. We propose that organoids cultured with the 2Ki medium could be used to rapidly generate in vitro a large number of rabbit intestinal epithelial stem cells while organoids cultured with the L-WRN CM represent a suitable model to study differentiated rabbit epithelium.

Weaning is a critical period for the health of rabbits, with a high sensitivity to digestive diseases. Allowing early consumption of solid feed in the nest of the suckling rabbit could help to maintain its health around weaning. In general, previous studies have focused on feed intake of rabbits when they are able to leave the nest, i.e. around 16 days. Herein, we provide a unique dataset of the dynamics of the onset of feed intake in suckling rabbits from 8 days to weaning. We quantified the solid feed intake behaviour and determined the dietary preferences for pellets according to their physical properties using nine pellets differing in diameter or compression rate. Additionally to the data provided in Paes et al. [1] we provide (i) the description of the nine pellets processing (ii) the description of the 3 point-scale system for nest quality evaluation, (iii) details on the device used to provide pellets in the nest, (iv) milk intake data and milk intake curve calculation and (v) pellet intake data according to physical characteristics. (c) 2020 Published by Elsevier Inc. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

International audience; n young rabbit, digestive disorders are frequently observed around weaning. Stimulating the onset of feed intake in the suckling rabbit might be a way to promote gut health. The aim of this study was to determine the rabbit's acceptability for different feed presentations and its preferences for flavours at an early stage of life. Two trials were conducted to evaluate the effects of physical form and flavouring on creep feed attractiveness. All the diets tested were provided in the nest from 3 to 17 days, and the daily intake per litter was recorded as of 8 days of age. In the first trial, five feed presentations were tested separately (n= 60 litters). Three dry presentations were chosen: commercial pellet (P), crumb from commercial pellet (cP) and crumb from beet pulp pellet (cBP). Hydrated feeds were also provided with either raw fodder beetroot (B) or a semi-solid feed in agar gel form produced with fodder beetroot juice and pulp (gB). In the second trial, double-choice tests were performed on four feed gels (n= 72 litters), leading to six comparison treatments. These agar gels were made of pellet mash without or with a sensory additive: one non-odorised control gel and three gels with 0.20% banana flavour, 0.06% red berry flavour and 0.10% vanilla flavour, respectively. In the first trial, kits ate more gB in fresh matter than other feed presentations (P< 0.001), with a total intake of 7.0 +/- 1.8 g/rabbit from 8 to 17 days. In DM, the total consumption of pellets P (1.6 +/- 0.4 g of DM/rabbit) was the highest together with the gB form (1.4 +/- 0.4 g of DM/rabbit), whereas cBP was barely consumed (0.3 +/- 0.1 g of DM/rabbit). Gel feed supplemented with vanilla was slightly more consumed than other flavoured and non-odorised gels (relative consumption of 57% when compared to control gel;P= 0.001). The gel feed intake was independent of the milk intake but was correlated with the litter weight at 3 days (r= 0.40,P< 0.001). In both trials, rabbit growth before and after weaning was not affected by the type of creep feed provided. Our results confirmed that providing creep feed promotes the solid intake of rabbits at early stages. Gel feed form motivated rabbits to eat and vanilla flavour supplementation increased the feed palatability. Those creep feed characteristics should be explored further for seeking effective stimulation of the onset of the feed intake in suckling rabbit.

International audience; Low-level contamination of food and feed by deoxynivalenol (DON) is unavoidable. We investigated the effects of subclinical treatment with DON, and supplementation with probiotic yeast Saccharomyces cerevisiae boulardii I1079 as a preventive strategy in piglets. Thirty-six animals were randomly assigned to either a control diet, a diet contaminated with DON (3 mg/kg), a diet supplemented with yeast (4 × 109 CFU/kg), or a DON-contaminated diet supplemented with yeast, for four weeks. Plasma and tissue samples were collected for biochemical analysis, 1H-NMR untargeted metabolomics, and histology. DON induced no significant modifications in biochemical parameters. However, lesion scores were higher and metabolomics highlighted alterations of amino acid and 2-oxocarboxylic acid metabolism. Administering yeast affected aminoacyl-tRNA synthesis and amino acid and glycerophospholipid metabolism. Yeast supplementation of piglets exposed to DON prevented histological alterations, and partial least square discriminant analysis emphasised similarity between the metabolic profiles of their plasma and that of the control group. The effect on liver metabolome remained marginal, indicating that the toxicity of the mycotoxin was not eliminated. These findings show that the 1H-NMR metabolomics profile is a reliable biomarker to assess subclinical exposure to DON, and that supplementation with S. cerevisiae boulardii increases the resilience of piglets to this mycotoxin.

International audience; The digestive microbiota plays a decisive role in shaping and preserving health throughout life. Rabbit younglings are born with a sterile digestive tract but then it gets progressively colonised by the microbiota of the nursing mother, by entering in contact with or ingesting the maternal droppings present in the nest. Here we posit that (i) offspring survival and (ii) lifespan of female rabbits are linked to how diverse their microbiota are. To test the hypothesis that maternal microbiota evolves in females having had different levels of offspring survival in their lifetime, we obtained 216 hard faecal samples from 75 female rabbits at ages 19.6, 31.6, 62.6 and 77.6 weeks. The annual mean offspring survival (MOS) at 64 days was calculated for each female then crossed against three alpha-diversity indexes (operational taxonomic units (OTUs), inverse Simpson index and Shannon index). Age was also analysed against these three parameters. The alpha-diversity indexes of the female faecal microbiota did not correlate with MOS, but they did decrease with age (e.g. from 712 OTUs at age 19.6 weeks to 444 OTUs at 77.6 weeks;P< 0.05). The age effect was also found in beta-diversity non-metric multidimensional scaling plots using the Bray-Curtis dissimilarity index and the unweighted UniFrac index but not for MOS. The ability of the microbiota composition from the faecal samples of young females (19.6 weeks old) to predict their lifespan was also evaluated. After subdividing the initial population into two classes (females that weaned a maximum of three litters and females living longer), we found no clear distinction between these two classes. To our knowledge, this is the first long-term study to characterise the gut microbiota of adult female rabbits through their reproductive life, thus laying foundations for using the gut microbiota data and its influence in studies on adult rabbits.

Collective housing is perceived as a possible way to improve rabbit welfare, especially among adult females, which are normally individually housed. Part-time group housing seems to allow a better balance between welfare and health than continuous group housing, but practical implementation and consequences for reproductive performance have not been extensively studied. The aim of this work was to compare weight, feed intake, litter size, injury occurrence, body integrity, and spatial location of female rabbits housed part-time in group housing (PGH group, n = 32) or housed individually (IH group, n = 8). Females were grouped by opening connecting hatches between four individual enriched cages (platform, wood stick and gnawing block). Collective housing started 12 days after artificial insemination and was interrupted at the 10th day (instead of the 15th day later as originally planned) due to high injury rates and severe injuries caused by fighting. The proportion of injured females increased from 25% on the first day of grouping to 63% on the 10th day. Female weight gain during the experiment was similar in the two groups. Litter size at weaning was 9% lower in the PGH group than in the IH group (9.2 vs 10.0, P

International audience; Les démarches participatives: un moyen pour faire évoluer conjointement les perceptions et les pratiques d'élevage dans la société et dans l'Institut ? Résumé Le bien-être des animaux d'élevage est une question qui interpelle l'ensemble de la société. Le mode de logement des animaux est particulièrement visé, notamment dans les systèmes ou les animaux sont confinés (truies, lapins, poules). Dans ce contexte, les unités expérimentales et le mode de production de connaissances de l'Institut doivent s'adapter pour accompagner les évolutions de la société. Le projet 3L (Living Lab Lapin ; 2018-2021) est un projet de recherche participative, basé sur la méthode du Laving Lab, qui a pour objectif de concevoir des systèmes cunicoles qui représentent une évolution notable pour le bien-être des lapins, perceptibles par les consommateurs et acceptables pour les éleveurs. Les acteurs impliqués sont des membres de la filière, des acteurs de la distribution, des représentants des consommateurs et 2 associations de protection animale. Après le mise en place des règles de fonctionnement pour favoriser le dialogue et la prise de décision (création de collège, consentement systémique), les idées émises par ces acteurs pour atteindre l'objectif se sont traduits par la mise en place de sept essais menés en 2018 sur l'IE PECTOUL. Il s'agissait d'évaluer les effets de la dimension du logement (hauteur, longueur), la nature du sol (grillage ou caillebotis), son enrichissement (terrier, matériaux à ronger), son agencement (toit ou non, plateforme, position des terriers) et la taille du groupe (femelles seules ou en groupe, lapereaux en petits ou grands groupes) sur l'expression des comportements propres à l'espèce et leurs performances (Fortun-Lamothe et al., 2019). Nous avons montré que certaines configurations permettent d'observer des comportements naturels non exprimables en système conventionnels (ronger, bondir, se dresser, se cacher, explorer, avoir des interactions sociales positives) ou d'être plus confortables (caillebotis) par des choix compatibles avec les contraintes d'élevage. Toutefois, en l'état actuel, l'élevage des femelles en groupe ne semble pas compatible avec la notion de bien-être (comportements agonistiques et blessures). En dernière partie du projet, les innovations produites seront testées en ferme commerciale. Au-delà de l'acquisition de connaissances sur la biologie du lapin et les systèmes cunicoles, les échanges inhérents à la démarche participative sont très riches d'enseignements et révèlent de fortes différences de perception de l'animal dans son système d'élevage entre acteurs d'origine variée. Cette démarche se révèle également féconde concernant nos pratiques de recherche. D'une part, les modalités testées ont permis de concevoir un nouveau logement modulable, pertinent à la fois pour les essais expérimentaux à visée agronomique et ceux à visée fondamentale, et compatible avec la réglementation sur l'expérimentation animale. D'autre part, les résultats obtenus viennent enrichir le fonctionnement de la structure chargée du bien-être animal de notre IE.

Efficacy of a new carvacrol-based product on Campylobacter jejuni in challenge test in vivo and impact on the whole caecal microbiota. 6. International Conference on Poultry Intestinal Health

Notice à reprendre pas de clé Ut au 13/09/2019; Weaning represents a critical period for rabbit, with a high susceptibility to gastrointestinaldiseases. Stimulating early solid feed intake could contribute to preserving health in rabbit. Thus,the aims of this study were, first, to quantify early solid intake and, second, to determine youngrabbit pellet preferences according to their physical properties. Double-choice tests of pelletsprocessed with different dies were conducted in two trials. An original feeding system was usedto specifically measure consumption of suckling rabbits in the nest independent of that of thedoes. Pellets were provided from 3 to 17 days in the nest box and intake was measured daily.From 15 to 35 days, kits received pellets in feeders and intake was measured every 4 days. In thefirst trial, four pellet diameters were tested in pairs against each other: (A) 2.0, (B) 3.0, (C) 4.0and (D) 6.0 mm. In the second trial, pellets of identical diameter (2.5 or 4.0 mm) were manufacturedwith three die channel lengths: (E) 10, (F) 12, (G) 14mm or (C) 18, (H) 20 and (I)24 mm. For a given diameter, pellets were tested in pairs. This resulted in six combinations pertrial (n=10 litters per combination). Solid feed intake began at 8 days for 89 out of 118 litters.Over the first 17 days of life, a rabbit ingested a total of 1.63 ± 0.76 g of dry matter in the nest inaddition to milk. The solid feed intake at 2 weeks of age was correlated with litter weight at thebeginning of the experiment (r=0.50 between 15 and 17 days; P < 0.05). In the feeders,rabbits selected pellet A (61%, 67% and 86% of relative consumption when compared with B, Cand D). In the second trial, pellet I was slightly disliked compared to C when provided in the nest(P < 0.05), and compared to H in the feeders (P < 0.05). It was concluded that suckling rabbitswere able to ingest solid feed in the nest box and to discriminate pellets according to theirpresentation when a choice was given. Providing young rabbits with an easy-access feedingsystem and an optimal pellet presentation may help to stimulate early solid intake and thus pavethe way for further studies on nutritional control of microbiota implantation

Simple Summary The weaning of young rabbits is a critical period that is often accompanied by digestive troubles. Innovations in feeding strategy are urgently needed to preserve rabbit health and to reduce the use of antibiotics. We show here that providing dehydrated alfalfa during weaning is a promising solution to manage health status by favoring the establishment of a proper digestive microbiota. Abstract The improvement of rabbit gut microbiota by modifying nutritional components of the feed or favoring its early intake of feed has been previously investigated. The early administration of dehydrated alfalfa (A) or fresh grass (G) for rabbits, during the peri-weaning period (30 and 45 days of age), and their effect on performance and caecal microbiota compared to a standard diet (C) were evaluated. Until 15 days of age, nine litters/group were housed in the maternal cage and milked once per day. From 15 to 30 days, the young rabbits could consume both milk and solid feed (pelleted for C or supplemental feed for A and G). At 30 days of age, the rabbits were weaned and, until 45 days, were kept in single cages following the same dietary protocol. No significant changes were found in the milk intake or the individual weight of young rabbits at 30 and 45 days. The caecal Firmicutes/Bacteroidetes (bacterial phyla ratio) increased with age (from 2.43 to 6.05 on average, at 30 and 45 days). The Ruminococcaceae/Lachinospiraceae (bacterial family ratio) was highest in the A group at both ages, followed by G then C. The early administration of dehydrated alfalfa is a promising solution to improve health status by favoring an appropriate digestive microbiota.

This study aimed to determine the influences of feeding strategy and diet for reproductive females on feed intake, BW, reproductive performances, and milk composition and their effects on kit performances from birth (d 0) to 70 d of age (d 70). A total of 133 does followed for 3 reproductive cycles and their offspring, 2,322 kits from 236 litters, were divided into 3 experimental groups that differed only by the diet offered to the doe. Three experimental diets were used: a reproduction (Repro) diet (11.01 MJ DE/kg, 24.0 g lipids/kg, 161 g starch/kg, and 343 g/kg NDF), a lactation (Lact) diet (11.88 MJ DE/kg, 49.0 g lipids/kg, 161 g starch/kg, and 302 g/kg NDF), and a fattening (Fatt) diet (9.73 MJ DE/kg, 23.0 g lipids/kg, 70 g starch/kg, and 415 g/kg NDF). In group RR, does received feed Repro throughout the study (d 0 to 42 of each cycle). In group RF, does received diet Repro from d 0 to 25 and d 35 to 42 and diet Fatt from d 25 to 35. In group LR, does received diet Lact from d 0 to 25 and diet Repro from d 25 to 42. Kits in all groups received diet F from d 18 to 70, where intake was restricted from d 35 to 63. Doe BW was similar throughout the study (4,495 g; P > 0.05). Doe feed intake differed only from weaning to the subsequent kindling (+7.8% in group RF; P = 0.042). Reproductive performances were similar, except for litter weight at birth (+3.6% in group LR; P = 0.029). From d 0 to 25, a negative energy balance was observed in does yet most markedly in group LR (-8.61 MJ vs. -3.15 and -2.39 for groups RF and RR, respectively; P 0.05). Feed intake per kit from d 18 to 25 was greater in groups RR and RF than in group LR (+26%; P 0.05) but was lowest in group RF after weaning compared to groups RR and LR (1.7 vs. 4.8 and 5.8%, respectively; P < 0.001). Our results suggest that stimulating milk production through the incorporation of fat at the beginning of lactation offers few benefits for females and had a negative effect on early solid feed intake, which could explain animal health after weaning.

Efficacy of formulated carvacrol on Campylobacter jejuni in challenge test in vivo and impact on the whole caecal microbiota. Colloque Adebiotech MBIO 2018 Les microbiotes et la santé humaine, animale et environnementale : Prévention et traitements du futur

International audience; Type B trichothecene mycotoxin deoxynivalenol (DON) is one of the most frequently occurring food contaminants. By inducing trans-activation of a number of pro-inflammatory cytokines and increasing the stability of their mRNA, trichothecene can impair intestinal health. Several yeast products, especially Saccharomyces cerevisiae, have the potential for improving the enteric health of piglets, but little is known about the mechanisms by which the administration of yeast counteracts the DON-induced intestinal alterations. Using a pig jejunum explant model, a whole-transcriptome analysis was performed to decipher the early response of the small intestine to the deleterious effects of DON after administration of S. cerevisiae boulardii strain CNCM I-1079. Compared to the control condition, no differentially expressed gene (DE) was observed after treatment by yeast only. By contrast, 3619 probescorresponding to 2771 geneswere differentially expressed following exposure to DON, and 32 signaling pathways were identified from the IPA software functional analysis of the set of DE genes. When the intestinal explants were treated with S. cerevisiae boulardii prior to DON exposure, the number of DE genes decreased by half (1718 probes corresponding to 1384 genes). Prototypical inflammation signaling pathways triggered by DON, including NF-B and p38 MAPK, were reversed, although the yeast demonstrated limited efficacy toward some other pathways. S. cerevisiae boulardii also restored the lipid metabolism signaling pathway, and reversed the down-regulation of the antioxidant action of vitamin C signaling pathway. The latter effect could reduce the burden of DON-induced oxidative stress. Altogether, the results show that S. cerevisiae boulardii reduces the DON-induced alteration of intestinal transcriptome, and point to new mechanisms for the healing of tissue injury by yeast.

Pigs are highly affected by dietary mycotoxin contamination and particularly by fumonisin. The effects of fumonisin on pig intestinal health are well documented, but little is known regarding its impact on gut microbiota. We investigate the effects of the fumonisin (FB1, 12 mg/kg feed) on the fecal microbiota of piglets (n = 6) after 0, 8, 15, 22, and 29 days of exposure. A control group of six piglets received a diet free of FB1. Bacterial community diversity, structure and taxonomic composition were carried out by V3&ndash, V4 16S rRNA gene sequencing. Exposure to FB1 decreases the diversity index, and shifts and constrains the structure and the composition of the bacterial community. This takes place as early as after 15 days of exposure and is at a maximum after 22 days of exposure. Compared to control, FB1 alters the ecological succession of fecal microbiota species toward higher levels of Lactobacillus and lower levels of the Lachnospiraceae and Veillonellaceae families, and particularly OTUs (Operational Taxonomic Units) of the genera Mitsuokella, Faecalibacterium and Roseburia. In conclusion, FB1 shifts and constrains age-related evolution of microbiota. The direct or indirect contribution of FB1 microbiota alteration in the global host response to FB1 toxicity remains to be investigated.

International audience; Motivation: Metagenomics leads to major advances in microbial ecology and biologists need user friendly tools to analyze their data on their own. Results: This Galaxy-supported pipeline, called FROGS, is designed to analyze large sets of amplicon sequences and produce abundance tables of Operational Taxonomic Units (OTUs) and their taxonomic affiliation. The clustering uses Swarm. The chimera removal uses VSEARCH, combined with original cross-sample validation. The taxonomic affiliation returns an innovative multi-affiliation output to highlight databases conflicts and uncertainties. Statistical results and numerous graphical illustrations are produced along the way to monitor the pipeline. FROGS was tested for the detection and quantification of OTUs on real and in silico datasets and proved to be rapid, robust and highly sensitive. It compares favorably with the widespread mothur, UPARSE and QIIME.; Avec le séquençage haut-débit (454, MiSeq), les pipelines de traitements de séquençage d'ARNr 16S actuels produisent de gros jeu de données. Le calcul des tables d'abondances d'OTU et leur affiliation taxonomique peinent à s'exécuter et les solutions les plus efficaces sont souvent dédiées aux spécialistes. Dans ce contexte, nous avons développé le pipeline "FROGS" : « Find Rapidly OTU with Galaxy Solution ». Développé sous environnement Galaxy, "FROGS" intègre un outil de prétraitement des données permettant le contigage de séquences, le nettoyage des données et la suppression des chimères. La déréplication des séquences se fait par un script python. L'étape de clusterisation s'effectue avec le logiciel SWARM. Un outil d'assignation retourne l’affiliation taxonomique de chaque OTU en utilisant à la fois l'algorithme RDPClassifier et NCBI blast+ sur la banque de données Silva SSU 119. Enfin, un outil de post-traitement permet aux utilisateurs de traiter la table d'abondance obtenue avec les filtres habituels, fournit des résultats statistiques et des illustrations graphiques. FROGS a été développé pour traiter de grandes quantités de données par l'utilisation d’outils innovants et une conception optimisée. De plus, il est portable sur toutes les plateformes Galaxy avec le minimum de dépendances informatiques et architecturales. FROGS a été testé sur plusieurs jeux de données simulées. L'outil se montre extrêmement rapide, robuste et hautement sensible pour la détection des OTU avec très peu de faux-positifs comparé aux autres pipelines largement utilisés par la communauté.

Les lapereaux naissent nus, incapables d’assurer seul une thermorégulation autonome suffisante, et ne sont qu’en partie mature sur les plans sensoriel, physiologique et moteur. Leurs interactions avec la mère sont limitées. En élevage, dès qu’ils sont capables de sortir du nid, ils accèdent à l’aliment de la lapine, bien qu’ils aient des besoins nutritionnels différents des siens. Face à ces apparentes fragilités, l’espèce a développé des adaptations physiologiques et comportementales efficaces comme l’existence de la phéromone mammaire, le comportement coprophage au nid et la dynamique de maturation du système digestif, qui sont autant d’atouts contribuant à la viabilité et robustesse des lapereaux au sevrage. Nous présentons ici certains leviers d’action envisageables en élevage (gestion des nids, homogénéisation des tailles et poids de portée, allaitement contrôlé, alimentation spécifique) pour valoriser ces atouts., Rabbits are born naked, unable to provide adequate self-thermoregulation if left alone and are only partly mature in sensory, physiological and motor terms. Interactions with the mother are limited. Solid food ingestion begins when the young are able to leave the nest and access their mother’s feeder, although their nutritional needs are different from hers. However, the species has developed physiological and behavioral adaptations such as the mammary pheromone, coprophagia in the nest and maturity of the digestive system that are all assets contributing to enhance viability and robustness around weaning. Husbandry practices potentially favorable to survival of the young may concern nest manipulation, homogenization of litters’ size and weight, controlled nursing and specific nutrition.

In rabbit breeding for meat production, the selection of future does for reproduction is based on the estimation of the genetic values of animals, which is based on the transmission of genetic information carried by DNA according to Mendelian laws. However, there are other pathways for transmission of traits from one generation to the next, such as epigenetic phenomena, behavioural heritage or microbiota. First, the mechanisms of action of these genetic and non genetic factors will be explained. In a second stage, consideration of these factors in the selection models is discussed. Finally, hypotheses and proposals of levers to optimize the transmission of maternal traits in breeding context are presented., Dans la filière cunicole, la sélection des futurs reproducteurs est réalisée à partir de l’estimation des valeurs génétiques des animaux qui repose sur la transmission selon des lois mendéliennes de l’information génétique portée par l’ADN. Toutefois il existe d’autres voies de transmission des caractères d’une génération à l’autre tels que les phénomènes épigénétiques, l’héritage comportemental ou le microbiote. Dans un premier temps, les mécanismes d’action de ces facteurs génétiques et non génétiques seront explicités. Dans un second temps la possibilité de prendre en compte ces facteurs dans les modèles de sélection est discutée. Enfin, des hypothèses et propositions de leviers d’action pour optimiser la transmission des caractères maternels en élevage sont présentées.