HAL ENVT (Ecole Nationale Vétérinaire de Toulouse)
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Estimer les infections à Eimeria spp. en atelier d’engraissement d’agneaux à l’aide d’analyses coprologiques de mélange et de litière
No full textOvine coccidiosis is a major problem in fattening houses. Its treatment relies on the use of anticoccidials, administered after diagnosis in accordance with new European regulations. However, individual diagnostic methods are costly and time-consuming. In this study, we developed the use of mixed coprological analyses of 5 animal samples, as well as coprological analyses on soiled litter. The trial was carried out in a fattening shed, monitored on an almost weekly basis for almost two months in 2 stalls, sampling 50 lambs per stall and three litter samples. The three diagnostic methods (individual, mixed 5-samples and litter) showed strong correlations in terms of total coccidia oocyst excretion intensity, as well as pathogenic species. These results demonstrate that it is possible to monitor coccidial infections in animals using these two new sampling methods, and to obtain a reliable representation of both the prevalence of infection and its intensity within a group of animals. In this way, these two methods not only reduce the cost of diagnosis, but also the time spent at the sampling site and in the laboratory.La coccidiose ovine est une problématique importante dans les systèmes d’engraissement. Son contrôle repose sur l’utilisation d’anticoccidiens, à administrer après diagnostic selon la nouvelle réglementation européenne. Or, les méthodes de diagnostic individuelles sont coûteuses et chronophages. Dans cette étude, nous avons développé l’utilisation d’analyses coprologiques de mélange de 5 prélèvements d’animaux, ainsi que des analyses coprologiques sur litière souillée. L’essai a été réalisé dans un atelier d’engraissement, suivi de manière hebdomadaire durant presque deux mois, sur 2 loges, en prélevant individuellement 50 agneaux par loge et trois échantillons de litière par loge. Les trois méthodes de diagnostic (individuelles, de mélange de 5 échantillons individuels et d’échantillons de litière) ont présenté de fortes corrélations en termes d’intensité d’excrétion des oocystes de coccidies, mais également dans les proportions d’espèces pathogènes. Ces résultats démontrent qu’il est possible de suivre les infections des animaux par les coccidies avec ces deux nouvelles méthodes d’échantillonnage et d’avoir une représentation fiable de la prévalence de l’infection, mais également de son intensité au sein d’un lot d’animaux. Ainsi, ces deux méthodes permettent d’alléger le coût du diagnostic, mais également de réduire le temps passé sur le chantier de prélèvement et au laboratoire
metagWGS, a comprehensive workflow to analyze metagenomic data using Illumina or PacBio HiFi reads
No full textTo study communities of micro-organisms taxonomically and functionally, metagenomic analyses are now often used. If there is no reference gene catalogue, a de novo approach is required. Because genomes are easier to interpret than contigs, the recovery of metagenome-assembled genomes (MAGs) by binning of contigs from metagenomic data has recently become a common task for microbial studies. However, during this process, there is a significant loss of information between the assembly and the binning of contigs. This is why it is important to produce taxonomic and functional matrices for all contigs and not just those included in correct bins. In addition, Pacbio HiFi reads (long and of good quality) are now a possible, albeit more expensive, alternative to short Illumina reads. We therefore developed a workflow that is easy to install with dependencies fixed using singularity images and easy to use on a computing cluster, that is capable of analyzing either short or long reads, and that should allow analysis at the contig and/or bin level, depending on the user’s choice. Following is a presentation of metagWGS, a fully automated workflow for metagenomic data analysis. It uses a new tool for refining bins (called Binette) that we will demonstrate is more efficient than competing tools. Methods metagWGS is a Nextflow workflow distributed with two singularity images and complete documentation to facilitate its installation and use. Because the main original features of metagWGS concern binning (short and long reads) and the analysis of HiFi reads, we compared metagWGS with the MAG construction workflow proposed by PacBio to a public dataset used by Pacbio to promote its workflow. Results metagWGS differs from existing workflows by (i) offering flexible approaches for the assembly; (ii) supporting short reads (Illumina) or PacBio HiFi reads; (iii) combining multiple binning algorithms with a new bin refinement tool, referred to as “Binette”, to achieve high-quality genome bins; and (iv) providing taxonomic and functional annotation for all genes, all contigs built and bins. metagWGS produces more medium (708) and high-quality (255) bins on 11 public metagenomic samples from human gut data than the Pacbio HiFi dedicated workflow, referred to as the HiFi-MAGS-pipeline (659 medium quality bins and 231 high quality bins), primarily due to the better performance of Binette
TRPV4 stimulates colonic afferents through mucosal release of ATP and glutamate
No full textInternational audienceBackground and Purpose Abdominal pain is a leading cause of morbidity for people living with gastrointestinal disease. Whereas the transient receptor potential vanilloid 4 (TRPV4) ion channel has been implicated in the pathogenesis of abdominal pain, the relative paucity of TRPV4 expression in colon‐projecting sensory neurons suggests that non‐neuronal cells may contribute to TRPV4‐mediated nociceptor stimulation. Experimental Approach Changes in murine colonic afferent activity were examined using ex vivo electrophysiology in tissues with the gut mucosa present or removed. ATP and glutamate release were measured by bioluminescence assays from human colon organoid cultures and mouse colon. Dorsal root ganglion sensory neuron activity was evaluated by Ca 2+ imaging when cultured alone or co‐cultured with colonic mucosa. Key Results Bath application of TRPV4 agonist GSK1016790A elicited a robust increase in murine colonic afferent activity, which was abolished by removing the gut mucosa. GSK1016790A promoted ATP and glutamate release from human colon organoid cultures and mouse colon. Inhibition of ATP degradation in mouse colon enhanced the afferent response to GSK1016790A. Pretreatment with purinoceptor or glutamate receptor antagonists attenuated and abolished the response to GSK1016790A when given alone or in combination, respectively. Sensory neurons co‐cultured with colonic mucosal cells produced a marked increase in intracellular Ca 2+ to GSK1016790A compared with neurons cultured alone. Conclusion and Implications Our data indicate that mucosal release of ATP and glutamate is responsible for the stimulation of colonic afferents following TRPV4 activation. These findings highlight an opportunity to target the gut mucosa for the development of new visceral analgesics
Le sexage in-ovo des volailles : évolutions sociétales, techniques et réglementaires
No full textThis review describes the development of ovo-sexing techniques for poltry species, driven by changes in public opinion and legislation concerning animal welfare, and more specifically the culling of male chicks at one day old. This practice, highly criticized for several decades, has prompted the egg industry to find other alternatives, such as sexing (and then eliminating) the embryos befort hatch. The sexing technologies should meet several criteria to enable a successful implementation in routine. These criteria are mainly ethical, economic, sanitary and ecological.Ce manuscrit traite du développement des outils d’ovo-sexage chez les volailles, poussé par une évolution de l’opinion publique et des lois concernant le bien-être animal, et plus précisément concernant l’abattage des poussins mâles à un jour d’âge. Cette pratique hautement décriée depuis maintenant plusieurs dizaines d’années a poussé les acteurs de la filière à trouver d’autres alternatives ; la principale étant le sexage (et l’élimination) des embryons avant éclosion. Les technologies développées se doivent de répondre à plusieurs critères si elles veulent être commercialisées et pérennes. Ces critères sont principalement éthiques, économiques, sanitaires et écologique
Acetate is a beneficial nutrient for E. coli at low glycolytic flux
No full textInternational audienc
Les interférences entre les anticorps d’origine maternelle et la vaccination en médecine vétérinaire
No full textVaccination is a preventative method to combat various infectious diseases whose consequences can be severe. Immunization is especially important in young animals, who are generally more prone to develop severe forms of these diseases. However, the transfer of passive immunity, while providing initial protection to newborns, interferes with the active immunity that develops after vaccination. The goal is to determine whether there are interferences between maternal antibodies and vaccination in several species for different infectious diseases but also to assess if modified live vaccines are more likely to cause this phenomenon compared to inactivated vaccines. Another goal is to determine if there are methods to overcome these interferences, particularly through other vaccination strategies.La vaccination est la pierre angulaire des programmes de lutte contre diverses maladies infectieuses dont les conséquences peuvent être redoutables. Elle est d’autant plus importante chez les jeunes animaux qui sont généralement plus susceptibles de développer des formes graves de ces maladies. Cependant, le transfert de l’immunité passive, bien que constituant une première protection aux nouveau-nés, interfère avec l’immunité active qui se met en place après la vaccination. L’objectif est de déterminer si les interférences entre les anticorps d’origine maternelle et la vaccination existent chez plusieurs espèces dans le cadre de différentes maladies, et de déterminer si les vaccins à agents vivants ont plus tendance à engendrer ce phénomène, contrairement aux vaccins inertes. L’objectif est également de déterminer s’il existe des moyens de pallier ces interférences, notamment par le biais d’autres stratégies vaccinales
Impact of the use of an indigenous starter on microbial community structuring and aromatic profile of rocamadour protected designation of origin cheese
No full textInternational audienceThe use of indigenous strains as starters offers new opportunities that challenge the use of industrial starters, especially to strengthen the link between Protected Designation of Origin (PDO) cheeses and their terroir. This study investigated the effect of two starters, industrial and indigenous, on the microbial ecosystem and volatile organic compounds (VOCs) in Rocamadour PDO cheese. Metabarcoding analysis showed that regardless of the type of starter used, Lactococcus lactis and Geotrichum candidum largely dominated the microbial communities of Rocamadour (>96 %). The analysis of β-diversity based on the Bray-Curtis indices differentiated the starters according to their bacterial communities. VOC analysis showed that the starters were distinguished by three fatty acids characteristic of the goat cheese aroma (p-value <0.05): decanoic, hexanoic, and octanoic acids. Hexanoic acid was not present in cheeses produced with the indigenous starter. This fatty acid was positively correlated with the presence of Paucilactobacillus nenjiangensis, Lactiplantibacillus sp. and Enterobacteriaceae, these microorganisms that were also characteristic of cheeses made with the industrial starter. Octanoic and decanoic acid, on the other hand, were suggested to be correlated with the presence of Leuconostoc mesenteroides.Cheeses produced with the indigenous starter differed in bacterial communities and aromatic signatures.</div
Fast and Quantitative 2D NMR for metabolomic applications within MetaboHUB
No full textInternational audienc
Étude rudologique de la gestion des déchets d’activité de soins au sein d’une structure hospitalière vétérinaire : exemple d’application au CHUVAC de l’ENVT
No full textCare activities in veterinary medicine generate a considerable amount of waste, particularly due to the single-use nature of many materials. Furthermore, many of these wastes require special treatment due to the risks they present. In light of the significant current ecological challenges, many hospitals and organizations have begun efforts to reduce their environmental impact. In this context, an audit of the waste management system at the Veterinary Hospital of the National Veterinary School of Toulouse was conducted based on site visits, interviews with various stakeholders, and a questionnaire distributed to each department. It includes a description of the waste management processes of the school, as well as suggestions aimed at optimizing waste management in terms of practicality, cost-effectiveness, and biosafety. The proposed solutions are structured around several key areas: regulatory compliance, optimization of sorting for different waste streams, reduction in the use of disposable materials, and training and information for staff and students.Les activités de soins en médecine vétérinaire génèrent un nombre considérable de déchets notamment en raison de l’usage unique de nombreux matériels. De plus, certains de ces déchets nécessitent un traitement spécifique en raison des risques qu’ils représentent. Ainsi face aux importants enjeux écologiques actuels, de nombreux hôpitaux et organismes ont entamé des travaux pour réduire leur impact environnemental. Dans ce contexte, un audit de la gestion des déchets du Centre Hospitalier de l’Ecole Nationale Vétérinaire de Toulouse a été réalisé à partir de visites des locaux, d’entretiens avec les différents acteurs et le recueil d’un questionnaire envoyé à chaque service. Ce rapport comprend une description de la gestion des déchets au sein de l’école, ainsi que des suggestions visant à l’optimisation de cette gestion sur les plans pratique, économique et de biosécurité. Les solutions proposées sont structurées autour de plusieurs axes principaux que sont la conformité à la réglementation, l’optimisation du tri des différents flux de déchets, la réduction de l’utilisation de matériel jetable, la formation et l’information du personnel et des étudiants
Analyse rétrospective des anesthésies réalisées et des complications péri-anesthésiques rencontrées à la clinique équine de l’École Nationale Vétérinaire de Toulouse entre janvier 2020 et décembre 2023
No full textHorse anaesthesia is associated with a high risk of morbidity and mortality, due to anaesthetic considerations specific to this species. According to the latest epidemiological studies, this risk is around 1 to 2% in the equine population. The aim of this thesis is to carry out a retrospective analysis of all anaesthesia procedures, including general anaesthesia and prolonged sedation, carried out at the Equine Clinic of the Toulouse National Veterinary School between January 2020 and December 2023. The aim is to study peri-anaesthetic complications in particular, both intra- and post-operatively. The first part of the report reviews current scientific knowledge of peri-anaesthetic complications and anaesthetic mortality. The records of 302 anaesthetics performed at the Clinique Equine were then analysed. The various peri-anaesthetic complications encountered and their incidence are presented in the second part.L’anesthésie du cheval est associée à un risque élevé de morbi-mortalité, lié aux considérations anesthésiques spécifiques de cette espèce. Selon les dernières études épidémiologiques, ce risque avoisine les 1 à 2 % dans la population équine. Cette étude est une analyse rétrospective de l’ensemble des anesthésies générales et des sédations prolongées, effectuées à la Clinique Équine de l’École Nationale Vétérinaire de Toulouse, entre janvier 2020 et décembre 2023. L’objectif principal est de décrire l’incidence de la mortalité et des complications péri-anesthésiques. Un bilan des connaissances scientifiques sur les complications péri-anesthésiques et la mortalité anesthésique, est présenté dans une première partie. Dans une seconde partie, les résultats de l’analyse des dossiers de 302 chevaux anesthésiés à la Clinique Équine sur la période sont décrits. Les différentes complications péri-anesthésiques rencontrées ainsi que leur incidence sont présentées