HAL ENVT (Ecole Nationale Vétérinaire de Toulouse)
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Infer selection and demography from genomic time series
No full textInternational audienceGenomic time series = allelic frequencies trajectories in a population. Population size (N ) and selection intensity on a locus (s) are two parameters shaping the evolution of its allele frequency ⇒ we aim to infer those parameters from observed trajectories.</div
The ruminal and faecal microbiota, digestion processes, and milk composition of dairy cows are modified by the botanical biodiversity of pastures
No full textInternational audiencePasture botanical diversity is known to change milk composition and improve dairy product quality. However, the chemical and physiological mechanisms behind this effect are only partially known and the role of ruminant's microbiota is still unclear. To study the effects of pasture botanical biodiversity on rumen microbiota, fermentation parameters and milk composition of dairy cows, an in vivo experiment, including in vitro measurements, was carried out with two balanced groups of seven dairy cows each. After a 5-week pre-experimental period on a common permanent grassland plot, the two groups of cows grazed for 4 weeks (experimental period) on two plots characterised by contrasting levels of plant biodiversity: low diversity (LD; 19 species, mainly grasses) and high diversity (HD; 56 species, mostly dicots). Samples of simulated bites, rumen fluid, faeces, and milk were collected at the end of the pre-experimental and experimental periods. The species richness (cc-diversity) of bacteria and fungi in the rumen and faeces of the cows did not differ between treatments, contrary to the composition and relative abundance ((3-diversity) of bacterial and fungal communities. In addition, during in vitro rumen fermentation, total gas production of HD herbage was lower compared with LD, probably because of the different chemical characteristics of the substrates and the partial inhibition of bacterial activity by tannins. Furthermore, methane production in vitro was reduced in the HD group compared to the LD one, as indicated by the higher CO2:CH4 ratio. Thus, the differences in (3-diversity may be explained both by herbage fibre and plant secondary metabolite contents. Plant tannins also protected dietary proteins from degradation, as indicated by the lower ammonia to CP ratio obtained in vitro in HD than in LD digesta. Comparable proportions of C18:3 n-3 were found in milk, despite the lower total fatty acid and C18:3 n-3 contents of the HD herbage. Plant secondary metabolites in the rumen could have partially inhibited the activity of ruminal bacteria responsible for the biohydrogenation of polyunsaturated fatty acids. This study explains how grazing dairy cows on permanent grasslands rich in plant biodiversity helps transferring polyunsaturated fatty acids from herbage to milk and likely reduces methane and ammonia emissions by influencing ruminal and faecal microbiota thanks to plant secondary metabolites. (c) 2025 The Author(s). Published by Elsevier B.V. on behalf of The animal Consortium
Comparison of country-specific predictions of feed intake and methane emissions in sheep using different proxies
No full textInternational audienceRuminants are often singled out as being the main culprits when it comes to greenhouse gas (GHG) emissions, for methane (CH4) in particular. However, with their diets based on forage and grazing, ruminants have a role to play to limit the feed-food competition. Sheep breeders are open to the prospect of including both feed efficiency and GHG emissions in their breeding programmes and whether or not it is for the purpose of genetic (or genomic) selection, the acquisition of new phenotypes for feed efficiency and GHG emissions are essential. Currently, devices recording GHG emissions and individual feed intake of animals reared indoors remains too expensive for most sheep breeders worldwide. In this study, research groups from six countries (UK (Scotland), France, Norway, Ireland, New Zealand and Uruguay) gathered their results obtained in different breeds to identify the most promising proxy measurements of feed intake and methane emissions. Despite the fact that each group set up their own protocol, there were several points in common: most feed intake trials were performed during 6 weeks on growing animals, and GHG emissions were all recorded with portable accumulation chambers (PACs). Different traits, in addition to feed intake and GHG emissions, were recorded and considered as putative proxies (body composition, growth, bodyweight, feeding behaviour, body condition score), as well as sheep genotypes and ruminal microbiota. Models' goodness of fit were estimated on training sets, whereas their prediction accuracy was assessed on actual validation datasets. The comparison of training and validation accuracies obtained with each dataset highlighted the well-documented problem of overfitting, particularly with microbiota data. In general, validation prediction accuracies were higher for feed intake than for the two feed efficiency criteria (residual feed intake and feed conversion ratio) investigated. The best predictions for feed intake were obtained when body weight and the average number of feeding events per day were included in the models (R2valid=0.78). Methane emissions were predicted with the highest accuracy when feed intake was considered among the proxies. Prediction accuracies for methane emissions obtained with the metagenome were higher than with this remains low (Rvalid=0.32)
Sclérose en plaques : perspectives d’utilisation des cellules dendritiques dans le rétablissement de la tolérance au Soi
No full textMultiple Sclerosis is a human dysimmune disease with a complex pathogenesis characterised in particular by a loss of tolerance. At present, a wide variety of treatments are used, but they do not always stabilise the most progressive forms of the disease, and above all, no treatment can restore self-tolerance. By describing the characteristics of dendritic cells, their implications in the immune response in multiple sclerosis and the data in the literature on their tolerogenic role, we have attempted to develop the uses of dendritic cells in the restoration of self-tolerance in multiple sclerosis.La Sclérose En Plaques est une maladie humaine dysimmunitaire à la pathogénie complexe caractérisée notamment par une perte de tolérance. A l’heure actuelle, les traitements utilisés sont très variés mais ne permettent pas toujours de stabiliser les formes les plus progressives de la maladie, et surtout, aucun traitement ne permet de rétablir la tolérance au Soi. En décrivant les caractéristiques des cellules dendritiques, leurs implications dans la réponse immunitaire dans la Sclérose en Plaques et les données de la littérature sur leur rôle tolérogène, nous avons tenté de développer les utilisations de ces dernières dans le rétablissement de la tolérance au Soi dans la Sclérose en Plaques
La sélection de souches de Caenorhabditis elegans résistantes aux lactones macrocycliques a révélé des mécanismes d'adaptation aux anthelminthiques.
No full textInternational audienceThe macrocyclic lactones (MLs) ivermectin and moxidectin are today the most widely used anthelmintics for treating nematode infections in both humans and animals. However, their extensive and frequent use has led to a significant rise in drug resistance. Despite sharing the same mode of action, differences have been reported in how they select for resistance. Our objective was to study and compare the changes occurring in the model nematode Caenorhabditis elegans when exposed to either ivermectin or moxidectin. To achieve this, C. elegans populations were subjected to stepwise selection with increasing doses of each drug. To minimize genetic drift during the selection process, we conducted three independent ivermectin resistance selection experiments in addition to moxidectin selection. In each resistant lineage, we observed key selection plateaus at several ML concentrations. However, despite their independent evolution, all resistant strains exhibited similar levels of ML resistance. Transcriptomic analysis of these lineages revealed several similarities in relation to resistance mechanisms. First, we observed an enrichment of dysregulated genes in the neural system of the worms' heads. Interestingly, all resistant lineages displayed Amphid defects, suggesting that neuronal changes are strongly associated to ML resistance. Additionally, nematodes possess multiple P-glycoproteins (PGPs), which have been associated with anthelmintic resistance and are believed to facilitate ML efflux from the worms. Expression analysis of pgp revealed no direct correlation between pgp expression levels and ML exposure or resistance at the end of the selection process. Finally, gene ontology analysis unveiled deregulation of lipid metabolism-related genes. Supporting this, oil-red staining assays showed altered triacylglycerol storage in ML-resistant C. elegans. In conclusion, despite independent evolution under ivermectin and moxidectin selection pressures, C. elegans populations exhibit similar resistance profiles, with shared neural system dysregulation, amphid defects, a potentially limited role of pgp gene expression, and a common dysregulation of lipid metabolism, highlighting the complex mechanisms underlying macrocyclic lactone resistance.Les lactones macrocycliques (ML), l'ivermectine et la moxidectine, sont aujourd'hui les anthelminthiques les plus utilisés pour traiter les infections à nématodes chez l'homme et l'animal. Cependant, leur utilisation fréquente et intensive a entraîné une augmentation significative de la résistance aux médicaments. Malgré un mode d'action similaire, des différences ont été observées dans leur mode de sélection de la résistance. Notre objectif était d'étudier et de comparer les changements survenant chez le nématode modèle Caenorhabditis elegans exposé à l'ivermectine ou à la moxidectine. Pour ce faire, les populations de C. elegans ont été soumises à une sélection progressive avec des doses croissantes de chaque médicament. Afin de minimiser la dérive génétique pendant le processus de sélection, nous avons mené trois expériences indépendantes de sélection de la résistance à l'ivermectine, en plus de la sélection à la moxidectine. Dans chaque lignée résistante, nous avons observé des plateaux de sélection clés à plusieurs concentrations de ML. Cependant, malgré leur évolution indépendante, toutes les souches résistantes présentaient des niveaux similaires de résistance aux ML. L'analyse transcriptomique de ces lignées a révélé plusieurs similitudes dans les mécanismes de résistance. Premièrement, nous avons observé un enrichissement en gènes dysrégulés dans le système nerveux des têtes des vers. Il est intéressant de noter que toutes les lignées résistantes présentaient des anomalies chez les amphidiens, suggérant que les modifications neuronales sont fortement associées à la résistance à la ML. De plus, les nématodes possèdent de multiples glycoprotéines P (PGP), associées à la résistance aux anthelminthiques et censées faciliter l'efflux de ML hors des vers. L'analyse de l'expression de la pgp n'a révélé aucune corrélation directe entre les niveaux d'expression de la pgp et l'exposition ou la résistance à la ML à la fin du processus de sélection. Enfin, l'analyse de l'ontologie génétique a révélé une dérégulation des gènes liés au métabolisme lipidique. À l'appui de cette hypothèse, des tests de coloration au rouge huileux ont montré une altération du stockage des triacylglycérols chez C. elegans résistant à la ML. En conclusion, malgré une évolution indépendante sous les pressions de sélection de l'ivermectine et de la moxidectine, les populations de C. elegans présentent des profils de résistance similaires, avec une dysrégulation partagée du système neuronal, des défauts d'amphide, un rôle potentiellement limité de l'expression du gène pgp et une dysrégulation commune du métabolisme lipidique, mettant en évidence les mécanismes complexes sous-jacents à la résistance aux lactones macrocycliques
Recurrent spontaneous miscarriages from sperm after ABVD chemotherapy in a patient with Hodgkin’s lymphoma: sperm DNA and methylation profiling
No full textInternational audienceLymphomas represent one of the most common malignant diseases in young men and an important issue is how treatments will affect their reproductive health. It has been hypothesized that chemotherapies, similarly to environmental chemicals, may alter the spermatogenic epigenome. Here, we report the genomic and epigenomic profiling of the sperm DNA from a 31-year-old Hodgkin lymphoma patient who faced recurrent spontaneous miscarriages in his couple 11–26 months after receiving chemotherapy with adriamycin, bleomycin, vinblastine, and dacarbazine (ABVD). In order to capture the potential deleterious impact of the ABVD treatment on mutational and methylation changes, we compared sperm DNA before and 26 months after chemotherapy with whole-genome sequencing (WGS) and reduced representation bisulfite sequencing (RRBS). The WGS analysis identified 403 variants following ABVD treatment, including 28 linked to genes crucial for embryogenesis. However, none were found in coding regions, indicating no impact of chemotherapy on protein function. The RRBS analysis identified 99 high-quality differentially methylated regions (hqDMRs) for which methylation status changed upon chemotherapy. Those hqDRMs were associated with 87 differentially methylated genes, among which 14 are known to be important or expressed during embryo development. While no variants were detected in coding regions, promoter regions of several genes potentially important for embryo development contained variants or displayed an altered methylated status. These might in turn modify the corresponding gene expression and thus affect their function during key stages of embryogenesis, leading to potential developmental disorders or miscarriages
Relationship between non-typhoidal Salmonella dose and food poisoning in humans: A systematic review
No full textInternational audienceFood safety is a major public health concern. The zoonotic pathogen non-typhoidal Salmonella, responsible for salmonellosis, is a leading cause of bacterial food poisoning globally, making its detection and control essential. Understanding the infectious dose of Salmonella is crucial for identifying appropriate risk management strategies; however, significant uncertainties remain, warranting a systematic review. Following PRISMA guidelines, we conducted a comprehensive search across multiple databases (Web of Science, PubMed, and CAB Abstracts) to identify relevant studies examining the relationship between Salmonella dose and foodborne illness in humans. Four main types of studies were identified: experimental trials, case reports, case series, and mathematical modelling. An analysis of these studies revealed their respective strengths and limitations. The data showed considerable variability, with the dose required to cause illness depending on factors such as Salmonella serovar, food type, and the health status of the exposed population. A key challenge identified was the lack of sufficient data on collective food poisoning incidents, which complicates the development of more reliable dose-response models. Despite these limitations, this review underscores the importance of targeted food safety interventions and risk assessments tailored to specific food products and population groups. The findings provide a foundation for enhanced food safety measures and support ongoing efforts to protect public health from foodborne illnesses
Epidemiological and clinical profiles of young and senior dogs fed a standard diet
No full textInternational audienceThis study aimed to explore age-related differences in epidemiological and clinical parameters in dogs consuming a standardized diet, focusing on factors relevant to veterinary practitioners. A total of 106 dogs were included, comprising young (2-5 years) and senior (≥8 years) individuals. Epidemiological data were collected through questionnaires and veterinary consultations, while clinical parameters were assessed via physical examinations and blood analyses. Compared to younger dogs, senior dogs were less active, more likely to live in houses, and more frequently received regular deworming. They were also more likely to consume food purchased from pet stores or supermarkets compared to younger dogs. Clinical evaluations revealed that senior dogs had higher plasma globulin and platelets and lower albumin, consistent with chronic low-grade inflammation associated with aging. Muscle loss, poor coat quality, and reduced lymphocyte counts were also prominent in senior dogs, potentially reflecting sarcopenia, malnutrition, and immunosenescence, respectively. Notably, dogs previously fed diets lacking a source of omega-3 fatty acids exhibited elevated plasma triglycerides even after transitioning for four weeks to a premium diet containing fish oil, underscoring the lasting impact of long-term dietary habits. These findings highlight the importance of regular veterinary follow-ups for senior dogs and the role of highquality nutrition, including sources of omega-3 fatty acids. By identifying key epidemiological and clinical differences, this study offers valuable insights to help veterinary practitioners distinguish between healthy and pathological aging
History of carbon supply shapes the metabolic response of photogranules to light shifts
No full textInternational audienceOxygenic photogranules mainly composed of cyanobacteria and heterotrophic bacteria, have gained attention fortheir ability to treat wastewater (removal of C, N, and P) without external aeration. Currently, the metabolicdynamics of photogranules to varying nutrient and light conditions in wastewater treatment systems remainspoorly studied. However, understanding how quickly the photogranule metabolism changes, and whether thischange is temporary or permanent is important for the optimal use of photogranules. Here, an NMR-basedmetabolomics approach was applied to investigate the temporal dynamics of photogranule metabolism in thepresence or absence of acetate and with or without light.Our findings revealed that under carbon-limited conditions, photogranules relied on alternative carbonsources, such as N-acetylneuraminate (a constituent of EPS) and amino acids like hypotaurine and L-alanine. Thisadaptation affected key metabolic pathways, including glycolysis, taurine and hypotaurine metabolism, and thetricarboxylic acid cycle. When acetate was provided, both heterotrophic and phototrophic activities weremaintained. Notably, the history of carbon supply influenced how photogranules responded to light shifts.Metabolic indicators showed that the lag in carbon addition altered fatty acid metabolism and carbon fixation,leading to shifts in amino acid concentrations and distinct metabolic profiles when the light was turned off. Thus,NMR metabolomics identified metabolic changes, induced by contrasting carbon conditions, lasting for severalhours, and significantly affecting the photogranule response to light fluctuations. These results suggest that thehistory of carbon supplementation may shape metabolic responses of photogranules to other environmentalchanges or stressors
Analyse transversale de 28 démarches de filières agrialimentaires : des dynamiques d'innovation variables au travers de leur engagement dans l'agroécologie
No full textLe secteur agroalimentaire fait l’objet d’une segmentation croissante du marché avec la multiplication de démarches dites de qualité, publique ou privée, qui engagent les filières dans la construction de pratiques de production, de transformation ou de distribution différenciées. Nous connaissons peu de choses sur la manière dont ces démarches inscrivent leurs pratiques dans l’agroécologie, et en particulier pour les filières ayant une mention valorisante autre que l’agriculture biologique. De 2022 à 2023, la Direction Scientifique Agriculture INRAE a engagé un chantier exploratoire, avec 11 groupes filières INRAE, pour analyser comment se construisent des démarches de filières différenciées sur le marché et leur engagement en faveur de l’agroécologie.National audienceSince the 2014 law dedicated to the development of agroecology, French plant and animal supply chains have mobilize agroecological principles in various ways. Twenty-eight case studies of initiatives claiming to differentiate themselves through practices related to agroecological principles have been analyzed across different production domains from animals and plants. The analytical framework used is based on innovation functions implemented by value chains : these different actions taken within the value chains can feed into a process of collective learning in the transition towards agroecology. The presented results show a variable transformative capacity of the value chains, but allow for the identification of several regularities on which the agroecological transition of the sectors in France seems to be taking place. The article builds suggestions for collective actions to support the agroecological transition in France.Depuis de la loi de 2014 dédiée au développement de l’agroécologie, les filières végétales et animales françaises mobilisent des principes de l’agroécologie de façon variée. Cet article synthétise l’analyse transversale de 28 cas de démarches de filières déclarant se différencier par des pratiques reliées à des principes de l’agroécologie, dans différents domaines de production de l’animal ou du végétal. Le cadre d’analyse mobilisé est basé sur des fonctions d’innovation mises en œuvre par ces filières. Ces différentes actions conduites dans la filière peuvent alimenter un processus d’apprentissage collectif dans la transition vers l’agroécologie. Les résultats présentés montrent une capacité transformative variable des filières, mais permettent d’avancer un ensemble de régularités sur lesquelles semble reposer la transition agroécologique des filières en France. L’article conclut par des pistes d’actions collectives pour soutenir la transition agroécologique en France