HAL ENVT (Ecole Nationale Vétérinaire de Toulouse)
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La sélection de l'hôte est efficace pour orienter le microbiote intestinal chez le porc
No full textInternational audienceThe microbiota, which represents all communities of microorganisms in an individual, influences the characteristics of its host. Its involvement in many metabolic processes of hosts has been widely demonstrated. To clarify the genetic determinism of the gut microbiota in pigs, we conducted a selection experiment based on the relative abundances of four bacterial genera estimated by 16S DNA sequencing data of bacterial genomes in the faeces of 60-day-old pigs. We selected two pig lines to increase the relative abundances of the genera Prevotella and Mitsuokella (HPM line) or Ruminococcus and Treponema (HRT line), which are the genera that differentiate the two enterotypes (PM and RT, respectively) observed in pigs in our experimental conditions. We confirmed that these relative abundances are traits with moderate heritability (ca. 0.3). We also estimated the contrasting evolution of all bacterial genera in the two pig lines, and observed a divergent increase in the frequency of RT and PM enterotypes in each line over the generations of selection. The relation between the relative abundance of Prevotella (i.e., the PM enterotype) and post-weaning growth was confirmed, but Prevotella had little influence on other growth or body-composition traits.Le microbiote, qui représente l’ensemble des communautés des microorganismes présents chez un individu, participe à l’élaboration des caractéristiques de son hôte. Son implication dans de nombreux processus métaboliques de son hôte ont été largement démontrés. Afin de préciser le déterminisme génétique du microbiote intestinal chez le porc, nous avons mené une expérience de sélection sur la base des abondances relatives de quatre genres bactériens, estimées à partir de données de séquençage de l’ADN 16S des génomes bactériens présents dans les fèces de porc de 60 jours d’âge. Nous avons sélectionné deux lignées de porcs avec comme objectif une augmentation de l’abondance relative des genres Prevotella et Mitsuokella (lignée HPM), ou des genres Ruminococcus et Treponema (lignée HRT), qui sont les genres différentiant des deux entérotypes (PM et RT, respectivement) observés chez le porc dans nos conditions expérimentales. Nous avons confirmé que ces abondances relatives sont des caractères avec des héritabilités modérées de l’ordre de 0,3 qui peuvent être sélectionnés. Nous avons également estimé l’évolution contrastée de l’ensemble des genres bactériens dans les deux lignées et observé l’augmentation de la fréquence des entérotypes RT et PM de manière divergente pour chaque lignée au fil des générations de sélection. La relation entre l’abondance relative de Prevotella (soit l’entérotype PM) et la croissance post-sevrage a été confirmée ; en revanche l’incidence sur d’autres caractères de croissance ou de composition corporelle est très limitée
Le chantier « Agroécologie & Marché » conduit par les groupes filières INRAE
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 audienceThe agri-food sector encountered an increasing market segmentation, with the proliferation of public and private quality labels, which commit the supply chains to the building of differentiated production, processing and distribution practices. We know very little about the way in which the value chains move towards agroecology, and in particular for the value chains with quality labels other than organic farming. From 2022 to 2023, INRAE's Scientific Division for Agriculture has launched an exploratory project, with 11 INRAE value-chain groups, to analyze how differentiated supply chains are committing toward agroecology. This project, entitled “Agroecology and Market”, was based on a desk research and interviews with over 60 actors from the interbranches and different streams in agrifood chains. This introductory article presents the initial thinking behind the project, the mission of the value-chain groups and the 28 case studies selected for illustrative purposes, in order to conduct this exploratory analysis within a diversity of production and supply chain contexts.Innovations agronomiques 100 (2025), 1-12 RésuméLe 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. Ce chantier dénommé « Agroécologie et Marché » s'est appuyé sur une analyse documentaire et une série d'entretiens auprès de plus de 60 acteurs, représentatifs d'interprofessions et de différents maillons de diverses filières. Cet article introductif présente la réflexion initiale de ce chantier, la mission des groupes filières et les 28 cas d'études retenus à titre illustratif, pour conduire cette analyse exploratoire au regard d'une diversité de contextes de production et de filières.</div
Long-read sequencing of hundreds of diverse brains provides insight into the impact of structural variation on gene expression and DNA methylation
No full textInternational audienceAbstract Structural variants (SVs) drive gene expression in the human brain and are causative of many neurological conditions. However, most existing genetic studies have been based on short-read sequencing methods, which capture fewer than half of the SVs present in any one individual. Long-read sequencing (LRS) enhances our ability to detect disease-associated and functionally relevant structural variants (SVs); however, its application in large-scale genomic studies has been limited by challenges in sample preparation and high costs. Here, we leverage a new scalable wet-lab protocol and computational pipeline for whole-genome Oxford Nanopore Technologies sequencing and apply it to neurologically normal control samples from the North American Brain Expression Consortium (NABEC) (European ancestry) and Human Brain Collection Core (HBCC) (African or African admixed ancestry) cohorts. Through this work, we present a publicly available long-read resource from 351 human brain samples (median N50: 27 Kbp and at an average depth of ∼40x genome coverage). We discover approximately 234,905 SVs and produce locally phased assemblies that cover 95% of all protein-coding genes in GRCh38. Utilizing matched expression datasets for these samples, we apply quantitative trait locus (QTL) analyses and identify SVs that impact gene expression in post-mortem frontal cortex brain tissue. Further, we determine haplotype- specific methylation signatures at millions of CpGs and, with this data, identify cis-acting SVs. In summary, these results highlight that large-scale LRS can identify complex regulatory mechanisms in the brain that were inaccessible using previous approaches. We believe this new resource provides a critical step toward understanding the biological effects of genetic variation in the human brain
Fibropapillomatosis Dynamics, Severity and Demographic Effect in Caribbean Green Turtles
No full textInternational audienceHabitat degradation induced by human activities can exacerbate the spread of wildlife disease and could hinder the recovery of imperiled species. The endangered green turtle Chelonia mydas is impacted worldwide by fibropapillomatosis (FP), a neoplastic infectious disease likely triggered by the Scutavirus chelonidalpha5 with coastal anthropogenic stressors acting as cofactors in disease development. Here, we studied fibropapillomatosis dynamics and its demographic consequences using an 11-year capture-mark-recapture dataset in Anse du Bourg d’Arlet/Chaudière (ABAC) and Grande Anse d’Arlet (GA), two juvenile green turtle foraging grounds in Martinique, French West Indies. Afflicted turtles had similar mortality and permanent emigration rates to the non-afflicted ones. Fibropapillomatosis was commonly observed in large individuals and disease recovery may take several years. Consequently, permanent emigration before full recovery from the disease is suspected and might affect the developmental migration success. Additionally, the results revealed that the FP had higher prevalence and severity, and progressed two times faster in ABAC than in GA despite the proximity (< 2 km) and the similarity of the two foraging grounds. The reasons for these differences remain unidentified. Locally, further studies should be focused on the determination of the external and internal cofactors related to the observed FP dynamics. Finally, the investigations should be extended at a global regional scale to determine potential deleterious effect of the FP on the adult life-stage. These perspectives improves upon our overall understanding on the interplay between wildlife diseases, hosts and environmental factors
Proficiency testing and cross-laboratory method comparison to support standardisation of diatom DNA metabarcoding for freshwater biomonitoring
No full textInternational audienceDNA metabarcoding of benthic diatoms has been successfully applied for biomonitoring at the national scale and can now be considered technically ready for routine application. However, protocols and methods still vary between and within countries, limiting their transferability and the comparability of results. In order to overcome this, routine use of DNA metabarcoding for diatom biomonitoring requires knowledge of the sources of variability introduced by the different steps of the procedure. Here, we examine how elements of routine procedures contribute to variability between European laboratories. A set of four experiments were performed focusing on DNA extraction and PCR amplification steps to evaluate their reproducibility between different laboratories and the variability introduced by different protocols currently applied by the scientific community. Under the guidance of a reference laboratory, 17 participants from 14 countries performed DNA extraction and PCR amplification in parallel, using the same fixed protocol and their own choice of protocol. Experiments were performed by each participant on a set of standardised DNA and biofilm samples (river, lake and mock community) to investigate potential systematic and random errors. Our results revealed the successful transferability of a protocol amongst labs and a highly similar and consistent ecological assessment outcome obtained regardless of the protocols used by each participant. We propose an “all for one but prove them all” strategy, suggesting that distinct protocols can be used within the scientific community, as long as their consistency is be proven by following minimum standard requirements
Identification of Circular RNA Variants by Oxford Nanopore Long-Read Sequencing
No full textInternational audienceCircular RNAs are an emerging class of noncoding RNAs playing important functions in gene expression regulation. While different detection methods exist, the information of their full sequence remains more difficult to reveal, but is crucial to understand their function. Here, we describe a protocol to enrich for circRNAs that are subjected to long-read sequencing with the Oxford Nanopore long-read sequencing platform. This allows to sequence circRNAs in full length and gives the possibility to detect eventual alternative splicing events. We further provide guidance for the bioinformatics analysis by two different tools, which will detect circRNAs of high confidence. This protocol is applicable to a wide range of disease contexts and will help to increase knowledge about this RNA class
Fast inference in copula models with categorical explanatory variables using the one-step procedure
No full textInternational audienceA fast calibration procedure is proposed for multivariate regression models with categorical explanatory variables. Generalized linear models (GLMs) are used to model the marginals, ensuring precise and applicable analysis. Additionally, the dependency between coordinates is captured through a parametric copula, providing a comprehensive framework for understanding the interrelations within multivariate data.Rather than using the MLE on the entire joint distribution, the inference for margins (IFM) estimator is often used in practice. This approach splits the estimation procedure into two steps: first, the marginal distributions are estimated independently, and then the copula or dependency structure is fitted separately. This method simplifies the estimation by handling the margins and dependency in a more manageable way compared to a full joint MLE. Nevertheless, the procedure IFM could still be time consuming with high number of marginal distributions and explanatory variables or modalities, or with a very high sample size.In this paper, a fast alternative to the IFM estimator is proposed. This method relies on a onestep procedure with a closed-form initial guess estimator, previously derived for unvariate GLMs with categorical covariates. The methodology is compared to the full MLE and classical IFM-MLE in terms of computation times and asymptotic variance. The results indicate that the proposed estimator significantly decreases the computation time as the number of covariates and modalities grows, while maintaining a similar asymptotic variance to that of the IFM-MLE procedure. The method is also applied in a real-world case study from the insurance industry.</p
Metabolic resilience in goats: Insights from nutritional challenge with metabolomic analysis
No full textInternational audienceThe aim of this study was to investigate metabolic resilience through milk of ruminants, to understand mechanisms related to resilience and to identify associated milk biomarkers associated with resilience. This study was conducted on 70 Alpine goats, classified into resilient (R) and non-resilient (NR) groups, based on a previous clustering of responses of 13 targeted milk metabolites and one enzyme measured around a 2-day nutritional challenge, with access to straw only. A metabolomics analysis (LC-MS) was conducted on milk morning samples collected before (D0) and after (D2) the challenge. Metabolome change (D2 / D0) was analyzed using univariate (ANOVA) and multivariate (sPLS-DA) methods to identify differences between R and NR goats. Metabolites related to amino acid metabolism showed greater reduction in NR goats (Pvalue – FDR < 0.05). This identified metabolite changes was significantly and positively correlated with the reduction of NH₂ groups and glucose-6-phosphate. These findings support total amino acid concentration and specific amino acids as markers of resilience. Additionally, goats in this study were derived from divergent functional longevity lines, based on estimated breeding values (EBV) of their sire. A metabolite change was identified in both resilience-based and longevity-based comparisons. The EBV of sire show a strong correlation with the mean of this metabolite change of his daughters, weighted by the number of daughters (r = -0.74, p < 0.001). This metabolite change is associated with both nutritional resilience and longevity, suggesting its role in metabolic adaptation, and warranting further investigation as a potential biomarker for genetic selection in ruminants. Metabolites were identified using internal and external databases and will be validated by MS/MS analysis
A multi-omics and modelling investigation reveals transgenerational, sex-specific effects of the obesogenic compound TBT on hepatic metabolism in mice
No full textInternational audienceMany chemical contaminants, including tributyltin (TBT), are suspected to act as metabolic disruptors, contributing to the onset and development of metabolic diseases such as insulin resistance and obesity. The effects of prenatal exposure to compounds such as TBT can be transmitted across several generations, increasing the susceptibility of subsequent generations to develop metabolic disorders. However, the mechanisms involved in adverse metabolic effects on non-directly exposed generations remain insufficiently understood. In this study, we investigated the transgenerational effects of past exposure to TBT on liver metabolism, both in male and female mice of the F3 generation. Aiming to gain a better understanding of the effects on hepatic metabolism, we conducted a multi-omics analysis, including metabolomics analyses of polar (NMR, LC-MS) and apolar metabolites (lipidomics via GC/LC-MS), and transcriptomics analyses (RNA-seq), performed on liver samples from these F3 mice.Multi-block statistical integration approaches are commonly used for the analysis of multi-omics data, but suffer from some limitations. On the one hand, they require that all data types be measured on exactly the same samples, which is rarely the case in practice. On the other hand, their main objective is to select variables that are both correlated and associated with a biological factor of interest, which often results in very reduced signatures that are not well-suited for in-depth exploration of underlying mechanisms of action. To tackle such limitations, we implemented an original two-step data integration approach. First, each omic-level dataset (transcriptomics, metabolomics, lipidomics) was analyzed independently using a combination of univariate and multivariate approaches (AMOPLS), enabling to model the interaction between the "sex" and "TBT" factors, so to identify the specific modulations attributable to each data block. This initial step revealed sex-specific signatures of TBT effects at each omics level. In a second step, we jointly analyzed these signatures by integrating them into the context of the whole metabolic network, using a graph-based approach, so to unveil connections between modulated elements (reactions and metabolites) and identify potential disrupted metabolic pathways
Avian influenza overview March–June 2025
No full textInternational audienceBetween 8 March and 6 June 2025, 365 highly pathogenic avian influenza (HPAI) A(H5) virus detections were reported in domestic (167) and wild (198) birds across 24 countries in Europe. HPAI A(H5N1) virus detections were predominant and mainly located in western, central and south-eastern Europe. Most detections in wild birds concerned waterfowl, particularly swans and geese, but also gulls were involved. Poultry establishments, particularly domestic ducks and chickens, continued to be affected in large numbers in Hungary and Poland. In mammals, HPAI A(H5N1) and A(H5N5) virus detections were reported in a domestic cat, red foxes, Eurasian otters and grey seals. For the first time ever, HPAI A(H5N1) viral infection was detected in a sheep in the United Kingdom. Outside Europe, the United States of America (USA) continued to report A(H5N1) virus detections in dairy cattle, while the virus was found for the first time in a gray fox (USA), a leopard cat (South Korea) and a long-tailed weasel (USA). Between 8 March and 6 June 2025, 20 cases of avian influenza virus infection in humans, including four deaths, were reported in six countries: Bangladesh (two A(H5N1) cases), Cambodia (two A(H5N1) cases), China (one A(H10N3), one A(H5N1), and 11 A(H9N2) cases), India (one A(H5N1) case), Mexico (one A(H5N1) case), and Viet Nam (one A(H5N1) case). Most of the A(H5N1) human cases (n = 5/8) reported exposure to poultry prior to detection or onset of illness. Given the widespread circulation of avian influenza viruses in animal populations, human infections remain rare. No human-to-human transmission has been documented during the reporting period. The risk of infection with the avian A(H5) clade 2.3.4.4b influenza viruses currently circulating in Europe remains low for the general public in the European Union/European Economic Area (EU/EEA) and low-to-moderate for those occupationally or otherwise exposed to infected animals or contaminated environments.</div