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Overview of LifeCLEF 2025: Challenges on Species Presence Prediction and Identification, and Individual Animal Identification
No full textInternational audienceBiodiversity monitoring using AI-powered tools has become vital for tracking species distributions and assessing ecosystem health on a large scale. Automated image- and sound-based species recognition, in particular, continues to accelerate conservation efforts by enabling rapid, low-cost surveys of vulnerable populations. However, the ever-growing variety of algorithms and data sources underscores the need for standardized benchmarks to assess real-world performance. Since 2011, the LifeCLEF lab has filled this role by organizing annual evaluations that promote collaboration among AI experts, citizen science, and ecologists. In this overview, we report on the LifeCLEF 2025 edition, which featured five distinct, data-driven tasks: (i) AnimalCLEF, focusing on open-set individual animal re-identification; (ii) BirdCLEF+, about species recognition in complex acoustic soundscape recordings; (iii) FungiCLEF, addressing few-shot classification of rare fungi species; (iv) GeoLifeCLEF, combining environmental and high-resolution remote sensing with occurrence records to predict plant species presence; and (v) PlantCLEF, aiming to identify multiple co-occurring plant species in vegetation-plot imagery. This paper provides an overview of the motivation, methodology, and main outcomes of the five challenges
Préférences des consommateurs pour l'huile de caméline : impact des perceptions sensorielles et de la divulgation d'informations sur l'acceptation d'une huile peu connue issue d'une culture mineure
No full textInternational audienceThis study aims to assess how French consumers evaluate the traditional but unfamiliar camelina oil, focusing on liking scores and willingness to pay (WTP) through sensory perception and information disclosure. In a controlled lab experiment (n = 132, Dijon, France), participants first blind-tasted camelina oil, with half of them evaluating extra virgin olive oil under similar conditions for comparison. After this blind step, stepwise information disclosure on product identity, health and environmental benefits, and possible gene-editing (GE) improvements was proposed.First, the blind tasting showed that 35 % of consumers disliked the camelina oil, while 45 % liked it. The correlations between liking scores and WTP are positive but relatively weak, particularly for the camelina oil, which had been previously seen in stores by only 12 % of participants.Second, information disclosure had a significant impact on WTP. (1) The identification of organic camelina oil led to a significant increase in WTP, while a similar disclosure for extra virgin olive oil had no effect. Additional messages about (2) the benefits of the camelina oil for human health and the environment led to significant increases in WTP. Conversely, (3) GE information reduced WTP for 46.2 % of participants, despite being framed with positive outcomes. These findings highlight the importance of targeted messages in promoting novel, sustainable food products and underline the need to address consumer concerns regarding biotechnology.Cette étude vise à évaluer la manière dont les consommateurs français apprécient l'huile de caméline, un produit traditionnel mais peu connu, en se concentrant sur les notes d'appréciation et la disposition à payer (WTP) à travers la perception sensorielle et la divulgation d'informations. Dans le cadre d'une expérience contrôlée en laboratoire (n = 132, Dijon, France), les participants ont d'abord goûté à l'aveugle de l'huile de caméline, la moitié d'entre eux évaluant également de l'huile d'olive extra vierge dans des conditions similaires à des fins de comparaison. Après cette étape à l'aveugle, des informations ont été progressivement divulguées sur l'identité du produit, ses bienfaits pour la santé et l'environnement, ainsi que les améliorations possibles grâce à l'édition génétique (GE). Tout d'abord, la dégustation à l'aveugle a montré que 35 % des consommateurs n'aimaient pas l'huile de caméline, tandis que 45 % l'appréciaient. Les corrélations entre les notes d'appréciation et la WTP sont positives mais relativement faibles, en particulier pour l'huile de caméline, que seuls 12 % des participants avaient déjà vue en magasin. Ensuite, la divulgation d'informations a eu un impact significatif sur la WTP. (1) L'identification de l'huile de caméline biologique a entraîné une augmentation significative de la WTP, tandis qu'une divulgation similaire pour l'huile d'olive extra vierge n'a eu aucun effet. Des messages supplémentaires sur (2) les bienfaits de l'huile de caméline pour la santé humaine et l'environnement ont entraîné une augmentation significative de la WTP. À l'inverse, (3) les informations sur la GE ont réduit la WTP pour 46,2 % des participants, bien qu'elles aient été présentées sous un angle positif. Ces résultats soulignent l'importance des messages ciblés dans la promotion de produits alimentaires novateurs et durables, et mettent en évidence la nécessité de répondre aux préoccupations des consommateurs concernant les biotechnologies
Cobalamin-mediated protection of Faecalibacterium duncaniae against oxidative stress: Insights from proteomic and membrane fatty acid profiles
No full textInternational audienceFaecalibacterium species are keystone commensals of the human gut, contributing to intestinal homeostasis, immune modulation, and epithelial health. However, their extreme sensitivity to oxygen and reactive oxygen species renders them highly vulnerable during inflammatory conditions, severely limiting their therapeutic application. Understanding the molecular mechanisms underlying their oxidative stress responses is therefore critical for harnessing these bacteria as next-generation probiotics to restore gut health. In this study, we investigated oxidative stress responses in Faecalibacterium duncaniae A2–165 using comprehensive proteomic and membrane fatty acid profiling. We demonstrated that increasing hydrogen peroxide (H₂O₂) concentrations extend the lag phase of growth and affect survival during the first hour of exposure, notably altering the redox potential. Exposure to H₂O₂ triggered a remodeling of the proteome, including detoxification systems, metal transporters, DNA repair systems, transcriptional regulators, and enzymes involved in cobalamin biosynthesis. Complementary RT-qPCR analyses revealed coordinated and time-dependent transcriptional activation of genes involved in oxidative stress response. Remarkably, cobalamin supplementation enhanced bacterial growth, mitigated H₂O₂-induced stress, and lowered superoxide levels in F. duncaniae, highlighting its direct antioxidant activity. By analyzing membrane fatty acid profiles, we showed that cobalamin preserves membrane fluidity, counteracting oxidative stress induced by H₂O₂ in F. duncaniae. These findings reveal the multifaceted strategies employed by F. duncaniae to withstand oxidative stress and provide a foundation for future efforts to optimize its production at industrial scales and its therapeutic potential as a next-generation probiotic
Transgenerational response to the ingestion of an endocrine disruptor: phenotypic, genetic, and epigenetic analyses in quail
No full textInternational audienceEpigenetic mechanisms such as DNA methylation can mediate the effect of the environment on an individual's phenotypes. While parental environments have also been shown to affect offspring phenotypes in several livestock species, evidence for transgenerational inheritance of environmentally induced epigenetic marks remains debated.This study aimed to assess the potential transgenerational inheritance of an environmental effect via epigenetic modifications in Japanese quails (Coturnix japonica). We investigated whether an initial dietary exposure to genistein - a natural phytoestrogen found in soybeans - could induce lasting phenotypic and epigenetic changes in subsequent generations.To disentangle genetic from epigenetic effects, we designed a balanced “mirror-crossing” scheme based on 20 founder families. In each family, two sisters were mated to the same male: one received a 30-day genistein supplementation (epi+ line), while the other was kept as a control, without genistein (epi– line). Their offspring were mated within each 'epiline' for three generations (G0–G2), ensuring a balanced representation of each genetic background in both epilines. Phenotypic data (body and tissue weights, egg production, and behavioral traits) were collected across all generations. DNA methylation profiles and genotypes were obtained from Reduced Representation Bisulfite Sequencing of 1,344 individual blood samples using BISCUIT, which allows jointly methylation and SNP calling. Differential methylation analysis was performed using the DSS package. Methylation heritability and methylation QTLs (metQTLs) were assessed with GCTA.Significant differences between epilines were detected for body weight. Epi+ females were consistently heavier than epi– controls at all ages, with the difference increasing across generations (up to +14 g in G2). A similar, though delayed, pattern was observed in males, becoming significant in G2 (+9 g at slaughter). Other traits, including reproduction and behavior, were not significantly affected. The proportion of phenotypic variance explained by the epiline increased over generations, suggesting either a genetic drift or non-genetic inherited effects.Methylation calling yielded 448,673 CpG sites in 1,267 individuals (mean coverage 34×). Among 111,168 variable CpGs (SD > 0.05), 22 and 72 were differentially methylated between epilines in G1 and G2, respectively, while no significant differences were detected in G0. A large number of CpGs showed significant sex × epiline interactions. The mean methylation heritability (h² = 0.24) supported moderate genetic control of methylation levels, with a high variability between CpGs.Ongoing analyses will contribute to a better understanding of the molecular mechanisms and biological significance of non-genetic inheritance in avian models.This project is funded by the European Union’s Horizon 2020 program GEroNIMO N°101000236, part of EuroFAANG (https://eurofaang.eu)
Beyond N and P fertilization: Tropical ground hexapod communities are tied to micronutrients
No full textInternational audienc
Mapping of a field: A systematic review of reviews on forestry and the forest-based sector in Europe
No full textInternational audienceThis study applies PRISMA guidelines to map and analyze trends and patterns in evidence synthesis within the field of Forestry and Forest-based Sector (F&FS). Given the role of evidence synthesis in shaping research priorities and informing policy, the study investigates potential biases in evidence synthesized by examining different forms of synthesis (i.e. systematic and non-systematic), topics covered and geographical distribution of underpinning studies. Following a thorough expert-led classification of F&FS topics, we identified 35,015 reviews from Europe, of which 642 were systematic. Although rapidly growing, systematic literature reviews (SLRs) still account for under 1% of all scientific production in F&FS (~5% of all evidence synthesis). Reviewed topics are dominated by management, biodiversity and climate change, even though the field is sprawling away from core silviculture themes and into more transdisciplinary issues. However, SLRs are more abundant in health-related and social science topics compared to non-systematic reviews, while syntheses of forest technologies and forest products are underrepresented. We also find an uneven geographical distribution of systematized evidence, South-eastern Europe the least and Mediterranean-Northern-Western Europe the most represented. Factors best explaining observed patterns are investment in Research & Development and economic contribution of value in million US dollars added in the forest sector. Our results show evidence synthesis within the F&FS field comes with structural biases in selected research themes, geographical distribution, and methodological approaches. The resulting partial understanding of the knowledge base may influence not only scientific agendas but also policy priorities, assuming such evidence is taken up by policymakers
Impact of Lactobacillus johnsonii CNCM I-4884 on canine giardiasis: a probiotic-based approach
No full textInternational audienceThis study reports a new therapeutic approach for canine giardiasis, the most common intestinal protozoan infection caused by Giardia intestinalis. It is based on the use of the probiotic strain Lactobacillus johnsonii CNCM I-4884 and, in particular, its bile salt hydrolase enzymatic activities. Clinical trials in dogs demonstrated that daily administration of L. johnsonii CNCM I-4884 significantly reduced Giardia cyst shedding after 14 days. These results highlight the potential of this probiotic as a promising alternative to antimicrobials, such as nitroimidazoles or benzimidazoles, for the treatment of giardiasis in dogs. Moreover, they provide a novel approach for the veterinary industry to develop innovative products targeting this parasite. In addition to its direct anti-Giardia effect, L. johnsonii CNCM I-4884 may also act as an adjuvant therapy, supporting intestinal homeostasis, enhancing host defense mechanisms, and promoting recovery of gut balance during or after antiparasitic treatments. This dual role suggests that the strain could be considered not only as a complementary therapy but, in specific cases, as a potential stand-alone probiotic treatment for canine giardiasis
Évaluer l’impact des jeux sérieux pour les transitions: Guide méthodologique
No full textThis guide is a resource for anyone using serious games (SGs) to support sustainability transitions and who wishes to understand their impact. It proposes a comprehensive evaluation approach enabling the analysis of change both in itinere (during implementation) and ex post.Ce guide s’adresse à toute personne mobilisant les jeux sérieux (JS) comme outil d’accompagnement des transitions et qui souhaite en évaluer l’impact. Il propose une démarche d’évaluation réflexive permettant d’analyser le changement in itinere et ex post
Clustering of the dynamics of milk lactose content throughout lactation and identification of variation factors
No full textInternational audienceInterest in milk lactose content (LC) has grown due to its potential as an indicator of udder health and metabolic disorders in dairy cattle. However, the variability of LC dynamics during lactation remains poorly described, and a better characterization of these dynamics could clarify our understanding of LC variations among cows, and potentially those due to udder health and metabolismrelated variations. The aim of this study was to identify distinct patterns of LC dynamics and assess their environmental and genetic determinants, as well as their phenotypic and genetic associations with milk yield, Na, K, SCC, and their phenotypic associations with fat-toprotein ratio (FPR) and BHB. A total of 1,980,693 testday records were analyzed from 183,150 Holstein cows in 2,239 herds across France. At least 2 records in the first 90 d and 4 records between 7 and 300 DIM were available for each cow, averaging 7.3 records per cow. Functional principal component analysis was used to describe LC dynamics throughout lactation. This approach involved smoothing the LC curves for each cow and then summarizing their overall shape using 3 principal components: average LC throughout lactation, LC slope and LC at mid lactation. Dynamics of LC were grouped into 6 clusters. Three clusters (3, 4, and 5) represented 86% of the data and shared similar dynamics with a flat trend after an initial rise in LC at early lactation and different average LC levels (cluster 3: 4.68%, cluster 4: 5.10%, cluster 5: 4.86%). Environmental and intrinsic animal factors explained 69% of the variability in average LC among clusters 3, 4, and 5, with cow parity and LC EBV identified as the main intrinsic contributors. The remaining clusters (1, 2, and 6) showed LC levels similar to the mean of the dataset (LC: 4.88% ± 0.19%) until 150 DIM. Thereafter, 2 clusters displayed negative LC slopes (cluster 1: -0.13% and cluster 6: -0.07% per month of lactation) and one a positive slope (cluster 2: +0.05% per month). Fifteen percent of the variations in the LC slopes of clusters 1, 2, and 6 was explained by environmental factors, mainly calving season: winter calving was associated with clusters 1 and 6, and summer calving with cluster 2. The remaining unexplained negative slope variation from mid lactation onward appears to be related to distinct patterns characterized by higher FPR and milk BHB concentrations preceding the decline in LC, followed by increased SCC after 150 DIM. The lactosebased clusters also corresponded to distinct curves for milk sodium contents, and there were slight correlations for potassium levels, indicating different equilibria between the 3 main osmotic agents (lactose, sodium, and potassium), probably to maintain milk osmolarity. As a result, LC clustering uncovered meaningful physiological profiles: average LC levels were primarily driven by parity and genetics, whereas LC slope variations appeared to be more sensitive to environmental and health-related factors. These findings support the potential of LC dynamics, accessible via mid-infrared spectra, to serve as functional biomarkers for udder health and, potentially, of metabolic status
Body weight variation is a good proxy of abdominal fat weight in laying hens at 90 weeks of age
No full textInternational audienceBody reserve levels are known to influence production performance and longevity in livestock species, and their management is therefore of interest for breeding programs. In laying hens, we have recently demonstrated that abdominal fat weight (AFW) at the end of the production cycle is genetically correlated with key economic traits, being positively correlated with laying rate and negatively correlated with egg weight at 90 weeks of age. While AFW is not a primary selection objective, controlling it can contribute to improving both metabolic efficiency and reproductive performance. Direct measurement of AFW, however, requires slaughter and dissection, preventing its use as a routine selection criterion. As an alternative, we evaluated in this study the potential of using body weight difference between two adult ages (DBW) as a non-invasive proxy for AFW in late-stage laying hens. In aging hens, body weight variation is expected to largely reflect changes in body reserves.Genetic parameters were estimated for AFW (measured at 90 weeks in 1,114 hens) and for DBW between 30 and 70 weeks (DBW70) or between 30 and 90 weeks (DBW90), traits available for much larger datasets (9,656 and 1,657 hens, respectively) due to their non-invasive nature. Very high genetic correlations were observed between AFW with DBW70 (0.75) and DBW90 (0.78), supporting the hypothesis that around three quarters of the genetic variance in AFW is captured by DBW. It can be noted that the correlation between back fat thickness (BFT) and DBW were lower, 0.45 and 0.46, respectively, suggesting that these two body reserve traits are distinct traits, despite the relatively high overall genetic correlation of 0.67 observed between them. This observation is consistent with a previous study (Bédère et al 2025). To go further in the genetic characterization of these traits, genome-wide association studies (GWAS) were conducted for DBW70, and DBW90 and compared with those obtained previously for AFW (3 QTLs on chromosomes 2, 8 and 28) using hens with available genotypes for a 60k SNP Array imputed on a 600k SNP array. We identified 3 QTLs for DBW70 and 2 for DBW90 and no QTLs were shared between the DBW traits and AFW.Overall, this study demonstrates that DBW traits are reliable and heritable non-invasive proxies for AFW in laying hens at 90 weeks. The strong genetic correlation between these traits, particularly with DBW70 as an earlier measurement, opens opportunities for indirect selection to control abdominal fat deposition at later production stages. The absence of common QTLs between AFW and DBW traits, suggests that major-effect genomic regions may differ between traits and their strong genetic correlation are largely polygenic in nature, driven most probably, by many small-effect causal variants that remain undetectable by GWAS at current sample sizes.These results provide practical insights for breeding programs aiming to optimize body reserve management and sustain production performance in extended laying cycles.This project is funded by the European program GEroNIMO N°101000236 and ANR ‘EFFICACE’ program