Biology subjects

Estelle, J.

Publications and source records attributed to Estelle, J..

4 recordsLinked to original sources

bioRxiv2025

Differential chromatin accessibility between pre- and post-natal stages highlights putative causal regulatory variants in pig skeletal muscle

Deciphering how chromatin dynamics shape the effects of regulatory variants on complex traits across development remains largely unexplored in farmed animals. Focusing on porcine skeletal muscle, we integrated chromatin accessibility (ATAC-seq), molecular QTL (molQTL), and GWAS data to identify putative stage-specific regulatory variants influencing agronomically important traits. We aggregated and analyzed 202 ATAC-seq libraries spanning prenatal (fetal) and postnatal (piglet) stages. We intersected consensus and differential peaks with cis-molQTLs from the Porcine Genotype-by-Tissue-by-Expression Atlas (PigGTEx) followed by functional enrichment analysis, promoter-focused functional annotation, integration with gene-trait pairs, and intersection with eGenes (i.e., genes whose expression is regulated by at least one cis-eQTL) to link variants previously associated with QTLs for production traits. We identified 132,275 differentially accessible peaks (DAPs) distinguishing fetal and piglet muscle. Fetal DAPs were enriched in promoter and intergenic regions, whereas piglet DAPs were enriched in intronic regions, indicating a shift from transcriptional priming to postnatal regulatory refinement. Overlaps between accessible regions and molQTLs were highly significant (p < 0.001), with the strongest eQTLs predominating in the fetal stage (14 fetal vs. 4 piglet). Gene Ontology analysis of promoter-accessible eGenes revealed enrichment for RNA metabolism and chromatin organization in fetuses, and for muscle contraction and lipid metabolism in piglets. The intersection with colocalized complex traits loci identified 107 fetal- and 30 piglet-stage regulatory elements, with only three eGenes shared between stages. These findings provide insights into developmental chromatin dynamics in skeletal muscle and an effective framework for prioritising putative regulatory variants affecting pig traits at prenatal stages.

genomics↗

bioRxiv2023

Characterization of bovine vaginal microbiota and its relationship with host fertility, health, and production

BackgroundBecause of its potential influence on the hosts phenotype, increasing attention is paid to organ-specific microbiota in several animal species, including cattle. However, ecosystems other than those related to the digestive tract remain largely understudied. In particular, little is known about the vaginal microbiota of ruminants despite the importance of the reproductive functions of cows in a livestock context, where fertility disorders represent one of the primary reasons for culling. ResultsIn the present study, we aimed at better characterizing the vaginal microbiota of dairy cows through 16S rRNA sequencing, using a large cohort of Holstein cows from Northern France. Our results allowed to define a core microbiota of the dairy cows vagina, and highlighted that 90% of the sequences belonged to the Firmicutes, the Proteobacteria, and the Bacteroidetes phyla. The core microbiota was composed of four phyla, 16 families, 14 genera and only one amplicon sequence variant (ASV), supporting the idea of the high diversity of vaginal microbiota within the studied population. This variability was partly explained by various environmental factors such as the herd, the sampling season, the lactation rank and the lactation stage. In addition, we investigated potential associations between the diversity and the composition of the vaginal microbiota and several health-, performance-, and fertility-related phenotypes. Our analyses highlighted significant associations between the and {beta}- diversities and several traits including the first insemination outcome, the productive longevity, and the culling. Besides, relevant phenotypes were correlated with the abundance of several genera, some of which, such as Leptotrichia, Streptobacillus, Methylobacterium-Methylorubrum, or Negativibacillus, were linked to multiple traits. ConclusionConsidering the large number of samples, which were collected in commercial farms, and the diversity of the phenotypes considered, this study represents a first step towards a better understanding of the close relationship between the vaginal and the dairy cows phenotypes.

microbiology↗

bioRxiv2021

Analysis of viromes and microbiomes from pig fecal samples reveals that phages and prophages are not vectors of antibiotic resistance genes

Understanding the transmission of antibiotic resistance genes (ARGs) is critical for human health. For this, it is necessary to identify which type of mobile genetic elements is able to spread them from animal reservoirs into human pathogens. Previous research suggests that in pig feces, ARGs may be encoded by bacteriophages. However, convincing proof for phage-encoded ARGs in pig viromes is still lacking, because of bacterial DNA contaminating issues. We collected 14 pig fecal samples and performed deep sequencing on both highly purified viral fractions and total microbiota, in order to investigate phage and prophage-encoded ARGs. We show that ARGs are absent from the genomes of active, virion-forming phages (below 0.02% of viral contigs from viromes), but present in three prophages, representing 0.02% of the viral contigs identified in the microbial dataset. However, the corresponding phages were not detected in the viromes, and their genetic maps suggest they might be defective. Furthermore, our dataset allows for the first time a comprehensive view of the interplay between prophages and viral particles.

microbiology↗

bioRxiv2018

Towards the quantitative characterization of piglets’ robustness to weaning: A modelling approach

Weaning is a critical transition phase in swine production in which piglets must cope with different stressors that may affect their health. During this period, the prophylactic use of antibiotics is still frequent to limit piglet morbidity, which raises both economic and public health concerns such as the appearance of antimicrobial-resistant microbes. With the interest of developing tools for assisting health and management decisions around weaning, it is key to provide robustness indexes that inform on the animals capacity to endure the challenges associated to weaning. This work aimed at developing a modelling approach for facilitating the quantification of piglet resilience to weaning. We monitored 325 Large White pigs weaned at 28 days of age and further housed and fed conventionally during the post-weaning period without antibiotic administration. Body weight and diarrhoea scores were recorded before and after weaning, and blood was sampled at weaning and one week later for collecting haematological data. We constructed a dynamic model based on the Gompertz-Makeham law to describe live weight trajectories during the first 75 days after weaning following the rationale that the animal response is partitioned in two time windows (a perturbation and a recovery window). Model calibration was performed for each animal. Our results show that the transition time between the two time windows, as well as the weight trajectories are characteristic for each individual. The model captured the weight dynamics of animals at different degrees of perturbation, with an average coefficient of determination of 0.99, and a concordance correlation coefficient of 0.99. The utility of the model is that it provides biological parameters that inform on the amplitude and length of perturbation, and the rate of animal recovery. Our rationale is that the dynamics of weight inform on the capability of the animal to cope with the weaning disturbance. Indeed, there were significant correlations between model parameters and individual diarrhoea scores and haematological traits. Overall, the parameters of our model can be useful for constructing weaning robustness indexes by using exclusively the growth curves. We foresee that this modelling approach will provide a step forward in the quantitative characterization of robustness.\n\nImplicationsThe quantitative characterization of animal robustness at weaning is a key step for management strategies to improve health and welfare. This characterization is also instrumental for the further design of selection strategies for productivity and robustness. Within a precision livestock farming optic, this study develops a mathematical modelling approach to describe the body weight of piglets from weaning with the rationale that weight trajectories provide central information to quantify the capability of the animal to cope with the weaning disturbance.

systems biology↗