A5022646283- Genetic Mapping and Diversity in Plants and Animals
- Genetic and phenotypic traits in livestock
- Gut microbiota and health
- Genomics and Phylogenetic Studies
- Livestock and Poultry Management
- Animal Nutrition and Physiology
- Agriculture, Soil, Plant Science
- Genetic diversity and population structure
- Nutrition, Genetics, and Disease
- Animal Behavior and Welfare Studies
- Aquaculture disease management and microbiota
- Salmonella and Campylobacter epidemiology
- Bioinformatics and Genomic Networks
University of the Basque Country
2020-2023
University of Copenhagen
2023
Observatoire Midi-Pyrénées
2023
U.S. National Poultry Research Center
2023
University of Missouri
2023
Rockefeller University
2023
Texas A&M University
2023
Université de Toulouse
2023
École Nationale Vétérinaire de Toulouse
2023
Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
2023
Abstract Background The red junglefowl, the wild outgroup of domestic chickens, has historically served as a reference for genomic studies chickens. These have provided insight into etiology traits commercial importance. However, use single genome does not capture diversity present among modern breeds, many which accumulated molecular changes due to drift and selection. While reference-based resequencing is well-suited cataloging simple variants such single-nucleotide short insertions...
Fast optimisation of farming practices is essential to meet environmental sustainability challenges. Hologenomics, the joint study genomic features animals and microbial communities associated with them, opens new avenues obtain in-depth knowledge on how host-microbiota interactions affect animal performance welfare, in doing so, improve quality production. Here, we introduce trials conducted broiler chickens H2020 project HoloFood, our strategy implement hologenomic analyses light initial...
Abstract Metagenomic datasets of host‐associated microbial communities often contain host DNA that is usually discarded because the amount data too low for accurate genetic analyses. However, genotype imputation can be employed to reconstruct genotypes if a reference panel available. Here, performance two‐step strategy tested impute from four types panels built using different strategies low‐depth genome (≈2× coverage) recovered intestinal samples two chicken lines. First, accuracy evaluated...
Abstract Understanding the development of functional attributes host-associated microbial communities is essential for developing novel microbe-based solutions sustainable animal production. We applied multi-omics to 388 broiler chicken caecal samples characterise and model dynamics 822 bacterial strains. Although community diversity metrics increased with age as expected, overall metabolic capacity activity microbiota exhibited an unexpected decrease. This drop occurred due spread...
Abstract Background. The red junglefowl, the wild progenitor of domestic chickens, has historically served as a reference for genomic studies chickens. These have provided insight into etiology traits commercial importance. However, use single genome does not capture diversity present among modern breeds, many which accumulated molecular changes due to drift and selection. While reference-based resequencing is well-suited cataloging simple variants such nucleotide short insertions deletions,...
<title>Abstract</title> Unravelling the colonisation dynamics and physiological effects of zoonotic bacteria such as <italic>Campylobacter</italic> is imperative to prevent foodborne diseases. We employed a hologenomic approach jointly analyse metabolic networks gene expression caecal microbiota, with intestinal 613 broiler chickens that did not undergo an opportunistic colonisation. report early development distinct microbial enterotype enriched <italic>Bacteroides fragilis_A</italic>,...
Abstract Metagenomic data sets of host-associated microbial communities often contain host DNA that is usually discarded because the amount too low for accurate genetic analyses. However, if a reference panel available, genotype imputation can be employed to reconstruct genotypes and maximise use such priori useless data. We tested performance two-step strategy input from four types panels, comprised deeply sequenced chickens low-depth genome (~2x coverage) recovered metagenomic samples...