Sofia Marcos

• University of the Basque Country

Background The red junglefowl, the wild outgroup of domestic chickens, has historically served as a reference for genomic studies of domestic chickens. These studies have provided insight into the etiology of traits of commercial importance. However, the use of a single reference genome does not capture diversity present among modern breeds, many o...

Unravelling the colonisation dynamics and physiological effects of zoonotic bacteria such as Campylobacter is imperative to prevent foodborne diseases. We employed a hologenomic approach to jointly analyse metabolic networks and gene expression of the caecal microbiota, with the intestinal gene expression of 613 broiler chickens that did and did no...

Background. The red junglefowl, the wild progenitor of domestic chickens, has historically served as a reference for genomic studies of domestic chickens. These studies have provided insight into the etiology of traits of commercial importance. However, the use of a single reference genome does not capture diversity present among modern breeds, man...

Understanding the development of functional attributes of host-associated microbial communities is essential for developing novel microbe-based solutions for sustainable animal production. We applied multi-omics to 388 broiler chicken caecal samples to characterise and model the functional dynamics of 822 bacterial strains. Although microbial commu...

Fast optimisation of farming practices is essential to meet environmental sustainability challenges. Hologenomics, the joint study of the genomic features of animals and the microbial communities associated with them, opens new avenues to obtain in-depth knowledge on how host-microbiota interactions affect animal performance and welfare, and in doi...

Metagenomic datasets of host‐associated microbial communities often contain host DNA that is usually discarded because the amount of data is too low for accurate host genetic analyses. However, genotype imputation can be employed to reconstruct host genotypes if a reference panel is available. Here, the performance of a two‐step strategy is tested...

From ontogenesis to homeostasis, the phenotypes of complex organisms are shaped by the bi-directional interactions between the host organisms and their associated microbiota. Current technology can reveal many such interactions, by combining multi-omic data from both hosts and microbes. However, exploring the full extent of these interactions requi...