Publications

Publication covering the HoloFood Data Portal

Rogers, A. B., Kale, V., Baldi, G., Alberdi, A., Gilbert, M. T. P., Gupta, D., Limborg, M. T., Li, S., Payne, T., Petersen, B., Rasmussen, J. A., Richardson, L., Finn, R. D. (2025). HoloFood Data Portal: holo-omic datasets for analysing host–microbiota interactions in animal production. In Database (Vol. 2025, Article ID: baae112), Oxford University Press. 10.1093/database/baae112

Nyholm, L., Koziol, A., Marcos, S., Botnen, A. B., Aizpurua, O., Gopalakrishnan, S., Limborg, M. T., Gilbert, M. T. P., & Alberdi, A. (2020). Holo-Omics: Integrated Host-Microbiota Multi-omics for Basic and Applied Biological Research. In iScience (Vol. 23, Issue 8, p. 101414). Elsevier BV. 10.1016/j.isci.2020.101414

Bozzi, D., Rasmussen, J. A., Carøe, C., Sveier, H., Nordøy, K., Gilbert, M. T. P., & Limborg, M. T. (2021). Salmon gut microbiota correlates with disease infection status: potential for monitoring health in farmed animals. In Animal Microbiome (Vol. 3, Issue 1). Springer Science and Business Media LLC. 10.1186/s42523-021-00096-2

Duangnumsawang, Y., Zentek, J., & Goodarzi Boroojeni, F. (2021). Development and Functional Properties of Intestinal Mucus Layer in Poultry. In Frontiers in Immunology (Vol. 12). Frontiers Media SA. 10.3389/fimmu.2021.745849

Eisenhofer, R., Odriozola, I., & Alberdi, A. (2023). Impact of microbial genome completeness on metagenomic functional inference. In ISME Communications (Vol. 3, Issue 1). Springer Science and Business Media LLC. 10.1038/s43705-023-00221-z

Duangnumsawang, Y., Zentek, J., Vahjen, W., Tarradas, J., & Goodarzi Boroojeni, F. (2022). Alterations in bacterial metabolites, cytokines, and mucosal integrity in the caecum of broilers caused by feed additives and host-related factors. In Frontiers in Physiology (Vol. 13). Frontiers Media SA. 10.3389/fphys.2022.935870

Tous, N., Marcos, S., Goodarzi Boroojeni, F., Pérez de Rozas, A., Zentek, J., Estonba, A., Sandvang, D., Gilbert, M. T. P., Esteve-Garcia, E., Finn, R., Alberdi, A., & Tarradas, J. (2022). Novel strategies to improve chicken performance and welfare by unveiling host-microbiota interactions through hologenomics. In Frontiers in Physiology (Vol. 13). Frontiers Media SA. 10.3389/fphys.2022.884925

Marcos, S., Parejo, M., Estonba, A., & Alberdi, A. (2022). Recovering High‐Quality Host Genomes from Gut Metagenomic Data through Genotype Imputation. In Advanced Genetics (Vol. 3, Issue 3, p. 2100065). Wiley. 10.1002/ggn2.202100065

Brealey, J. C., Lecaudey, L. A., Kodama, M., Rasmussen, J. A., Sveier, H., Dheilly, N. M., Martin, M. D., & Limborg, M. T. (2022). Microbiome “Inception”: an Intestinal Cestode Shapes a Hierarchy of Microbial Communities Nested within the Host. In A. August (Ed.), mBio (Vol. 13, Issue 3). American Society for Microbiology. 10.1128/mbio.00679-22

Brealey, J. C., Kodama. M., Rasmussen. J. A., et al (2024). Host-gut microbiota interactions shape parasite infections in farmed Atlantic salmon. In Msystem (s. 2024). American Society for Microbiology. 10.1128/msystems.01043-23