Animal-microbiota interactions

@ the AlberdiLab
Center for Evolutionary Hologenomics
GLOBE Institute, University of Copenhagen

Latest publications

  1. Marcos S, Parejo M, Estonba A, Alberdi A. 2022 Recovering high-quality host genomes from gut metagenomic data through genotype imputation. Advanced Genetics: 2100065. doi: 10.1002/ggn2.202100065.
  2. Nyholm L, Odriozola I, Martin G, Aizpurua O & Alberdi A. 2022. Gut microbiota differences between paired mucus and digesta samples in three small species of fish. PeerJ 10:e12992. doi: 10.7717/peerj.12992.
  3. Alberdi A, Bideguren GM, Aizpurua O. 2021. Diversity and compositional changes in the gut microbiota of wild and captive vertebrates: a meta‐analysis. Scientific Reports. 11: 22660. doi: 10.1038/s41598-021-02015-6.
  4. Aizpurua O, Nyholm L, Morris E, Chavarri G, Herrera-Montalvo LG, FLores-Martinez JJ, Lin A, Razgour O, Gilbert MTP, Alberdi A. 2021. The role of the gut microbiota in the dietary niche expansion of fishing bats. Animal Microbiome 3: 76. doi: 10.1186/s42523-021-00137-w.
  5. Alberdi A, Andersen SB, Limborg MT, Dunn R, Gilbert MTP. 2021. Disentangling host-microbiota complexity through hologenomics. Nature Reviews Genetics. doi: 10.1038/s41576-021-00421-0.

Relevant publications

A guide to the application of Hill numbers to DNA-based diversity analyses

Alberdi A, Gilbert MTP. 2019. Molecular Ecology Resources 19: 804-817,

Scrutinizing key steps for reliable metabarcoding of environmental samples

Alberdi A, Aizpurua O, Gilbert MTP, Bohmann K. 2018. Methods in Ecology and Evolution 9: 134-147

Holo-omics: Integrated Host-Microbiota Multi-omics for Basic and Applied Biological Research

Nyholm L, Koziol A, Marcos A, Bolt-Botnen A, Aizpurua O, Gopalakrishnan S, Limborg MT, Gilbert MTP, Alberdi A. 2020. iScience 23(8): 101414.

Disentangling host–microbiota complexity through hologenomics

Alberdi A, Andersen SB, Limborg MT, Dunn R, Gilbert MTP. 2021. Nature Reviews Genetics.

Main projects


Hologenomics for sustainable foor production

Poultry and salmon aquaculture are our two model systems to showcase the power of hologenomics for improving the quality and sustainability of animal food production.

Earth Hologenome Initiative

Mapping animal-microbiota interactions worldwide

We are generating paired genomic and metagenomic data of wild organisms from all over the world.


Reconstructing animal-microbiota interactions in 3D

We are merging animal sciences, microbiology and structural genomics to reconstruct animal-microbiota multi-omic interactions at the micro scale in three dimensions.


GLOBE Institute
University of Copenhagen
Øster Farimagsgade 5,
Building 7
1353 Copenhagen, Denmark


Assoc. Prof. Antton Alberdi