Animal-microbiota interactions

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

Latest publications

  1. Alberdi A, Limborg MT, Groussin M, Aizpurua O, Gilbert MTP. 2025. Metagenomic spaces: a framework to study the effect of microbiome variation on animal ecology and evolution. Journal of Evolutionary Biology. doi: 10.1093/jeb/voaf063.
  2. Romeo C, Brenner E, Wauters LA, Alberdi A. 2025. The role of microbiomes in animal invasions: a scoping review. Neobiota. doi: 10.3897/neobiota.98.145939.
  3. Hernández M, Langa J, Aizpurua O, Navarro-Noya YE, Alberdi A. 2025. Contrasting recovery of metagenome‑assembled genomes and derived bacterial communities and functional profiles from lizard fecal and cloacal samples. Animal Microbiome. doi: 10.1186/s42523-025-00381-4.
  4. Aizpurua O, Bolt Botnen A, Eisenhofer R, Odriozola I, Nielsen L, Bjørnsen M, Gilbert MTP, Alberdi A. 2025. Functional insights into the effect of feralisation on the gut microbiota of cats worldwide. Molecular Ecology. doi: 10.1111/mec.17695.
  5. Rogers A, Kale V, Baldi G, Alberdi A, Gilbert MTP, Gupta D, Limborg M, Li S, Payne T, Petersen B, Rasmussen J, Richardson L, Finn R. 2025. HoloFood Data Portal: holo-omic datasets for analysing host-microbiota interactions in animal production. Database. doi: 10.1093/database/baae112.
  6. Pietroni C, Gaun N, Leonard A, Lauritsen J, Martin-Bideguren G, Odriozola I, Aizpurua O, Alberdi A, Eisenhofer R. 2025. Hologenomic data generation and analysis in wild vertebrates. Methods in Ecology and Evolution. doi: 10.1111/2041-210X.14456.

Relevant publications

Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data

Aizpurua O, Dunn RR, Hansen LH, Gilbert MTP, Alberdi A. 2023. Critical Reviews in Biotechnology. 

10.1080/07388551.2023.2254933

Unravelling animal–microbiota evolution on a chip

Aizpurua O, Blijleven K, Trivedi U, Gilbert MTP, Alberdi A. 2023. Trends in Microbiology.

10.1016/j.tim.2023.04.010

Mammals show distinct functional gut microbiome dynamics to identical series of environmental stressors

Koziol A, Odriozola I, Leonard A, Eisenhofer R, San Jose C, Aizpurua O, Alberdi A. 2023. MBio.

10.1128/mbio.01606-23

Disentangling host–microbiota complexity through hologenomics

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

10.1038/s41576-021-00421-0

Main projects

Earth Hologenome Initiative

Mapping animal-microbiota interactions worldwide

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


3D'omics


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.


HoloFood


Hologenomics for sustainable
food 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.

Address

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

Contact

Assoc. Prof. Antton Alberdi
Email: antton.alberdi@sund.ku.dk

Links

Earth Hologenome Initiative
3D'omics
GLOBE Institute
University of Copenhagen