Publication list of the Alberdi Group at the University of Copenhagen

Under review

Eisenhofer R, Odriozola I, Alberdi A. 2022. Impact of microbial genome completeness on functional metagenomics. Research Square. doi: 10.21203/ Under Review. 


Koziol A, Odriozola I, Nyholm L, Leonard A, San José C, Pauperio J, Ferreira C, Hansen AJ, Aizpurua O, Gilbert MTP & Alberdi A. 2022. Enriching captivity conditions with natural elements does not prevent the loss of wild-like gut microbiota but shapes its compositional variation in two small mammals. MicrobiologyOpen 11: e1318.
Núria Tous, Sofia Marcos, Farshad Goodarzi Boroojeni, Ana Pérez De Rozas, Jürgen Zentek, Andone Estonba, Dorthe Sandvang, M Thomas P Gilbert, Enric Esteve-Garcia, Robert Finn, Antton Alberdi, Joan Tarradas. 2022. Novel Strategies to Improve Chicken Performance and Welfare by Unveiling Host-Microbiota Interactions through Hologenomics. Frontiers in Physiology. doi: 10.3389/fphys.2022.884925. Accepted. 
Alberdi A, Odriozola I, Eisenhofer R, Aizpurua O (2022) Measuring biodiversity with eDNA metabarcoding. Chapter in Applied Environmental Genomics. Berry O, Holleley C, Jarman S eds. CSIRO Publishing. In Press.
Alberdi A, Aizpurua O. 2022. Alpine Long-Eared Bat Plecotus macrobullaris (Kuzjakin, 1965). Chapter in Handbook of the Mammals of Europe. Hackländer K, Zachos FE (eds). Springer, Cham.
Marcos S, Parejo M, Estonba A, Alberdi A. 2022 Recovering high-quality host genomes from gut metagenomic data through genotype imputation. Advanced Genetics: 2100065.
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.
Alberdi A, Andersen SB, Limborg MT, Dunn R, Gilbert MTP. 2022. Disentangling host-microbiota complexity through hologenomics. Nature Reviews Genetics 23: 281–297.


Alberdi A, Martin G, Aizpurua O. 2021. Diversity and compositional changes in the gut microbiota of wild and captive vertebrates: a meta-analysis. Scientific Reports 11: 22660. 
Aizpurua ONyholm 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 batsAnimal Microbiome 3: 76.
Roberto Novella-Fernandez R, Juste J, Ibañez C, Rebelo H, Russo D, Alberdi A, Kiefer A, Graham L, Paul H, Doncaster CP, Razgour O. 2021. Broad-scale patterns of geographic avoidance between species emerge in the absence of fine-scale mechanisms of coexistence. Diversity and Distributions 27: 1606–1618.
Rampelli S, Turroni S, Debandi F, Alberdi A, Schnorr S, Horman C, Taddia A, Helg R, Biagi E, Brigidi P, D'Amico F; Cattani M, Candela M. 2021. Bronze Age Coprolites Unveil the Buffering Role of the Gut Microbiota in the Dietary Adaptation of Dogs to Domestication. iScience 24(8): 102816


Aizpurua O, Alberdi A. 2020. Mapping the pressure of natural predators on pest arthropods. Preprint. Authorea preprint. doi: 10.22541/au.158981075.53963117.
Nyholm L, Koziol A, Marcos S, Bolt-Botnen A, Aizpurua O, Gopalakrishnan S, Limborg MT, Gilbert MTP, Alberdi A. 2020. Holo-omics: integrated host-microbiota multi-omics for basic and applied biological research. iScience 23(8): 101414.
Li Z, Wang X, Alberdi A, Deng J, Zhong Z, Si H, Zheng C, Zhou H, Wang J, Yang Y, Wright ADG, Mao S, Zhang Z, Guan LL, Li G.. 2020. Comparative Microbiome Analysis Reveals the Ecological Relationships between Rumen Methanogens, Acetogens, and their Hosts. Frontiers in Microbiology 11: 1311.
Moreno-Mateos D, Alberdi A, Morrien E, van der Putten WH, Rodríguez-Uña, Montoya D. 2020. The long-term restoration of ecosystem complexity. Nature Ecology and Evolution 4: 676–685.
Alberdi A, Razgour O, Aizpurua O, Novella-Fernandez R, Aihartza J, Budinski I, Garin I, Ibáñez C, Izagirre E, Rebelo H, Russo D, Vlaschenko A, Zhelyazkova V, Zrncic V, Gilbert MTP. 2020. DNA metabarcoding and spatial modelling link diet diversification with distribution homogeneity in European bats. Nature Communications 11: 1154.


Alberdi A, Gilbert MTP. 2019. A guide to the application of Hill numbers to DNA based diversity analyses. Molecular Ecology Resources 19: 804-817.
Razgour O, Forester B, Taggart J, Bekaert M, Juste J, Ibáñez C, Puechmaille SJ, Novella Fernandez R, Alberdi A, Manel S. 2019. Considering intraspecific climatic adaptations reduces species range loss projections. PNAS 116(21): 10418-10423.
Alberdi A, Aizpurua O, Bohmann K, Gopalakrishnan S, Lynggaard C, Nielsen M, Gilbert MTP. 2019. Promises and pitfalls of using high-throughput sequencing for diet analysis. Molecular Ecology Resources, 19(2), 327-348.
Hooper R, Brealey J, van der Valk T, Alberdi A, Durban J, Fearnbach H, Robertson K, Baird R, Hanson B, Wade P, Gilbert M, Morin P, Wolf J, Foote A, Guschanski K. 2019. Host‐derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin. Molecular Ecology, 28(2): 484-502.


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


Assoc. Prof. Antton Alberdi