under review
Marcos S, Odriozola I, Langa J, Baldi G, Sahin E, Mak SST, Pless L, Tarradas J, Estonba A, Alberdi A. Nov 2023. Priority effects and microbial cross-feeding shape zoonotic agent spread in broiler chickens. Under review at Microbiome. pre-print at Research Square. doi: https://doi.org/10.21203/rs.3.rs-3588367/v1
Bideguren G, Razgour O, Alberdi A. Nov 2023. Quantitative synthesis of microbe-driven acclimation and adaptation in wild vertebrates. pre-print at Research Square. doi: https://doi.org/10.21203/rs.3.rs-3577507/v1
Alberdi A, Limborg MT, Groussin M, Aizpurua O, Gilbert MTP. 2023. Metagenomic spaces: a framework to study the effect of microbiome variation on host ecology and evolution. Under review at Journal of Evolutionary Biology.
Eisenhofer R, Nesme J, Santos-Bay L, Koziol A, Sørensen SJ, Alberdi A, Aizpurua O. Oct 2023. A comparison of short-read, HiFi long-read, and hybrid strategies for genome-resolved metagenomics. pre-print at biorxiv. doi: 10.1101/2023.10.04.560907v1.
Rice ES, Alberdi A, Alfieri J, Athrey G, Balacco JR, Bardou P, Blackmon H, Charles M, Cheng HH, Fedrigo O, Fiddaman SR, Formenti G, Frantz L, Gilbert MTP, Hearn CJ, Jarvis ED, Klopp C, Marcos S, Velez-Irizarry D, Xu L, Warren WC. Jun 2023. A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants. pre-print at Research Square. doi: 10.21203/rs.3.rs-3086064/v1
Marcos S, Odriozola I, Aizpurua O, Eisenhofer R, Mak SST, Martin G, Kale V, Baldi G, Finn R, Tarradas J, Estonba A, Gilbert MTG, Alberdi A. 2023. Reduced metabolic capacity of the gut microbiota is associated with host growth in broiler chickens. Under Review at Science Advances.
2023
Aizpurua O, Dunn RR, Hansen LH, Gilbert MTP, Alberdi A. 2023. Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data. Critical Reviews in Biotechnology. doi: 10.1080/07388551.2023.2254933.
Alberdi A, Odriozola I, Eisenhofer R, Aizpurua O. 2023. Measuring biodiversity with eDNA metabarcoding. Chapter in Applied Environmental Genomics. Berry O, Holleley C, Jarman S eds. CSIRO Publishing. In Press.
Hernández M, Hereira-Pacheco S, Alberdi A, Diaz de la Vega-Pérez AH, Estrada-Torres A, Ancona S, Navarro-Noya YE. 2023. DNA metabarcoding reveals seasonal changes in diet composition across four arthropod-eating lizard species (Phrynosomatidae: Sceloporus). Integrative Zoology. doi: 10.1111/1749-4877.12755.
Froidevaux et al. 2023. A species-level trait database of bats in Europe and beyond. Scientific Data 10: 253.
Aizpurua O, Blijleven K, Trivedi U, Gilbert MTP, Alberdi A. 2023. Unravelling animal-microbiota evolution on a chip. Trends in Microbiology. doi: 10.1016/j.tim.2023.04.010.
Koziol A, Odriozola I, Leonard A, Eisenhofer R, San Jose C, Aizpurua O, Alberdi A. 2023. Mammals show distinct functional gut microbiome dynamics to identical series of environmental stressors. MBio. doi: 10.1128/mbio.01606-23.
Eisenhofer R, Odriozola I, Alberdi A. 2023. Impact of microbial genome completeness on functional metagenomics. ISME Communications 3: 12.
Pirolo M, Espinosa-Gongora G, Alberdi A, Eisenhofer R, Soverini M, Eriksen EO, Pedersen KS, Guardabassi L. 2023. Bacterial topography of the upper and lower respiratory tract in pigs. Animal Microbiome 5: 5.
Botnen AN, Bjørnsen MB, Alberdi A, Gilbert MTP, Aizpurua O. 2023. A simplified protocol for DNA extraction from FTA cards for faecal microbiome studies. Heliyon: e12861.
2022
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.
Tous N, Marcos S, Goodarzi Boroojeni F, Pérez De Rozas A, Zentek J, Estonba A, Sandvang D, Gilbert MTP, 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. Frontiers in Physiology 13: 884925.
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.
2021
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 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.
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.
2020
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.
2019
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.