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. pre-print at Research Square. doi: https://doi.org/10.21203/rs.3.rs-3588367/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. May 2023. Reduced metabolic capacity of the gut microbiota is associated with host growth in broiler chickens. pre-print at Research Square. doi: https://doi.org/10.21203/rs.3.rs-2885808/v1
2025
Alberdi A, Limborg MT, Groussin M, Aizpurua O, Gilbert MTP. 2025. Metagenomic spaces: a framework to study the effect of microbiome variation on host ecology and evolution. Journal of Evolutionary Biology voaf063.
Romeo C, Brenner E, Wauters LA, Alberdi A. 2025. The role of microbiomes in animal invasions: a scoping review. NeoBiota 98: 335-360.
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 7: 15.
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 34(6): e17695.
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 16(1): 97-107.
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 baae112.
2024
Augusto AM, Pereira S, Rodrigues S, Marques F, Aizpurua O, Alberdi A, Jones G, Razgour O, Marques TA, Russo D, Rebelo H. 2024. Landscape influences bat suppression of pine processionary moth: Implications for pest management. Journal of Environmental Management 373: 123803.
Bordenstein SR, Gilbert MTP, Ginnan N, Malacrinò A, Martino ME, Bahrndorff S, Mundra S, Martin MD, Theis KR, Hird SM, Caro-Quintero A, Sharpton TJ, Kohl KD, Eisenhofer R, Aizpurua O, Andersen SB, Brealey JC, Noer CL, Medina M, Limborg MT, Alberdi A. 2024. The disciplinary matrix of holobiont biology. Science 386(6723): 731-732.
Eisenhofer R, Alberdi A, Woodcroft BJ. 2024. Quantifying microbial DNA in metagenomes improves microbial trait estimation. ISME Communications 4(1): ycae111.
Hussain M, Aizpurua O, Perez de Rozas A, París N, Guivernau M, Jofre A, Tous N, Ng'ang'a ZW, Alberdi A, Rodríguez-Gallego E, Kogut MH, Tarradas J. 2024. Positive impact of early-probiotic administration on performance parameters, intestinal health and microbiota populations in broiler chickens. Poultry Science 103(12): 104401.
Martin-Bideguren G, Razgour O, Alberdi A. 2024. Quantitative synthesis of microbe-driven acclimation and adaptation in wild vertebrates. Evolutionary Applications 17(10): e70025.
Hernández M, Hereira-Pacheco S, Alberdi A, Diaz de la Vega-Pérez AH, Estrada-Torres A, Ancona S, Navarro-Noya YE. 2024. DNA metabarcoding reveals seasonal changes in diet composition across four arthropod-eating lizard species (Phrynosomatidae: Sceloporus). Integrative Zoology 19(3): 480-495.
Tranquillo C, Santicchia F, Romeo C, Bisi F, Panzeri M, Preatoni D, Martinoli A, Alberdi A, Wauters LA. 2024. Going urban: variation in personality traits of an invasive species along an urbanization gradient. Journal of Mammalogy 105(6): 1300–1308.
Odriozola I, Rasmussen JA, Gilbert MTP, Limborg MT, Alberdi A. 2024. A practical introduction to holo-omics. Cell Reports Methods 4(7): 100820.
Eisenhofer R, Alberdi A, Woodcroft BJ. 2024. Large-scale estimation of bacterial and archaeal DNA prevalence in metagenomes reveals biome-specific patterns. pre-print at bioRxiv doi: 10.1101/2024.05.16.594470.
Hernández M, Ancona S, Hereira‐Pacheco S, Díaz de la Vega‐Pérez AH, Alberdi A, Navarro-Noya YE. 2024. Seasonal dietary changes relate to gut microbiota composition depending on the host species but do not correlate with gut microbiota diversity in arthropod‐eating lizards. Molecular Ecology e17426.
Leonard A, Earth Hologenome Initiative Consortium, Alberdi A. 2024. A global initiative for ecological and evolutionary hologenomics. Trends in Ecology and Evolution 39(7): 616-620.
Eisenhofer R, Nesme J, Santos-Bay L, Koziol A, Sørensen SJ, Alberdi A, Aizpurua O. 2024. A comparison of short-read, HiFi long-read, and hybrid strategies for genome-resolved metagenomics. Microbiology Spectrum 12(4): e03590-23.
Augusto AM, Raposeira H, Horta P, Mata VA, Aizpurua O, Alberdi A, Jones G, Razgour O, Santos SAP, Russo D, Rebelo H. 2024. Bat diversity boosts ecosystem services: Evidence from pine processionary moth predation. Science of the Total Environment 912: 169387.
Aizpurua O, Dunn RR, Hansen LH, Gilbert MTP, Alberdi A. 2024. Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data. Critical Reviews in Biotechnology 44(6): 1164-1182.
2023
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. BMC Biology 21(1): 267.
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 19: 480-495.
Alberdi A, Odriozola I, Eisenhofer R, Aizpurua O. 2023. Measuring biodiversity with eDNA metabarcoding. 2nd Chapter in Applied Environmental Genomics. Berry OF, Holleley CE, Jarman SN eds. CSIRO Publishing. pp14-17. ISBN: 978-1-4863-1494-2.
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 31(10): 995-1002.
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 14:e01606-23.
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.
Alberdi A, Aizpurua O. 2023. Alpine Long-Eared Bat Plecotus macrobullaris Kuzjakin, 1965. Handbook of the Mammals of Europe. Russo D (editor). Chiroptera (pp. 671-684). Springer.
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.
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.