We love to conduct interdisciplinary research in which methods and ideas from different fields are merged to address new scientific questions. The main topics we cover in our research are outlined below. 



We are interested in understanding how the interactions between animals and their associated microorganisms, revealed using multi-omic approaches, shape ecological and evolutionary processes.

Trophic ecology

We analyse trophic niche variation across taxa and environments usind DNA metabarcoding to understand its relation with other aspects of animal biology and ecosystem services.

Community ecology

We use genomic and metagenomic tools to understand ecological community variation across space and time. 

Research projects

Ongoing projects in the Alberdi Lab


Micro-scale multi-omics

Carlotta Pietroni, Marta Contreras,
Jonas Lauritsen

The project combines the newest technologies & equipment to investigate microorganisms in their 3D spatial structures within their host-microbiome relation on a microscale.


Hologenomic adaptation

Garazi Martin Bideguren,
Ostaizka Aizpurua

We aim to study the role of gut microbes in the adaptation of lizards to different environments. We will perform an experimental study with wall lizards (Podarcis muralis) and doing faecal microbiota transplants we will be able to see if the gut microbes enhance lizards adaptability to new environments.


Squirrel hologenomics

Aoife Leonard

We aim to study the relationships between ecological niche properties of the squirrels Sciurus vulgaris and Sciurus carolinensis, their genomic features, and their gut metagenomic characteristics, across their entire geographical distributions, including regions in which the species can be found in sympatry and allopatry.


Hybridisation hologenomics

Isolde van Riemsdijk

We aim to understand the dynamic relationships between the occurrence of chytrid fungus, the hybrid zone between the yellow-bellied toad (Bombina variegata) and the fire-bellied toad (Bombina bombina), and their microbiomes. 


Convergence hologenomics

Raphael Eisenhofer

We aim to generate population-level paired genomic and metagenomic data of paired marsupial and placental species with similar ecological characteristics, to understand the impact of animal-microbiota interactions in the evolution of ecological features of mammals.


Invasion hologenomics

Claudia Romeo

We aim to investigate whether metagenomic plasticity plays a role in invasions, i.e., whether invasive species may be able to quickly adapt to their new environment and oust native species thanks to a higher diversity and/or dynamism of their gut microbial community.


Behavioral hologenomics

Luisa Nielsen

More details coming soon


Chicken hologenomics

 Sofia Marcos, Iñaki Odriozola,
Jorge Langa

More details coming soon



Kees Blijleven, Michael Miskelly, Ostaizka Aizpurua

Our goal is to generate intestinal organoid models from a range of animals (both wild and captive) in order to assess the specific effects of gut microbiota-host interactions in the intestinal epithelium.


Elevation hologenomics

Garazi Martin Bideguren, Aoife Leonard

We aim to generate population-level paired genomic and metagenomic data of vertebrates across elevational gradients in various mountain ranges to understand the hologenomic underpinnings of adaptation to different climatic regimes.


Podarcis inbreeding

Garazi Martin Bideguren, Aoife Leonard

We aim to establish if there are consistent genomic and gut metagenomic signatures in lizard populations that are restricted to tiny islets.


Habitat degradation hologenomics

We aim to generate population-level paired genomic and metagenomic data of neotropical vertebrates (birds, bats, and amphibians) which inhabit ecosystems with similar ecological characteristics in the cloud forest of Honduras to understand the role of the gut microbiota in facilitating adaptive responses in inhabits with different degrees of anthropic perturbation.


Newt conservation metagenomics

Restored and newly created ponds are a critical resource to counteract amphibian population declines in areas with severe anthropic pressure. While many amphibian species are able to colonise and take advantage of such microhabitats, we do not know whether and how microbiome features are affected. This project aims to ascertain whether newt microbiome features are correlated with host health and pond attributes.


Vultures hologenomics

Scavenging is an extreme dietary strategy that requires immune adaptations to cope with the diverse microorganisms that grow in animal carcases. This project aims to study the specialised microbiome of New World vultures that was hypothesised could enable them to cope with such conditions, by not only investigating the genomic features of bacterial communities, but also their gene expression and the expression of host vultures.


Field, laboratory, and informatic infrastructure


To conduct controlled captivity experiments

We run controlled captivity experiments to understand the interactions between animals and their gut microorganisms.


To process thousands of samples

We use automated tools that enabe high-throughput processing of hundreds or thousands of samples per projects


To generate cool results!

We make use of HPCs dedicated to live sciences to run the heaviest bioinformatic procedures.


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


Assoc. Prof. Antton Alberdi