Microbiomes
We investigate how microbial communities vary among animals and environments, and how they contribute to host biology, ecology and evolution.
How we work
How we study animals and their microbiota
We collect animals and environmental samples, run controlled experiments and analyse genomes, metagenomes and other molecular data together.
Organism · community · environment
Research themes
The three questions
we return to.
Our projects examine microbiomes, their relationships with animal genomes and the spatial organisation of microbial communities at the smallest scales.
Hologenomics
We combine host genomic and microbiome data to understand how animals and their associated microorganisms interact and respond to ecological and evolutionary pressures.
Micro-scale spatial ecology
We use spatially resolved molecular approaches to explore how microorganisms are organised and interact within the microscopic landscapes of their hosts.
In the lab now
What we are working on.
These projects are being developed by our current group members and collaborators.
Project 01
Micro-scale multi-omics
Carlotta Pietroni, Amalia Bogri, Jonas Lauritsen
Project note
Combining new technologies and equipment to investigate microorganisms in their three-dimensional spatial structures within host–microbiome relationships.
Project 02
Hologenomic adaptation
Garazi Martin Bideguren, Ostaizka Aizpurua
Project note
Studying the role of gut microbes in lizard adaptation through experiments with wall lizards and faecal microbiota transplants.
Project 03
Invasion hologenomics
Claudia Romeo
Project note
Investigating whether the diversity and dynamism of gut microbial communities contribute to the rapid adaptation of invasive species.
Project 04
Hybridisation hologenomics
Isolde van Riemsdijk
Project note
Exploring the relationships among chytrid fungus, a fire-bellied and yellow-bellied toad hybrid zone, and the animals’ microbiomes.
Project 05
Convergence hologenomics
Raphael Eisenhofer
Project note
Comparing paired genomic and metagenomic data from ecologically similar marsupial and placental mammals.
Project 06
Gut-on-a-chip
Michael Miskelly, Ostaizka Aizpurua
Project note
Developing experimental intestinal models that make animal–microbiota interactions observable under controlled conditions.
Project 07
Elevation hologenomics
Garazi Martin Bideguren
Project note
Generating paired genomic and metagenomic data across mountain gradients to understand adaptation to different climatic regimes.
Project 08
Podarcis inbreeding
Garazi Martin Bideguren
Project note
Looking for consistent genomic and gut metagenomic signatures in lizard populations restricted to tiny islets.
Project 09
Chicken hologenomics
Sofia Marcos, Iñaki Odriozola, Jorge Langa
Project note
Applying hologenomics to animal production systems and the complex microbial ecology of broiler chickens.
Project 10
Newt conservation metagenomics
Conservation ecology
Project note
Testing whether newt microbiome features correlate with host health and the attributes of restored and newly created ponds.
Project 11
Vulture hologenomics
Comparative multi-omics
Project note
Studying the specialised microbiomes and gene expression that help New World vultures thrive on an extreme scavenging diet.
Project 12
Habitat degradation hologenomics
Neotropical vertebrates
Project note
Exploring how gut microbiota may facilitate adaptive responses to different degrees of human disturbance in cloud-forest habitats.
How we do the work
The facilities we use
and have developed.
We run animal experiments, process large sample collections with automated laboratory workflows and analyse the results on dedicated computing systems.
Controlled experiments
Animal experimentation
Captivity experiments reveal interactions between animals and their gut microorganisms under controlled conditions.
Thousands of samples
High-throughput laboratory
Automated tools enable consistent processing of hundreds or thousands of samples per project.
Heavy computation
Bioinformatic platform
Dedicated life-science computing systems support our most demanding bioinformatic procedures.