EarthHologenomics: Unveiling global patterns of gut microbiome-animal interactions in light of environmental variation

Name of applicant

Antton Alberdi


University of Copenhagen


DKK 5,096,595



Type of grant

Semper Ardens: Accelerate


In EarthHologenomics we will perform the first global mapping of spatial variation of animal-microbiome interactions. We will screen climatic, habitat and dietary gradients in 50 widespread animal taxa spanning the four main vertebrate clades (mammals, birds, reptiles and amphibians) to identify general patterns across animal phylogeny and geographic space. We will leverage the network of over 120 researchers that are already collecting samples within the Earth Hologenome Initiative. We will employ whole genome sequencing and shotgun metagenomics to characterise genomic features of animal hosts and associated gut microbial communities. This will enable us not only to perform taxonomic inferences, but to understand the functional capabilities of animal genomes and microbial metagenomes.


Research carried out in the last decade has unveiled that biology of animals is largely impacted by microorganism associated with them. However, the global impact of such interactions in animal ecology and evolution has not been quantified yet. The data we will generate in EarthHologenomics will enable us to address questions such as how animal genomes and microbial metagenomes interact to provide adaptive capacity of animals towards climate change, or why genomically related species often exhibit contrasting geographic range sizes. In addition, the metagenomic characterisation of wild animals will allow us to screen for zoonotic diseases with an unparalleled resolution, while the large catalogue of bacterial genomes we will generate will enable identifying potential probiotic strains.


EarthHologenomics will leverage the Earth Hologenome Initiative, a global endeavour founded and coordinated by the PI, which will provide access to the largest catalogue of faecal, oral, blood and tissue samples of over 120 vertebrate taxa from all over the world. We will select 50 widespread animal species, and collect samples to generate paired genomic and metagenomic datasets across environmental gradients. These data will include whole-genome genotypes of animal hosts, and high quality genome reconstructions of associated bacteria. Data analysis will be conducted using a range of phylogenomic, spatial and community ecology tools to unveil relationships between microbial and animal genomic properties and their association with environmental features, among others.

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