Microorganisms associated to complex organisms are not longer considered passive passengers but active crew, who can affect and even condition a myriad of biological processes of their hosts. Although such effects have been so far mainly explored in applied contexts (e.g. medicine, agrisciences), an increasing amount of evidence is indicating that they could also be relevant in basic ecological and evolutionary processes. The hologenomic approach I will introduce in this talk takes advantage of the newly developed high-throughput DNA/RNA sequencing methods, to study host-microbiota interactions at different ‘omic levels (e.g. genomes, transcriptomes), and eventually understand their impact on eco-evolutionary processes such as acclimation, adaptation or speciation. In this talk, I will present basic concepts about the host-microbiota interplay and introduce the work we are carrying out on the topic, before providing an overview of the research approaches we are using on chickens, deers, shrews, mice, wolves and toothcarps, among others, to address different ecologically and evolutionary relevant topics. I will also introduce the Centre for Evolutionary Hologenomics that will kick off in Copenhagen in early 2020, and I will encourage researchers to join the Earth HoloGenome Initiative (EHI), an endeavour we are now launching aiming at promoting, facilitating, coordinating and standardising hologenomic research on wild organisms worldwide. In the initial phase of EHI, we are coordinating a large research network to generate geographically expansive coupled host genome and microbial metagenome data from 10,000 animals belonging to 100 European vertebrate species, aiming at addressing major questions regarding adaptation to climate change and disease transmission, among others