Microbiomes comprise communities of microorganisms (i.e., microbiota that includes bacteria, archaea, protists, fungi and microalgae) and their "theatre of activity" (i.e., structural elements, metabolites, signal molecules, mobile genetic elements, as well as surrounding environmental conditions). Microbiomes play a key role in maintaining life on Earth by providing a range of essential ecosystem services and are indispensable for the health of plants, animals and humans. Thus, there is a wide consensus that by harnessing microbiome functions society would be better placed to tackle global challenges such as food security, health and wellbeing, food waste management, and climate change mitigation. To facilitate the science necessary to achieve key advances in microbiome research, methodologies and technologies to capture or create, ensure stable long-term maintenance, and experimentally perturb microbiomes are required. Research infrastructures currently lack optimized methodologies and technologies to preserve and provide access to microbiome samples and massive amounts of associated data MICROBE is designed to address these issues by building upon and connecting: (1) technical solutions for microbiome preservation, propagation and functionality assessment, (2) novel ecological concepts (i.e. “core microbiome” and “microbial keystone taxa”), and (3) data infrastructures. In addition, MICROBE will address essential framework issues such as standardization, ethical and legal requirements and new business opportunities. Participation of relevant European research infrastructures, i.e., BBMRI-ERIC, MIRRI, ELIXIR and EMBRC-ERIC, to ensure that community needs are properly addressed and that developed solutions are efficiently taken up by the infrastructures themselves and by their user communities. Long term ambition is to ensure widespread uptake in microbiome research communities and thus support the development of novel microbiome-based applications.