Microbes are the most ancient, abundant, and diverse life forms on Earth. They have coevolved with and shaped our planet. This transversal research theme aims to systematically dissect microbial functions, lifestyles, and communities, and especially how microbes interact with and influence their environments across time and space. By focusing primarily on microbes that impact humans, the aim of this theme is to generate the foundational knowledge that will enable us to rationally modulate human microbial communities to achieve desired traits and to combat pathogens.

Microorganisms colonise, proliferate on, and impact every surface and subsurface of the planet. They do this mostly in the form of complex communities. The Microbial Ecosystems theme aims to explore microorganisms and their interactions, with each other and with their environments. EMBL research has placed a strong emphasis on human-associated microbiomes (i.e. microbial communities on and within the human body), building both computational and experimental capacities to elucidate the complex role that microbes play in human health and disease. Examples of this include how medication impacts the gut microbiota composition, and how microbes themselves affect drug availability. Regardless of the specific microbiome, a fundamental goal of this theme is to understand how the composition of a microbiome may be modulated, whether to enhance a particular trait or to return the microbiome to its original state after perturbation.

An important aspect of understanding microbiomes is increasing our knowledge of their composition, their individual constituents – from viruses to bacteria to single-celled eukaryotes – and the functions these encode. For example, there are thousands of bacterial species that have been identified in the gut microbiota from metagenomics datasets, yet less than a third have been cultured in the laboratory, let alone functionally characterised. EMBL is interested in pioneering ways to tap into this vast store of functional information to understand the underlying molecular mechanisms of microbiome–host–environment interactions.

EMBL’s future directions include exploring microbes in any domain of life and from any environment, especially how they form communities and interact with their natural environment or host. This includes related topics such as infection biology and antimicrobial resistance, for which the focus is on understanding the underlying mechanisms and transmission paths in their natural context, and devising novel strategies to combat them.

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