Microbes are this planet’s most ancient, abundant, and diverse life forms. They have coevolved with and shaped our planet. This theme will systematically dissect microbial functions, lifestyles, and communities – especially how microbes interact with and influence their environments across time and space.

With an eye towards 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 towards desired traits and compositions. 

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 focused largely on human-associated microbiomes (i.e. microbial communities on and within the human body), and has built 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 – from viruses to bacteria to single-celled eukaryotes – and the functions they encode. For example, there are thousands of bacterial species that have been identified in the human gut microbiota from metagenomics datasets, yet most of these species are still terra incognita in terms of the functions they encode. EMBL is interested in pioneering ways to tap into this vast functional diversity to understand the underlying molecular mechanisms of microbiome–host–environment interactions. Such functional and mechanistic understanding is necessary for protecting, rationally modulating, or even exploiting microbiomes.

EMBL’s future directions include exploring microbes from all domains of life as well as from different environments, and understanding how they form communities and interact with their natural environment, their host, or their predators (other microbes, phages).

Read the Programme chapter

“By focusing further on microbial ecosystems, we can delve into the secret lives of microbes – what functions they encode and how these help them survey the environment, interact with each other, and live together in diverse, complex communities. Ultimately, we want to understand how the balance in these versatile communities impacts human health.”

News

Global microbial signatures for colorectal cancer

Understanding soil through its microbiome

Molecular cuisine for gut bacteria

Combining antibiotics changes their effectiveness

Potential way to limit antibiotic resistance

Understanding the influenza virus

Cell death trigger in tuberculosis bacteria

Toxin responsible for Legionella growth identified

EMBL’s contribution to fighting the coronavirus pandemic

Tools

MGnify

Microbiome analysis tools developed at EMBL