Microbial Ecosystems

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 Transversal Theem 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. The bidirectional interactions of the gut microbiota has been an area of extended research at EMBL. Examples of this include how medication impacts the gut microbiota composition, including both antibiotics and non-antibiotic drugs, and in turn how microbes themselves affect drug availability by breaking down drugs or bioaccumulating them intracellularly. Interestingly, the response of microbes to drugs can be emergent and benefit the entire community, the effect of medication on gut microbiome composition can be passed from fathers to their offspring, and the effects of microbes to carcinogenic compounds can promote cancer.

Commonly used drugs accumulate in human gut bacteria, which can affect the drugs' effectiveness and change the bacteria's metabolism.

Credit: Aleksandra Krolik

At EMBL, the study of microbes spans diverse environments through an interdisciplinary approach. Scientists at EMBL have pioneered genome-wide genetics and proteomics methods to explore gene functions and  mechanisms of antimicrobial drug action. Investigations into bacterial genomes have revealed mechanisms of cell death and immunity against viruses, paving the way for new strategies to combat bacterial pathogens. Additionally, EMBL research delves into environmental microbes, examining interactions between soil microbes and protozoan predators, the role of marine microbes, genome packaging in archaea, and how microbes in extreme environments handle toxic metals. 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.

EMBL’s data services, including MGnify, SPIRE, and the European Nucleotide Archive, support global microbiome research. Our computational groups lead in recovering genomes from metagenomics datasets, covering viruses, archaea, bacteria, and single-cell eukaryotes. EMBL researchers use these extensive catalogs, along with experimental and data-mining approaches, to validate computational results. Studies on the human gut and skin have revealed novel species and shown the microbiome’s compositional variability across different body sites, providing unprecedented insights into the human microbiome. The extensive data can be exploited to uncover new functions, including  enzymes, natural products and biomarkers.

Additionally, the extensive data can be exploited to uncover new functions, including enzymes, natural products and biomarkers These discoveries aim to prevent or treat diseases and address environmental challenges.

EMBL is expanding its microbiome research, from exploring environmental contexts through the TREC expedition to fostering clinical collaborations for better human health. We are developing new technologies to quantify and visualise microbial life and establishing high-throughput, automated setups to study diverse microbiomes. EMBL leadership in the field has culminated in the establishment of a new Microbial Automation and Culturomics Core Facility in 2024. EMBL’s future directions include exploring microbes from all domains of life as well as from different environments. These studies offer clues for better therapies and diagnostics and enhance our understanding of microbial behaviour and interactions in ecosystems and can be exploited for interventions to restore planetary health and improve disease outcomes.

Global warfare between bacteria and fungi in soil

IMAGE: Falk Hildebrand and Aleksandra Krolik in collaboration with Campbell Medical Illustration/EMBL