Mapping microbiomes: the power of microbial communities

EMBL research aids understanding of microbial communities and their interconnection with human and planetary health.

Communities of microbes, known as microbiomes, are being increasingly studied by researchers around the world. EMBL researchers are contributing to this effort by characterising and analysing diverse microbial ecosystems, as well as offering automated analysis pipelines and archiving microbiome data.

In 2021, EMBL-EBI and collaborators in the United States, Germany, and the United Kingdom sequenced the genomes of microorganisms detected within 594 samples taken from various skin surfaces of 12 healthy volunteers. From this data, they created the Skin Microbial Genome Collection (SMGC) – a collection of reference genomes for the human skin microbiome. The collection includes 174 previously unknown bacterial species, four new eukaryotes, and 20 new jumbo phages – viruses with a genome larger than 200 kilobases. This study singlehandedly expanded the catalogue of known skin bacteria by 26 %. All of these data will be made freely accessible as a new genome catalogue in the MGnify data resource, where researchers can find a huge range of microbiome datasets including those for the human gut.

A previous study from the Patil and Bork groups used advanced metabolic modelling with data from thousands of microbial communities across the globe to understand microbial relationships. They learned groups of cohabitating bacteria tend to be either highly competitive or highly cooperative, seemingly determined by survival advantages. For this, they used data from the Earth Microbiome Project (EMP), a massively collaborative effort to characterise microbial life on the planet.

In another study, the Bork group and collaborators launched the Global Microbial Gene Catalog. With more than 2 billion genes, identified from samples collected from 14 different environments, the catalogue helps with comparative analyses of genetic features of myriad microbiomes. Researchers can explore how specific functionalities emerge, develop, and spread in these various microbial worlds.

Microbial communities are not only an integral part of ecosystems surrounding us, they also are central to health and disease. As part of another international collaboration, EMBL-EBI is hosting and making freely available a database needed to effectively study drug resistance in tuberculosis. The Comprehensive Resistance Prediction for Tuberculosis: an International Consortium (CRyPTIC) aims to find the causes of drug resistance in bacteria that cause tuberculosis and enable rapid diagnostics that could radically improve future tuberculosis treatments.

These studies capture the genomic, taxonomic, and physiological diversity of the microbiomes surrounding us everywhere. More importantly, as they expand, they significantly add to the biologist’s toolkit for studying life ‘in context’.