Discovering new genomes from terrestrial microbiomes

The artist’s interpretation of how microbial genome sequences from the GEM catalog can help fill knowledge gaps about the microbes that play key roles in Earth’s microbiomes. (Credit: Zosia Rostomian / Berkeley Lab)

Despite advances in sequencing technologies and computational methods over the past decade, researchers have discovered genomes for only a small fraction of the Earth’s microbial diversity. Since most microbes cannot be grown under laboratory conditions, their genomes cannot be sequenced using traditional approaches. Identifying and characterizing the planet’s microbial diversity is key to understanding the role of microorganisms in regulating nutrient cycles, as well as gaining insight into the potential applications they may have in a wide range of research fields.

Now, thanks to a massive project involving more than 200 scientists from the DOE Joint Genome Institute and DOE Systems Biology Knowledgebase (KBase), an archive of 52,515 microbial genomes generated from environmental samples around the world has been made public. This new resource, known as the Genomes from Earth’s Microbiomes (GEM) catalog, expands the known diversity of bacteria and archaea by 44%.

“Using a technique called metagenome binning, we were able to reconstruct thousands of metagenome (MAG) assembled genomes directly from sequenced environmental samples without the need to cultivate the microbes in the laboratory,” said Stephen Nayfach, a JGI scientist and first. author of the study describing the GEM catalog published today in Nature Biotechnology. “What really sets this study apart from previous efforts is the remarkable environmental diversity of the samples we analyzed,” he added.

Metagenomics is the study of microbial communities (microbiomes) in environmental samples without the need to isolate individual organisms, using various methods of processing, sequencing and analysis.

Much of the data in the catalog was generated from environmental samples sequenced by the JGI through the Community Science Program and was already available on the JGI Integrated Microbial Genomes & Microbiomes (IMG / M) platform. But the team behind GEM wanted to make this data more organized and accessible to the international microbial community.

The large team worked to sort and label the vast pool of metagenomic data so that users could search the resulting catalog for features of interest – such as the presence of genes needed to produce interesting compounds – and predict how these inculturable microbes interact with the environment and other organisms.

“With this dataset I can see where each microbe is and how abundant it is. This is a great resource for the community that will facilitate many more studies, ”said co-author Kostas Konstantinidis, who is already using the catalog in his research on how microbes respond to climate change.