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JGI at 25: Expanding Metagenomics to Capture Viral Diversity

2022 marks the JGI’s 25th anniversary. Over the last year, we’ve been revisiting a number of notable achievements that showcase our collaborations and capabilities to enable great science that will help solve energy and environmental challenges.

Artist rendering of genome standards being applied to deciphering the extensive diversity of viruses. (Illustration by Leah Pantea)

Artist rendering of genome standards being applied to deciphering the extensive diversity of viruses. (Illustration by Leah Pantea)

Viruses are everywhere — in soil, the sea and, of course, the cells of other organisms. As they infect microbes like bacteria, algae and protists, all kinds of viruses impact many ecological processes, including carbon cycles.

“Whether or not you planned it, viruses are most likely in your system and in your data, and they’re probably influencing the microbes there,” said Simon Roux, the Viral Genomics Group Lead at the JGI.  To understand the microbiome systems underpinning a broad range of environmental challenges, characterizing viruses is a key step. 

For decades, though, many viruses have been somewhat invisible to the sampling experiments probing Earth’s ecosystems. Viruses rarely grow well in environmental samples brought back to a lab, because they often need unique conditions and a specific microbial host to replicate. Sequencing genetic material directly from samples sidesteps these challenges, since it doesn’t require this kind of lab culture. 

Beginning in the early 2000’s, these environmental metagenomes began to offer a window into viral existence. Along with highlighting the viruses in a given sample, metagenomics shed light on another key aspect of viruses in the environment — their sheer genetic diversity. 

As pioneers of this field, the JGI has leveraged metagenomics to boost understanding of environmental viruses. In 2016, Nikos Kyrpides at the JGI led a team that combed datasets from around the world, finding over 125,000 partial and complete viral genomes. That study multiplied the number of known viral genes by a factor of 16.

The same year, the JGI expanded its existing Integrated Microbial Genomes & Microbiomes database to include a dedicated section for viruses, so researchers around the world would have better, easier access to these viral genomes. The new database was called IMG/VR. It featured samples from different ecosystems all over the world, including 3,908 isolate reference DNA viruses and 264,413 computationally identified viral contigs.

Since then, IMG/VR has grown exponentially. The latest release, IMG/VR v4 features over 15 million viral genomes, and  this most recent version is six times larger than the previous one . To identify so many genomes, JGI researcher Antonio Camargo developed a new pipeline for identifying viruses across many thousands of genomes and metagenomes, called geNomad (watch Antonio Camargo present on IMG/VR v4 at the 2022 VEGA meeting below). Another JGI-developed tool, CheckV, assesses viral genomes, and grades their quality based on completeness.

Along with expanding the viral diversity that IMG/VR features, teams at the JGI are focused on what those viruses can do. For example, understanding virus-host dynamics in soil microbiomes could allow for more accurate ecosystem modeling. In a different vein, characterizing CRISPR defense and anti-CRISPR mechanisms in a broader range of viral genomes would give researchers more ways to engineer microbial genes. 

Eventually, whether the goal is improving soil microbiomes for carbon capture or removing harmful substances from the environment, viruses could play a role. 

“If you want to do anything with a microbiome — you know, target specific microbes or change the behavior of this bacteria — most likely there is a virus that is already doing what you want in a sense, and can inform on how this can be done” Roux said. And in just 6 years, IMG/VR has built a foundation for finding more of those details from all kinds of viruses. 

 

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