JGI at 25: Cow rumen and the early days of metagenomics

2022 marks the JGI’s 25th anniversary. Over the next few months, we’ll be revisiting a number of notable achievements that showcase our collaborations and capabilities to enable great science that will help solve energy and environmental challenges.

Oh, the magical world of the cow stomach. Rumen – and its microbes – are really a powerhouse. Rumen microbes have the ability to break down hardy plant cell walls and therefore hold clues to how humans could do the same on an industrial scale to produce biofuels. Since one of the challenges of developing alternative fuels from plants is the high cost and resource requirements of processing these sturdy materials, rumen microbes and their enzymes are an optimal study subject that could lead to more sustainable energy production. 

However, less than 10% of the microbes found in any environment can be grown in a laboratory — and rumen microbes are no exception.

Back in 2011, JGI-supported researchers published a paper in the journal Science. It detailed how they’d used metagenomics — a then-novel approach which allows scientists to study microorganisms that can’t be cultured by analyzing and then extrapolating data obtained from environmental samples — to identify over 27,000 microbial genes. These genes were identified based on their potential to efficiently degrade lignocellulose in cow rumen, essentially what makes them so powerful that they can process tough cell walls. 

“The JGI was really leading the development of these approaches that are still vital to facilitate the assembly of small DNA fragments into larger and coherent pieces called contigs — into genes and even into genomes — from these environmental samples,” said Matthias Hess, first author on the paper and now an associate professor and head of the Hess Lab at UC Davis. “It was a really huge effort in tool development and … that was really the foundation for many of the tools that are available these days and that are widely used by many, many scientists.” 

Using samples of rumen-digested switchgrass, researchers isolated and sequenced DNA from rumen microbes involved in the digestion process. 

“We wanted to find the enzymes that make the rumen such an efficient biomass-degrading environment and transfer that ability into industry, specifically to generate biofuels,” Hess said. 

(Only 90 of those genes were actually tested in the 2011 paper. In 2015, the study’s dataset became material for a hands-on undergraduate research course for all biotechnology majors at CSU-San Marcos. That course has since expanded into three other universities. You can learn more about how JGI data supports higher education in this JGIota, a Genome Insider podcast minisode.) 

“The ultimate target has shifted from just finding enzymes that produce biofuel, to the general ability of these enzymes to break down these recalcitrant carbohydrates into more versatile molecules that can be then utilized to generate other end products,” Hess explained. “That is a very valid goal — not necessarily for biofuel production anymore, but for other bioproducts.”

This is Part 2 of our three-part “Guts R Us” series. You can find Part 1 here. 

Related Links: 

• JGIota: “Looking back at how our cow rumen study drives higher learning”
• JGI News Release: “How Now, Inside the Cow: Nearly 30,000 Novel Enzymes for Biofuel Production Improvements” 
• Publication: “Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen”; Science, Jan 2011
• “JGI at 25: Fueling investigation into methane-making microbes”; JGI, Oct 2022