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Image courtesy of Rekha Seshadri (Joint Genome Institute) and Zosia Rostomian (Berkeley Lab Creative Services)

A global scientific project led by New Zealand researchers, which has generated a reference set of genome sequences of microbes found in the stomachs of sheep and cattle, has been published in the respected international scientific journal Nature Biotechnology.

The project, called the Hungate1000, was led by former AgResearch scientist Dr Bill Kelly, and AgResearch scientist Dr Sinead Leahy. The pair brought together nearly 60 scientists from 14 research organisations across nine countries, who collaborated to generate a reference catalogue of 501 rumen microbial genomes—before Hungate1000, just 15 rumen microbial genomes were available to the scientific community.

Dr Kelly says the project was named after Bob Hungate, an American scientist who trained the first generation of New Zealand rumen microbiologists in the 1960s and 1970s.

“Bob Hungate developed the pioneering technique of growing anaerobic bacteria—that technique of culturing the microbes that then have their genomes sequenced has been the cornerstone of our project.”

Dr Kelly says the project gives a new understanding of what exactly is taking place inside a rumen.

“Hungate1000 means we can now start to reveal the intricacies of how the rumen microbial community functions, and provides a roadmap for where to take the science next,” he says. “This data can be translated into interventions that are useful, such as identifying targets for vaccines and inhibitors to reduce methane emissions and improve productivity, among other things.”

Dr Leahy, who is currently seconded to the New Zealand Agricultural Greenhouse Gas Research Centre (NZAGRC) as its International Capability and Training Coordinator, says the project represents a major scientific advancement in the field of rumen microbiology, an area of science that up until recently had largely been unexplored.

“These microbes in the stomachs of ruminants are crucially important—they convert grass and other dietary components into smaller compounds that the sheep or cow uses to make meat and milk,” she says. “The data we’ve made available with Hungate1000 will underpin the development of technologies to target these microbes and aid productivity or reduce greenhouse gas emissions—you need to know what you’re targeting to make a specific impact on the rumen microbiome environment.”

Dr Andy Reisinger, the NZAGRC’s Deputy Director (International), says Hungate1000 is central to the work that the NZAGRC is managing.

“Hungate1000 shows what a powerhouse the rumen is in converting digestible plant material to energy, and gives us a much better understanding of how we might be able to use science to influence that process,” he says. “This will help us find ways not only to enhance productivity but also to achieve emissions reductions and deliver solutions to farmers—such as inhibitors and vaccines—that don’t affect their bottom lines.”

The Hungate1000 data is available as a community resource on the United States Department of Energy’s Joint Genome Institute website.

“We had an open release policy, which meant the data was made available as soon as we generated it,” explains Dr Leahy. “That aligns with the GRA’s ethos of science for the greater good—Hungate1000 is about coming together to advance global knowledge.”

The Hungate1000 was funded by the New Zealand Government through the Ministry for Primary Industries in support of the Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gases (GRA), which is administered by the NZAGRC. The genome sequencing and analysis component of the project was supported by the United States Department of Energy’s Joint Genome Institute (JGI), via its Community Science Program.

Dr Harry Clark, the Director of the NZAGRC who also co-chairs the GRA’s Livestock Research Group, says Hungate1000 would not have come about without the financial support of the New Zealand government.

“The investment by MPI to support good science delivers multiple benefits, not just to New Zealand but globally too,” he says. “This project shows the power of international collaboration—we’ve been able to bring scientists together from around the world to create this resource that can benefit all countries, and New Zealand can be proud that we made it happen.”

Dr Kelly says he and the rest of the Hungate1000 team are delighted to see their work published in Nature Biotechnology.

“It’s the culmination of a long journey and a lot of work, and we have achieved something that I think is really worthwhile,” he says. “The kudos of getting something published in a high-impact journal like Nature Biotechnology is enormous, and highlights the value of this work to a global audience.”

Source: New Zealand Agricultural Greenhouse Gas Research Centre 

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