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Rumen Microbe Genome Set May Serve as Resource for Biofuel Production

Aubrac cattle

NEW YORK (GenomeWeb) – Researchers are getting a closer look at the microbes found in the first stomach of ruminant livestock animals — a chamber known as the rumen, which holds clues to digesting sturdy, complex plant materials such as lignocellulose that have been proposed as possible biofuel substrates.

"The combination of DNA and RNA sequence analysis and laboratory experiments with genome-sequenced, characterized, cultivated strains can now be used to begin to reveal the intricacies of how the rumen microbial community functions," William Kelly, a researcher formerly affiliated with New Zealand's Grasslands Research Centre and who is currently based at the New Zealand Agricultural Greenhouse Gas Research Centre, said in a statement. 

In a paper appearing online today in Nature Biotechnology, Kelly and his colleagues from centers in New Zealand, the US, and elsewhere described new reference genome sequences for 410 cultured bacterial or archaeal species from the rumen of ruminant livestock animals. The genomes are part of a larger, growing collection known as Hungate1000, named for deceased microbiologist Robert Hungate, who was an early developer of anaerobic bacterial culturing methods used to study the bovine rumen and other oxygen-poor environments.

"The rumen represents one of the most rapid and efficient lignocellulose depolymerization and utilization systems known, and is a promising source of enzymes for applications in lignocellulose-based biofuel production," the authors wrote, adding that the fermentation that takes place in ruminant animal intestines "is also the single largest anthropogenic source of methane."

The team's initial analyses of the Hungate1000 set provided insights into rumen microbe pathways contributing to everything from methanogenesis to polysaccharide breakdown and the production of short-chain fatty acids. The group also compared the Hungate data with available gut microbe metagenomic data for humans and other organisms, and got a look at genes or pathways with rumen-specific representation, including genes capable of synthesizing vitamin B12 from scratch.

"Understanding the functions of the rumen microbiome is crucial to the development of technologies and practices that support efficient global food production from ruminants while minimizing greenhouse gas emissions," the researchers wrote.

Through a Rumen Microbial Genomics Network established within the Global Research Alliance's Livestock Research Group, Hungate1000 collaborators set out to produce a catalogue of rumen microbes, encompassing reference genome sequences for archaea and bacteria in the organ, along with cultured representatives for these microbes.

Over the past six years or so, the researchers have analyzed the 410 new reference genomes for bacteria or archaea in the rumen, along with 91 previously sequenced genomes. After doing strain-level identification of each cultured isolate with 16S ribosomal RNA sequencing, they provided genomic DNA to collaborators at the Department of Energy's Joint Genome Institute for sequencing with Illumina and/or Pacific Biosciences RS instruments, followed by reference genome assembly and annotation.

Along with phylogenetic analyses done with Hungate1000 16S rRNA profiles and 16S rRNA amplicon data for hundreds of rumen microbes previously reported for the Global Rumen Census, the team began characterizing the Hungate genomes, identifying tens of thousands of enzymes involved in glycoside or polysaccharide breakdown and components from a range of other metabolic pathways.

When the team compared the Hungate genomes with thousands of metagenomic sequence collections, meanwhile, it saw overlaps for some 60 percent of the almost 893,000 coding sequences in the Hungate set. Two dozen rumen samples contained 336 characteristic strains, while 134 strains turned up in both the rumen and previous human gut samples.

"Researchers have access to Hungate Collection strains," the authors wrote, "which enable a better understanding of carbon flow in the rumen, including the breakdown of lignocellulose, through the metabolism of substrates to [short-chain fatty acids] and fermentation end products, to the final step of [methane] formation."