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Gut reactions: Sequencing ruminal bacteria


Cows have the ability to digest cellulose—the carbohydrate that strengthens the cell walls of plants—because of "fibrolytic ruminal bacteria," which represent just a few of the hundreds of species of microbes in the digestive systems of ruminants.

Ruminococcus albus.

With the goal of better understanding the complex process by which those microbes handle cellulose, a scientific consortium is now making headway in sequencing two of those ruminal bacteria: Fibrobacter succinogenes and Ruminococcus albus.

The group, called the North American Consortium for Genomics of Fibrolytic Ruminal Bacteria, includes more than a dozen researchers from The Ohio State University (the lead institution), The Institute for Genomic Research (TIGR), Cornell University, the University of Illinois, and the University of Guelph in Canada. The consortium is sponsored by the US Department of Agriculture.

This spring, many of those scientists gathered at TIGR—where the sequencing is done—to discuss and coordinate their research. The scientists are focusing mainly on annotating both genomes and collecting additional genomic information using 'subtractive hybridization' methods for related strains of bacteria.

Microbiologist Mark Morrison, an associate professor at Ohio State's Department of Animal Sciences who is the consortium's coordinator, says its main goals are to pinpoint those parts of the bacterial genomes that play a role in degrading cellulose and other plant polysaccharides, and also to identify other genetic traits that are critical to the bacteria's colonization and persistence in the digestive systems of the host animals.

"More than 200 microbial species live in the digestive systems of cows and other ruminants," says Karen Nelson, a microbial genomics researcher at TIGR. "And we know very little about those microbes."

Researchers don't yet know the exact enzymatic mechanism by which those ruminal bacteria break down cellulose—even though cellulose is one of the most important plant products. But scientists believe that determining the genomic sequence of those microbes is likely to help explain some of those secrets.

Why is there so much interest in bacteria that can break down cellulose? "From the intensive dairy farms in North America to the nomadic cattle herds in sub-Saharan Africa, improving cellulose degradation is a top priority because of the potential impacts it can have on animal productivity," says Morrison.

There are also potential industrial and environmental uses: Cellulose and woody stems from plants—in the form of paper, wood, and related materials—account for more than half of the biomass in waste dumps worldwide. With genomic information collected from ruminal and other bacteria and fungi that break down fibers, scientists might be able to develop better methods to speed the recycling of such materials.

But up to now, Morrison says, biochemists so far have found it difficult to match existing enzymes with the needed rates of cellulose conversion, and to make the process cost-effective. He hopes the genome sequencing projects can help change that.

By this summer, the consortium plans to set up a new Ruminant Microbial Genome Database on TIGR's website. Eventually, that database will be the main resource for genomic data related to the bacteria that break down cellulose.

Meanwhile, researchers of the University of Illinois at Urbana-Champaign are working on a low-redundancy sequence of a related microbe, Ruminococcus flavefaciens, which also breaks down cellulose, and TIGR has recently started to sequence Prevotella ruminicola, which degrades non-cellulose polysaccharides such as xylan and starch.

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