WALNUT CREEK, CA - The next time you chow down on a sausage pizza, enjoy a refreshing frozen yogurt, or savor a fine wine, remember to thank the bugs.
Lactic acid bacteria (bacteria that ferment sugars into lactic acid) play an essential role in the production of wine, as well as such fermented foods as cheese, yogurt, pickles, sausage and salami. From October 7-11, about three dozen scientists from around the nation will gather at the Joint Genome Institute (JGI) in Walnut Creek to examine the genomes of nine of these economically and scientifically important microbes.
Analyzing the DNA of lactic acid bacteria can help food scientists enhance the preservation and safety of fermented foods, said JGI Director Eddy Rubin.
"Besides their importance in food production," Rubin said, "these 'probiotic,' or 'good' bacteria can be beneficial in other ways - contributing to the health and balance of the intestinal tract and helping fight illness and disease. Learning about the genetic makeup of probiotic bacteria can help in the prevention and treatment of a variety of gastrointestinal disorders."
The gathering is the second genome "jamboree" sponsored by the JGI this year. In April, about 50 scientists from Japan, Australia, Italy, France, Scotland and the United States met to study the genome of the sea squirt Ciona intestinalis, sequenced by the JGI last year. Later in October, researchers will examine the genome of diatoms - microscopic ocean dwellers that could help combat global warming by capturing carbon dioxide near the ocean's surface and carrying it into deeper waters.
As part of the U.S. Department of Energy's Microbial Genome Program, the JGI has completed the sequencing of the genomes of the 11 lactic acid bacteria targeted by the Lactic Acid Bacteria Genome Consortium, a group of molecular scientists from a dozen U.S. universities. One of the bacteria, Oenococcus oeni, is especially important to wine growers because it contributes to flavor, aroma, and texture and can help retard spoilage and taint in some wines (see http://www.
Dr. David Mills, a food microbiologist and assistant professor of viticulture and enology at the University of California-Davis, said the bacteria under study are used in the production of $20 to $30 billion worth of fermented products per year in the United States. "Looking at the genomes will aid in finding and exploiting those genetic traits that make a better cheese, wine, sausage, etc.," Mills said. "Conversely, we can learn more about those lactic acid bacteria that spoil products, to help identify them earlier and perhaps prevent their growth and the resulting spoilage."
Mills said the Jamboree could shed light on the common genetic mechanisms that enable the bacteria to use sugars, nitrogen, and other substances in fermentation, as well as the genetic differences that allow them to live in such "markedly different environments" as milk, wine, beer, vegetables, and the human gastrointestinal tract. "We can compare the genetic plans and identify common gene sets that help us understand how they work so well in those environments," he said.
Along with the economic value of learning more about how the bacteria function, Mills said, the scientists hope to answer a number of open questions about how they evolved and where they fit on the evolutionary tree.
"To our knowledge, no one has ever sequenced such a large number of genetically related microbes before," Mills said. "This gives us an unprecedented opportunity to learn about genome evolution with a defined, related group - can we use genome information to understand how a small, related, section of the tree of life evolved?"
The JGI, one of the largest and most productive public genome sequencing centers in the world, is operated jointly by three DOE national laboratories managed by the University of California - Lawrence Berkeley and Lawrence Livermore in California, and Los Alamos in New Mexico. In addition to the lactic acid bacteria and other microbe projects, the JGI has whole genome sequencing programs that include vertebrates, fungi, and plants.
With its main headquarters and Production Genomics Facility in Walnut Creek, JGI employs about 240 people and has programs in genomic sequencing, computation, functional genomics, genomic diversity, and new technology development. Funding is provided predominantly by the Department of Energy's Office of Science, Office of Biological and Environmental Research. Other agencies that have contributed to funding JGI include DOE's National Nuclear Security Administration, the National Institutes of Health, the National Science Foundation, and the U.S. Department of Agriculture.
Additional information and progress reports on JGI projects, including daily updates of sequence information and assembly statistics, are available at www.jgi.doe.gov.