Researchers have developed a new method to sequence and analyze the dark matter of lifethe genomes of thousands of bacteria species previously beyond scientists' reach, from microorganisms that produce antibiotics and biofuels to microbes living in the human body.
Scientists from UC San Diego, the J. Craig Venter Institute and Illumina Inc., published their findings in the Sept. 18 online issue of the journal Nature Biotechnology. The breakthrough will enable researchers to assemble virtually complete genomes from DNA extracted from a single bacterial cell. By contrast, traditional sequencing methods require at least a billion identical cells, grown in cultures in the lab. The study opens the door to the sequencing of bacteria that cannot be culturedthe lion's share of bacterial species living on the planet.
"This part of life was completely inaccessible at the genomic level," said Pavel Pevzner, a computer science professor at the Jacobs School of Engineering at UC San Diego and a pioneer of algorithms for modern DNA sequencing technology.
Pevzner, in collaboration with UC San Diego mathematics professor Glenn Tesler and computer science postdoctoral researcher Hamidreza Chitsaz, developed an algorithm that dramatically improves the performance of software used to sequence DNA produced from a single bacterial cell. These programs traditionally recover 70 percent of genes.
"The new assembly algorithm captures 90 percent of genes from a single cell. Admittedly, it is not 100 percent. But it's almost as good as it gets for modern sequencing technologies: today biologists typically capture 95 percent of genes but they need to grow a billion cells to accomplish it," said Tesler.
Bacteria play a vital role in human health. They make up about 10 percent of the weight of the human body and can be found anywhere from the stomach to the mouth. Some, like E. coli, can wreak havoc. Others help us digest. Yet ot
|Contact: Ioana Patringenaru|
University of California - San Diego