Genetic sequencing helps scientists mine soil for antibiotics

Published: June 13, 2018 at 3:32 PM

Brooks Hays

June 13 (UPI) -- Scientists have developed a more efficient way to search for potential antibiotics living in the soil.

The new method, called metagenomic sequencing, allows scientists to sequence the genomes of multiple microbes living in a small soil sample.

Scientists can use the survey method to identify gene sequences related to the production of molecules with antibiotic or antifungal qualities -- defense mechanisms evolved by microbes that could also help humans battle infections.

Many studies show problematic bacteria, including MRSA, E. coli and others, are becoming increasingly resistant to common antibiotics.

To test the new genome sequencing method, scientists collected 60 10-gram samples of dirt from a few inches beneath the surface of a Northern California meadow. Researchers used metagenomic sequencing to identify the genomes of 1,000 different microbes, 360 of which were found to be new species.

"Soil is the last frontier from the perspective of genome-resolved metagenomics," Jill Banfield, a professor at the University of California, Berkeley's Innovative Genomics Institute, said in a news release. "It is just full of many, many, many different types of organisms, a lot of them closely related and present in fairly low abundances, so it is hard to tease them apart."

Scientists are currently analyzing the newly sequenced genomes, searching for gene sequences related to the production of unique and complex molecules. These genes can be inserted into other organisms to see if they do indeed code for the production of a potentially useful protein or enzyme.

These proteins and enzymes could yield molecules with a variety of medicinal qualities.

"Most of these new biosynthetic molecules are coming out of what people know to be the most abundant bacteria in soil, they just hadn't been found because people didn't have genomes for them," Banfield said. "We expect to find novel antibiotics, which could help humanity, but also novel pharmaceuticals more broadly."

Researchers detailed their new sequencing technology this week in the journal Nature.

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