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Soil Microbes Yield Rich Antibiotic Sources

Researchers taking soil samples

Research team taking soil samples in the Angelo Coast Range Reserve (Jill Banfield, Univ of California – Berkeley)

14 June 2018. A group of geo- and bioscience researchers analyzed microbes residing in soil under northern California and discovered many new potential sources of antibiotics, well beyond current sources. The team from University of California in Berkeley and Lawrence Berkeley National Laboratory report their findings in yesterday’s issue of the journal Nature (paid subscription required).

Researchers from the lab of earth and planetary sciences professor Jill Banfield are seeking new sources of antibiotics, as many current antibiotics become inoperative due to constant evolution of microbes targeted by those drugs. The authors cite data from the U.S. Centers for Disease Control and Prevention showing 2 million people a year in the U.S. become infected with antibiotic-resistant bacteria, leading to some 23,000 deaths.

Banfield and colleagues explored soil from the Angelo Coast Range reserve in Mendocino County, California, part of a natural reserve owned by University of California. The site is already monitored as part of a climate change study. The team sample took 60 samples of soil in grasslands from the reserve, each about 10 grams, at depths of 4 to 16 inches. The researchers used a technique known as metagenomic sequencing that analyzes the genomes of all organisms present in environmental samples, like those extracted in the California soil.

With this analysis, the Berkeley team sequenced and assembled some 1,000 genomes found in the samples. The genomes represent a wide range of organisms, with only a few of the species representing even 1 percent of all microbes identified, but most of those identified are much more rare. While many of the organisms are classified under existing categories of soil microbes, many of the bacteria are newly identified, or are associated with other soil microbes in different, unexpected ways.

The researchers tested the genomes looking for genetic patterns similar to current antibiotics, and report on 360 of the organisms. About one-third of the microbes examined produce more than 1,000 genes similar to polyketides and nonribosomal peptides that make up the chemistries in many current antibiotics. A large number of the newly discovered organisms are acidobacteria, a common type of bacteria found in soil. Two of the new organisms, say the researchers, each encode 15 gene clusters resembling antibiotics.

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

The researchers plan to synthesize more than 20 of the newly discovered genes, and use them for genetic engineering of organisms to produce new types proteins leading to new antibiotics and other drugs.

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