Berkeley Lab, UC Berkeley researchers find method for creating potential antibiotics from soil microbes

Alex Crits-Christoph/Courtesy

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A team of researchers from UC Berkeley and Lawrence Berkeley National Laboratory is working on producing antibiotics through previously unknown soil microbes and released a study in the journal Nature on June 13.

The search for new antibiotics is becoming more crucial as the development of new antibiotics has slowed and certain disease-causing bacteria are developing resistance to modern drugs, according to a press release.

“The biosynthetic potential of abundant and phylogenetically diverse soil microorganisms has previously been underestimated,” the study said. “These organisms may represent a source of natural products that can address needs for new antibiotics and other pharmaceutical compounds.”

UC Berkeley microbiology graduate student Alex Crits-Christoph, a member of the research team behind the study, said the team took soil samples of approximately 10 grams from the Angelo Coast Range Reserve, which is part of the UC Natural Reserve System and is located on the South Fork Eel River in Mendocino County. He said one side of the site has received more rain than the other for 20 years, and researchers are studying how it affects the microbes that are found there.

“We take the DNA to the lab and sequence it,” Crits-Christoph said, “and we get this huge mixture of DNA from all of the different microbes.”

Crits-Christoph added that the end result is like “a big puzzle” in which the researchers have to match the various genomes to the different microbes from the soil sample. The study is similar to finding the blueprints for robots that produce cars, where the blueprints are the genes, the robots are the proteins and the car is the antibiotic, according to Crits-Christoph.

Crits-Christoph noted that one of the team’s two goals is to learn how to grow these certain types of bacteria that typically do not grow in labs through “targeted growth.” The other is to know the sequence of the microbe, create that sequence in the lab and then produce it in a lab strain.

“To isolate some microbes, we’re taking a small bit of that soil and putting it in a petri dish,” Crits-Christoph said. “But only a small percentage of microbes — less than 1 percent — will grow (in the lab).”

According to Crits-Christoph, his previous work was a study on microbes that focused on whether or not microbes were able to grow and whether different microbes appeared in different places. His work was centered in the Atacama Desert in Chile — the “driest in the world.”

Crits-Christoph said that while it is traditional for researchers to go to the soil and isolate the microbes that produce antibiotics, his current research team is trying a new approach, in which they study the microbes in their natural ecosystem.

“In the future, we can really be more targeted when we are finding antibiotics,” Crits-Christoph said.

Contact Margaret Black at [email protected].