Turning to dirt for antibiotics in the fight against superbugs

Chemical biologist Sean Brady at The Rockefeller University in New York City and his team in 2018 discovered new antibiotics, called malacidins, by applying genetic sequencing techniques to bacteria in soil samples.

(CNN)Think about aphids — those little, green, garden-destroying bugs. The bane of the begonia. But aphids exist in an ecosystem. Which is to say, those little suckers have enemies. When gardeners see aphids, it's often ladybugs to the rescue.

There is another plague out there right now: the antibiotic-resistant bacteria currently making a home in our health care system that kills thousands each year.
But by thinking like a gardener and looking to the ecosystem those microbes originally came from, we may be able to find new ways to fight them.
    For instance, researchers at Vanderbilt University recently unearthed a new kind of chemical compound that may one day help fight off antibiotic-resistant bacteria. The source? Dirt.
      Dirt, it turns out, contains an entire microbial ecosystem, with a wealth of intriguing compounds. And while there are major hurdles between discovering a new drug and using it, scientists are hopeful new techniques could pay off.

      Stuck in the mud

      Antibiotic-resistant microbes, commonly called superbugs, have become a major health problem across the world. More than 2.8 million infections happen every year in the United States alone; more than 35,000 people will die from those infections.
        The answer for an infection is often antibiotics. Or stronger antibiotics.
        But we're not the original inventor of this class of compounds — for time immemorial, antibiotics have been deployed by the microbes themselves. Microbes, such as the myriad species of fungi, bacteria and other critters that live in the soil, live in a complex ecosystem where chemical defenses are often necessary in order to fend off or attack competitors.
        In fact, soil was actually one of the great historical sources for new antibiotics.
        "The vast majority of antibiotics we use today come from growing bacteria out of soil," said Sean Brady, a chemical biologist and professor at The Rockefeller University in New York City. Though we came up with ways to make them ourselves, it was in dirt that these antibiotics were first discovered.
        Streptomycin, which is often used to treat tuberculosis, came from a sample of New Jersey soil back in the 1940s, for instance.
        At the time, a wealth of new medicines seemed just within reach.
        Unfortunately, it turned out that soil microbes are finicky. Only a handful grow well in traditional laboratory setups, and what we could get out of them was limited. Stuck discovering the same compounds over and over again, the pharmaceutical industry's focus shifted to tweaking the antibiotics we already had.

        Returning to our roots

        However, in the last few years, a number of researchers have been going back to the soil with new techniques.
        One potential breakthrough came when Kim Lewis, a microbiologist and university distinguished professor at Northeastern University, and his colleague Slava Epstein, a professor of biology, figured out how to "domesticate" wild microbes. The duo loaded soil bacteria into a special device called the "iChip" (short for isolation chip), then buried it back into their native soil until the bacteria grew into usable colonies.
        Microbiologist Kim Lewis of Northeastern University and Yu Imai, a postdoctoral research associate, observe a petri dish encasing darobactin, a new type of antibiotic that can selectively kill gram-negative bacteria in October 2019.