Sean Brady, associate professor in the Laboratory of Genetically Encoded Small Molecules at Rockefeller University in New York, has a simple request: He’s asking people to go out into their backyards, collect a bit of dirt, put it in a Ziploc bag and send it to his lab.
He wants dirt samples from just about anywhere so they can be analyzed for organisms that may guide the discovery of new antibiotic compounds—small, genetically encoded molecules. Those molecules could help address what the Geneva-based World Health Organization (WHO) and many others in the medical and scientific fields believe to be one of the most pressing issues of our time: the growing resistance to antibiotics that is taking root throughout the developed world.
Antibiotics have helped millions of people fight illnesses that not so long ago could have been drawn-out and debilitating, if not fatal. Over time, however—and, many argue, largely because of their overusage—human beings have become much more resistant to antibiotics. This has reduced their effectiveness and has led us toward what the WHO terms “a post-antibiotic era” in which common infections that have been quickly treatable with antibiotics, like stomach bugs, ear, nose and throat issues, and urinary tract infections, could once again rear their ugly, dangerous heads.
The developed world, where the fallout from increased resistance to common antibiotics is going to hit the hardest, is only just beginning to feel its impact, Brady said.
“There’s a pressing need for new antibiotics because what we’re seeing today is going to become an even greater problem for the first world in the future,” he said.
Most drugs, from antibiotics to anti-cancer drugs, come from bacteria in nature, Brady said, but because repeated analysis has thrown up the same kinds of bacteria, “people assumed we’ve found them all, and therefore there are no more drugs to be made.”
The world is a huge place, though, with richly varied soil. Brady is convinced that there’s a plethora of uncultured bacteria that produce molecules research has thus far missed and that could, if properly studied and analyzed, be used to make brand new drugs—or, new and better derivatives of existing drugs that have become less effective.
“Just think that under your feet, in your backyard, there are bugs that are going to make brand new versions of drugs we currently use,” Brady said. “Or, maybe there is a better version of any of the billion-dollar drugs currently on the market. Nature is the greatest lab and, as far as we’re concerned, we haven’t even scratched the surface of what is out there. We do believe, though, that there’s great potential with studying soil samples from around the world.”
Brady’s lab uses a process called next-generation sequencing to profile the DNA in soil samples. The process rapidly sequences and resequences genomes because the genome of a single individual of a species will not indicate all of the genome variations among other individuals of the same species, and it can help identify new biosynthetic systems in molecules.
Being able to mine the entire planet for soil samples, though, is more than one lab can do. That’s why the “Drugs from Dirt” project (DrugsFromDirt.org) is enlisting the help of global citizens—anyone, anywhere. By analyzing a broad swath of soil samples, the lab hopes to be able to zero in on areas that look to be the most promising for new gene sequencing. Thus far, it has identified two biodiversity hot spots where soil bacteria looks to be particularly rich and diverse, and therefore highly conducive to future drug research. One of those is the American Southwest, where the team believes it could find compounds that resemble rifamycins, a class of antibiotics used to treat tuberculosis, strains of which have proven increasingly resistant to existing treatments. The other is Brazil, where analysis of soil samples have revealed genes that could be used to make new anti-cancer drugs.
“We want to eventually get soil from all over the U.S. and the world to see how the chemistry changes in anything from hot springs and caves and islands, or in a forest that is endogenous to certain areas,” Brady said. “We believe there are hot spots for new diversity in many places.”
All the information the lab obtains from different soil samples will be stored on a publicly accessible resource. “It’s important to note that we will not be cloning DNA from any soil sample we get. Ours is a purely observational study that we hope will guide future molecule discovery efforts,” Brady said.
He’s hoping, though, that the collaborative nature of the project will help to bring more money into areas of medical research such as antibiotic resistance, a problem that has implications for everyone. Private investment and philanthropy has typically tended to focus on funding cancer research, he said. While he’s hoping that the analysis of soil samples from various biodiversity hot spots could also throw up bacteria for new sorts of cancer drugs, Brady believes that resistance to antibiotics is a far more pressing issue and one that has been overlooked, “so it would be great to see more funding going there.”
According to the WHO, antibiotic resistance causes people to be sick for longer and increases the risk of death. And of course, increased resistance to drugs also increases the cost of health care—long-term health care is a key issue for long-term financial planning—through lengthier stays in hospital and a need for greater, more intense medical care.
Last year, the WHO released its first-ever report on the problem of antibiotic resistance, calling attention to the need to develop new diagnostics, antibiotics and other tools to allow health care professionals to stay ahead of the issue.
The report kick-started a global effort led by the WHO that involves the development of tools and standards, and improved collaboration around the world to track drug resistance, measure its health and economic impacts, and design targeted solutions.