UCSF scientists explore the bacterial communities that live in and on our bodies.
Long ago, when Andrew Goldberg, M.D., was a resident, the ear, nose and throat specialist had a patient who came in repeatedly with a chronic infection in one ear. The man had been prescribed all manner of treatments – from vinegar drops to antibiotics to antifungals to steroids – none of which provided lasting relief. Then one morning, the patient walked into the office and asked Goldberg to take a look in his ear – the infection was wiped out. “Don’t you want to know what I did?” Goldberg recalls the patient asking, with a grin.
“So he tells me,” Goldberg continues, “I took some wax from my healthy ear and stuck it in my bad ear. Within a few days, my problem was gone and never came back.’ Of course I laughed it off, thinking that the infection had spontaneously cleared and that the guy was crazy,” reflects Goldberg, who is now the director of rhinology and sinus surgery at UC San Francisco.
Decades later, when he began investigating the myriad bacterial communities thriving in the human body, Goldberg realized what a clever, if not desperate, move his patient had made. His good ear hosted an abundant and stable microbial community, while his bad ear had a depleted population of microbes that left it in a chronic inflammatory state. The bacteria in the wax from his good ear had brought the other ear back to healthy harmony.
That patient’s recovery hints at the enormous therapeutic potential of the human microbiome – the 100 trillion bacterial cells living in and on our bodies. Such cells outnumber the body’s own cells 10:1. They are housed primarily in our gut, where roughly 70 percent of the components of our immune system reside. Scientists are hard at work trying to leverage the extraordinary healing powers of the microbiome, mining it for treatments of a variety of conditions, including asthma, irritable bowel syndrome and obesity.
And for good reason, according to microbiologist Michael Fischbach, Ph.D. “One-third of all human medicines are made by bacteria,” he says. “Clearly, they are the best chemists on the planet.” His lab studies how simple microorganisms create drugs with such proficiency. “Over the past 20 years, people have done seminal work uncovering which genes enabled microorganisms to synthesize wildly complex drugs,” he says. “For me, the trick is to be able to find other genes that look similar enough that I know they are there to make a drug.” The process used to be an arduous one, involving a great deal of luck while combing for bacteria through the soil or the ocean, where the vast majority of such drugs have traditionally been found.
That all changed with improvements in genetic sequencing and computational technology. Now, Fischbach uses his computer to scan every bacterium whose genome has been sequenced for drug-producing genes. As expected, his searches have turned up many drug-producing genes in ground- and marine-dwelling bacteria. “But I was shocked to see so many in the human microbiota. You used to have to travel to the coast of Palau to mine the ocean sediment for drugs,” says Fischbach, an assistant professor of bioengineering and therapeutic sciences. “Now we can just check our gut!”