Bugs that Prescribe

Illness: Common infections that require antibiotics.
Goal: A saliva test to check if an antibiotic is the right one.

Decades of misuse and overuse of antibiotics have enabled many types of bacteria to adapt to the drugs, leading to a global rise in harmful bugs that are difficult to treat and can become so-called superbugs. Ideally, new antibiotics would be under development to treat them, but in reality what’s coming onto the market are simply modifications of existing families of antibiotics, which provide only short-term solutions.

But what if doctors could use currently available antibiotics more effectively, and without contributing to resistance, by finding an easy and timely way to monitor their effect?

Peter Belenky, an assistant professor of molecular microbiology and immunology, believes we should be able to do that by tracking changes to the microbiome in the saliva of patients taking antibiotics. Reading saliva in this way, he says, could provide doctors with a fast, effective way to tweak treatment if they discover the current protocol is killing beneficial organisms.

Earlier research had shown that the “good” microbes in our saliva are much less sensitive than gut microbes to such things as dietary changes or hospitalization, which can wreak havoc in your gut. As Belenky and his team reported last fall in Nature, the salivary microbiome is dramatically affected by antibiotics—in this case, azithromycin.

“This was surprising considering that azithromycin isn’t a particularly aggressive antibiotic,” Belenky says.

Collecting a saliva sample is simple, and it also allows doctors to see shifts in the bacterial community right away. “You’d have to wait several hours for food to move through the gut to obtain a fecal sample,” Belenky says, “and by that point it may be too old to provide useful information.”

Doctors would now be able to respond more quickly to any changes and adjust treatment simply by analyzing saliva.”

Bugs that Protect Your Lungs

Illness: Respiratory infections and diseases such as the flu and asthma.
Goal: Shield the lungs by adding the good bacteria that illness takes away.

Amanda Jamieson never planned to study the microbiome of the lungs. Why should she? Until recently, scientists didn’t think there was a lung microbiome, at least not in healthy people. For starters, their lungs lack the microbe-friendly mucosal lining found in the mouth and gut. And researchers also struggled to grow bacteria from lung tissue samples in culture. As a result, scientists assumed that, in the absence of infection or disease, lungs were sterile.

Jamieson, an assistant professor of molecular microbiology and immunology, has shown that there is a community of microbes in healthy lungs and that they shift in response to respiratory illnesses. In particular, Jamieson has studied the effect of influenza A virus infections on lung microbes, an illness that can cause an estimated 500,000 deaths every year.