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Seven decades after penicillin revolutionized the treatment of infections by killing bacteria, medicine is poised for another revolution.

The central idea: Many bacteria, rather than creating disease, actually protect against it. So, rather than indiscriminately killing all bacteria, a growing number of researchers say we should be taking an ecological approach — by supporting good bacteria, either in addition to, or instead of destroying the bad.

“Balance is the key,” said Dr. Martin Floch, an assistant clinical professor of medicine at the Yale University School of Medicine. “The internal environment is an ecology.”

Yogurt has long been known as a probiotic — fostering the growth of healthy bacteria in the immune system. But now doctors and researchers are looking at promoting bacteria more aggressively. One recent study suggests that adding bacteria to the sinuses might help fight an active infection, and other research has shown that fecal transplants — getting a suppository of a healthy person’s poop — can be extremely effective at treating one kind of intestinal infections.

Early research has been so convincing that even mainstream institutions like Massachusetts General Hospital are experimenting with the techniques.


“There’s a lot of interest in trying to understand how these bacterial products educate the immune system,” said Dr. Ramnik Xavier, a senior associate member of the Broad Institute and chief of gastroenterology at Massachusetts General Hospital, which is seeking approval to begin a study on fecal transplants in patients with gastrointestinal diseases.

In recent generations, we’ve killed off many weaker strains of bacteria with antibiotics and antibacterial soaps and detergents, leaving the most dangerous strains — many of which have grown more resistent to treatment. And we’ve simultaneously stopped eating the probiotic foods of our ancestors, which provided our great-grandparents with a steady diet of healthy microbes to keep their intestinal flora in balance.


“Over time, this results in highly unstable communities that are perhaps more vulnerable to infection or chronic inflammation,” said Susan Lynch, an associate professor of medicine in the division of gastroenterology at the University of California San Francisco.

This may explain the rise of chronic inflammatory diseases and autoimmune disorders including type 1 diabetes, asthma, and allergies. Even some cancers have been shown to be influenced by the microbiome, the community of microbes that live inside each person.

Lynch recently conducted a study showing that people with chronic sinus infections had less diversity in their bacterial communities than healthy people. Promoting bacterial diversity may therefore be a better way to fight disease than prescribing antibiotics that blast both the good and bad bacteria, she said.

After being given antibiotics, a typical person’s bacterial community will bounce back to normal within a week, research has shown. If given antibiotics a second time, the community takes roughly two weeks to return to normal, and even longer after the third round.

“There are always organisms that never come back,” Lynch said, adding that the resulting lack of diversity of bacteria might make people more vulnerable to infections and chronic illnesses.

Scientists aren’t suggesting that antibiotics are bad — antibiotics are essential to fight dangerous bacterial illnesses. But taking antibiotics when not absolutely necessary could be dangerous.

Sarkis Mazmanian, a professor of biology at the California Institute of Technology, said the key is to learn to harness the benefits of the microbes that evolved along with us.


“If we knew what the bugs already know, we could cure diseases,” said Mazmanian, who was awarded a MacArthur Foundation Fellowship earlier this month for his work. “They know how to flip the switches of our immune system, our metabolic systems, in a way that could be harnessed as therapy.”

In his own life, Mazmanian said he follows the principle: “Do things we’ve done for millions of years, not the last 50-100 years.”

Eating heavily processed foods and killing bacteria with dishwashing detergent could be harmful to your microbiome, Mazmanian said.

“At the end of the day, they may provide a convenience, but they are an unnatural shift in our association with the microbial world,” he said. He does not use dishwashing detergent — instead running his dishwasher with water only — because research shows detergent doesn’t clean any better than water, Mazmanian said, and leaves a chemical residue that may be dangerous.

“It’s easy to make small shifts in your life that would allow your indigenous organisms to not be harmed by things that are most likely unnecessary.”

Mazmanian said he also supports his microbiome by eating as our ancient ancestors did: organic foods, mostly plant-based, and meat only occasionally.

Some foods, like greens, oats, barley, beans, and artichokes naturally spur the growth of good bacteria, said Floch, of Yale, who has led a national effort to systematically gather information on probiotics.

Yogurt is the most frequently cited probiotic, and Floch, Xavier, and Lynch said they regularly eat yogurt, in part for its probiotic benefits. Mazmanian said he doesn’t eat much dairy because humans didn’t begin raising cattle until relatively recently in evolutionary history.


Most cultures have developed fermented foods that promote probiotic activity, including German sauerkraut, Korean kimchi, and French cheeses, said Dr. Marc Micozzi, of Rockport, a physician and anthropologist who wrote the medical school textbook “Fundamentals of Complementary and Alternative Medicine.” Beer and wine are probiotics, too, said Micozzi.

“They’ve been around for thousands of years,” he said, and “are part of our dietary history.”

Micozzi and others said they’re skeptical of the probiotic supplements sold at many natural food and grocery stores.

Most of the organisms in probiotic supplements come from dairy products, Mazmanian said, and most were chosen mainly because they have a long shelf life or for other reasons having nothing to do with effectiveness.

“There is exceedingly little evidence that anything on the shelves today, that there’s any benefit from them,” Mazmanian said.

Luckily, he and others said, there’s also “no evidence they do any harm,” particularly to people with healthy immune systems.

A few individual bacteria have been identified as helpful for particular diseases. There is good evidence, for example, that lactobacillus reuteri can be helpful against childhood diarrhea, according to research Floch published last year.

Science is nowhere near the point yet, though, of being able to prescribe specific bacteria to treat or prevent specific illnesses. That’s why most researchers suggest that the best approach for now is for each person to promote the health of his or her own microbial ecosystem.


“You have to think like an ecologist,” Micozzi said.

Karen Weintraub can be reached at