It’s Not Yet Clear How to Boost the Microbiome. But Diet Is the Best Bet

The gut microbiome—the billions of bacteria that live inside the human digestive tract—is the focus of some of today’s most exciting and compelling medical research. Studies have linked microbiome-related imbalances to health conditions ranging from depression and Parkinson’s disease to heart disease. Some researchers have even started referring to the microbiome as a “forgotten organ” because of the indispensable role it plays in human health.

It’s fairly clear that the foods a person eats—or doesn’t eat—can affect the composition of his or her microbiome. Research on mice has shown that switching from a fiber-and-antioxidant rich Mediterranean diet to a Western diet heavy in fat and protein can alter the microbiome’s population within a day. Also, diets high in sugar are able to decrease microbiome diversity within a week—a shift that has been associated with irritable bowel syndrome and diabetes. Researchers have also found that antibiotics or antibacterials are able to knock down or disrupt the human body’s microflora in ways that could promote disease or illness.

All of these new discoveries are changing the way doctors think about and treat disease, says Krzysztof Czaja, an associate professor of veterinary biosciences at the University of Georgia.

Czaja’s research in rodents has shown that diet-induced changes to the microbiome can “rewire” communication between an animal’s brain and gut in ways that could promote obesity. These and other microbiome related discoveries “will change modern medicine,” he says.

But when it comes to strengthening or restoring the microbiome in ways that promote optimal health in humans, Czaja says there are promising theories but no hard-and-fast answers yet. “Our understanding of mechanisms regulating the gut-microbiome-brain axis is negligible,” he says. “We are not even sure about the number of microbes in the human body.”

He points out that the skin, gut and reproductive organs are home to roughly 1,000 different species of bacteria and 5,000 different bacterial strains. Figuring out which foods or probiotics could help reshape or harmonize the microbiome for improved health is like baking a perfect cake using 5,000 different ingredients, he says. The idea that eating this fruit or popping that supplement will do the trick is a woeful oversimplification of the microbiome’s complex role in human health.

Others agree. “We’re still learning what is a ‘healthy’ microbiome,” says Dr. Vincent Young, a professor in the department of microbiology and immunology at the University of Michigan Medical School. “There’s tremendous promise, and the research is being done, but right now, we don’t know what’s deranged or lacking, or how to fix it.”

Young points to the studies that have tied certain microbiome characteristics with disease states. The assumption is that by altering the microbiome to resemble a healthy person’s, we can cure or combat those diseases. This is the theory behind fecal transplants, which are basically transfusions of gut bacteria from a healthy person into a sick one. “But so far, fecal transplants are only proven to be effective for patients with recurrent C. difficile infection,” Young says, referring to a common type of infection that occurs in some people who have had their microbiome disrupted, typically by antibiotics. “People are trying these transplants for everything from autism to depression, but the results are uncertain and anecdotal.”

Often lost amid the fecal transplant hype is the considerable risk involved. “The potential to be harmed by this procedure is very high,” says Daniel McDonald, scientific director of the American Gut Project and a post-doctoral researcher at the University of California, San Diego School of Medicine.

The medical science community is only “scratching the surface” when it comes to understanding the microbiome’s role in human health, McDonald says, and experts who study it still can’t even say what a healthy or unhealthy microbiome looks like. “A lot of the technology we’re applying now is of relatively low precision,” he says. “We are not even in a position to say that one person’s microbiome is more or less healthy than another’s.”

The same is true of diet or probiotic supplements intended to strengthen or improve a person’s gut bacteria. “We have data to show that diets change the microbiome, but not that specific foods will change the microbiome in a specific way for a specific individual,” he says.

This is frustrating news to hear—especially if you keep reading about the microbiome and want to take steps to strengthen or safeguard your own. But even at these early stages of research, there may be some broad guidelines to consider.

“I tell people a healthy diet high in complex carbohydrates and fiber may benefit the microbiota,” Young says. He says whole grains in particular may be beneficial, as well as eating a wide variety of plant foods. But he points out that these recommendations aren’t any different from what you’d hear from a family physician or nutritionist without training on the microbiome.

Likewise, he says eating probiotic-containing fermented foods like kefir and kimchi and sauerkraut may be beneficial; these foods have long been eaten and associated with good health.

On the other hand, if you’re worried about harming your microbiome, Czaja says it’s a good idea to avoid diets high in sugar and simple carbs. That means cutting out soda, sweets and most snack foods. But again, this guidance is based in part on broader nutrition research, not solely on microbiome studies. If your goal is to encourage healthy gut bacteria communities, “there is no perfect food or perfect bacteria cocktail,” he says.

“You will always have unexpected side effects, some of which you can’t predict, when manipulating a complex system,” Young adds. The human microbiome is extremely complex. And as of today, experts who study it can’t predict what side effects—good or bad—may result from attempts to tweak its composition.