By Amanda MacMillan
Updated: April 1, 2019 11:56 AM ET | Originally published: March 25, 2019

It’s hardly news that the gastrointestinal tract is important to human health: It transports food from the mouth to the stomach, converts it into absorbable nutrients and stored energy, and shuttles waste back out of the body. If you don’t properly nourish yourself, you don’t live. It’s that simple.

But in recent years, scientists have discovered that the GI system has an even bigger, more complex job than previously appreciated. It’s been linked to numerous aspects of health that have seemingly nothing to do with digestion, from immunity to emotional stress to chronic illnesses, including cancer and Type 2 diabetes.

“We now know that the GI tract is full of trillions of bacteria that not only help us process food but that also help our bodies maintain homeostasis and overall well-being,” says Dr. Tara Menon, a gastroenterologist at the Ohio State University Wexner Medical Center. The key, experts say, may lie in the microbiome—the makeup of bacteria and other microorganisms in the stomach and intestines, or, informally, the gut.

Research on the microbiome is still in its infancy. But studies have already found that certain environments, foods and behaviors can influence gut health for better or worse. Here’s why that matters and what you can do to improve yours.

Why is gut health important?

Everyone’s microbiome is unique, but there are a few generalities about what’s healthy and what’s not. “In healthy people, there is a diverse array of organisms,” says Dr. Gail Hecht, chair of the American Gastroenterological Association Center for Gut Microbiome Research & Education. (Most of those organisms are bacteria, but there are viruses, fungi and other microbes as well.) “In an unhealthy individual, there’s much less diversity, and there seems to be an increase of bacteria we associate with disease.”

Hecht stresses the word associate because scientists don’t know for sure which comes first—whether bacteria influence disease risk or whether existing disease influences gut bacteria. Most likely, she says, both are true. “We’re still lacking specific proof of how this connection works, but we know it’s there.”

Some bacteria fight inflammation, while others promote it. When the gut works as it should, these two types keep each other in check. But when that delicate balance gets skewed, inflammatory bacteria can take over—and they can produce metabolites that pass through the lining of the gut and into the bloodstream, spreading the inflammation to other parts of the body.

Specific types of bacteria in the gut can lead to other conditions as well. Studies in both animals and humans have linked some bacteria to lower immune function; others to greater risk of asthma and allergies; and still others to chronic illnesses like diabetes, heart disease, multiple sclerosis and some cancers.

Gut health has even been linked to anxiety and depression, and to neurological conditions like schizophrenia and dementia. The makeup of gut bacteria also varies between lean and overweight people, suggesting that it may play a role in causing obesity in the first place.

What affects gut health?

The food you eat obviously plays a role in the bacterial makeup of your gut, but so do a lot of other factors, including the nature of your birth. Research shows that babies delivered vaginally grow up to have more diverse microbiomes than those delivered via C-section, thanks to the exposure they get to different bacteria as they pass through the birth canal. Breastfeeding has also been shown to foster beneficial gut bacteria.

The environment you grow up in matters too. “We are way too clean of a society,” says Hecht. More exposure to germs and bacteria, within reason, can strengthen our microbiomes. “Go outside, dig in the dirt, play with animals … it’s all good. These are things that will help establish a healthy gut.”

Emotional stress can also affect gut bacteria. Scientists refer to the “gut-brain axis,” a pathway through which signals from the gut can affect neurotransmitters in the brain, and vice versa. Research is still early, but a person’s microbiome and mental state appear to be able to influence each other to some extent.

Then, too, there is the role of medications, including over-the-counter painkillers and drugs used to treat acid reflux, diabetes and psychiatric conditions; all have been linked to microbiome changes. But the best-known gut-altering drugs are antibiotics: though they’re prescribed to kill harmful bacteria, they can also wipe out bacteria of all kinds.

“I’ve seen patients on antibiotics develop allergies, or become more susceptible to infection, or have motility issues, all because their microbiota composition suddenly changes,” says Hecht. Antibiotics should be prescribed when they’re needed to fight bacterial infections, she adds, but doctors and patients should be careful about overuse.

Can you tell if you’re having health problems in your gut?

When the microbiome is thrown out of balance for any reason, it’s often easy to tell. Bloating, gas, diarrhea, stomach pain or nausea are all pretty direct signs that something in the gut isn’t working as it should. The imbalances often fix themselves after a short time, but if they become chronic, they may require a medical diagnosis and treatment. (Gastroenterologists can test for specific conditions associated with the microbiome, like an overgrowth of certain bacteria.)

But more and more, doctors are discovering irregularities in gut bacteria that don’t cause immediate symptoms—at least not gastrointestinal ones. “You can have bacteria in your gut that aren’t overproducing gas or altering your motility or anything you’d notice but that, for example, are associated with an increased risk of colon cancer,” says Hecht.

For people curious about their microbiome, commercial testing kits will analyze a stool sample and provide information about the strains of bacteria detected. But if you’re looking for advice about your health, doctors say the kits are not worth the money. “We don’t know enough to make those readouts meaningful yet,” says Dr. Robert Hirten, assistant professor of medicine at the Icahn School of Medicine at Mount Sinai. “We know in general what looks like inflammatory and noninflammatory bacteria, but in a practical sense we can’t really measure it or match specific bacteria to specific diseases.”

How can I maintain my gut health?

You don’t have to know exactly what’s going on in your gut at all times. And as long as you’re following doctor’s orders for overall health, you’re likely benefiting your microbiome. “We tell people to follow a balanced diet, stay hydrated, exercise regularly and get a good night’s sleep,” says Menon, “because we think staying healthy overall will help you maintain a healthy gut.”

Similarly, the same habits that are bad for your heart, lungs and brain—like cigarette smoking and excessive alcohol intake—can also hurt the microbiome. (Some data does suggest, however, that moderate amounts of red wine may be beneficial.) Avoid taking unnecessary medications, says Hecht, and talk to your doctor about how your current drug regimen might affect your gut health.

Limiting dairy, red and processed meats, and refined sugars can also improve gut health. So can getting the recommended amount of fiber—20 to 40 g a day, depending on your age and gender. Most Americans don’t meet these guidelines, but you can increase your amount by adding fruits, vegetables, whole grains, nuts and seeds to your diet.

Menon recommends keeping a food diary to track fiber intake, as well as GI symptoms related to food. A sudden switch to high-fiber foods can cause bloating, so introduce them gradually and keep track of how your body reacts to anything new. “Sometimes you can identify specific trigger foods that make you feel bad every time you eat them,” says Menon, “and you can find alternatives that work better for you.”

Some studies have looked at how regular consumption of specific foods—including mangoes, cherries, cranberries, broccoli, walnuts and leafy greens—appear to benefit the gut. But rather than narrowing your options to these items, it’s more important to look at what they (and plenty of other foods) have in common, says Hirten: they’re high in nutrients and fiber, and low in saturated fats and refined ingredients.

Overall, says Hecht, eating a wide variety of foods—including plenty of fiber-rich fruits, vegetables and whole grains—is the best way to encourage a diverse and healthy microbiome. “Your gut bacteria lives off whatever’s left over in your colon after your cells have digested all of the nutrients and amino acids,” she says. “You want to feed them complex fiber, not bad, processed stuff.”

Should I take probiotics?

Many commercial dietary supplements claim to boost gut health and introduce good bacteria. But the science is still out on the real-life benefits of probiotic pills and capsules. One potential problem is that even though probiotics should contain live bacterial cultures, the supplement industry isn’t well regulated—and there’s no guarantee that what’s in the bottle matches what’s on the label.

What’s more, studies have been inconclusive about whether probiotic supplements actually improve gut health for everyone. The evidence is stronger for people with specific health conditions, such as inflammatory bowel disease (IBD) and antibiotic-associated diarrhea. “A lot of probiotic strains are not what you would naturally find in large quantities in the human intestine,” says Hecht. “So you can eat them or drink them, but they won’t necessarily stay and colonize, and they won’t necessarily do you any good.”

Instead of pills, Hecht recommends getting beneficial bacteria from fermented food sources—like yogurt, kefir, sauerkraut and kimchi—that have other nutritional benefits as well. Hirten also advises his patients to focus more on a healthy diet and lifestyle rather than on pills. “I’m always cautious of new diets or supplements that claim to alter gut health in some way,” he says.

Finally, there are the cutting-edge ways in which doctors are beginning to manipulate the gut microbiome directly. Fecal transplants, which introduce donor stool material containing healthy bacteria into the intestinal tract of a recipient, have been used to treat IBD as well as C. difficile, a dangerous infection that causes recurrent diarrhea. Researchers are also studying how bacteria-killing viruses can target strains of E. coli associated with Crohn’s disease. “We’re actually giving people viruses to see if we can treat this specific bacteria,” says Hirten.

With so much still unknown about the microbiome, he adds, the best advice is stick to the basics. “I think that at this point, the most important thing we can do is follow a healthy diet and lifestyle,” he says. “If it’s good for you, it’s probably good for your gut.”

Correction, April 1

The original version of this story mischaracterized the health condition IBD. It is inflammatory bowel disease, not irritable bowel disease.

Contact us at editors@time.com.

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