The Truth About Probiotics and Gut Health

The start of each year is a time many of us think about resetting our health and trying to be more mindful about what we put in our bodies. One enduringly popular wellness trend for this is probiotics, or live microorganisms that are meant to have helpful effects on the body.

It makes sense people prioritizing their health are drawn to their microbiome. For thousands of years, healers across cultures have recognized that much of human health begins in the gut.

Science backs this up: From a cellular perspective, we are as much or more bacteria as we are human. From a genetic standpoint, we have about 100 times more microbial genetic material than our own DNA. These trillions of cells, representing thousands of species, are integral to metabolic health, immune regulation, neurodevelopment, and more.

So keeping our body’s microbiome in balance is crucial. Probiotics can be helpful in specific circumstances. But they are just one piece of a much larger story about microbial health, and research about many of their potential benefits is still ongoing. Here is our primer on maintaining a healthy gut for overall well-being.

Why having a diverse microbiome is important

Modern life has fundamentally changed our relationship with microbes. Historically, humans were exposed to diverse microbial communities through soil, unprocessed foods, and the environment. Today, we’ve largely sanitized that exposure away.

Studies comparing populations in industrialized societies to those in relatively preserved hunter-gatherer or indigenous communities show we have far fewer microbial species than those eating more traditional diets. This loss appears linked to practices including antibiotic use, pesticides in agriculture, and a diet dominated by ultra-processed foods.

The health implications of all this are significant, says Dr. Akash Goel, a gastroenterologist at the Atria Health Institute. The United States and other Western countries have seen major increases in allergies, inflammatory conditions, and autoimmune diseases in recent years, and some experts think this may be driven by our declining microbial diversity. Microbes educate our immune system about what to tolerate, and without that proper education, the immune system can become overactive.

On the flip side, more diverse microbial ecosystems help strengthen the gut’s lining, make bowel movements more regular, and are associated with less obesity, diabetes, and other positive health outcomes across multiple studies.

What we know about probiotics and prebiotics

Probiotics are live microbes that come from food or supplements. They are meant to join your body’s existing microbe population and improve the balance of the communities there. Prebiotics are the nutritional elements (mainly fermentable fibers) that feed those microbes and can encourage good bacteria to grow in your gut. Postbiotics are the compounds produced when your body digests prebiotics and postbiotics, and they can be made into products that help certain conditions.

When probiotics work, they can help balance the ecology of the gastrointestinal tract, often offering benefits to GI and overall health and symptom improvement. Researchers are still studying how probiotics affect a range of health conditions, and studies vary widely in quality and their findings. The most robust evidence shows probiotics are effective for:

• Irritable bowel syndrome (particularly for bloating and bowel irregularity)
• Reducing cold symptom duration and severity
• Gum disease
• Eczema and acne (including prenatal use to reduce the risk of eczema in infants)
• Vaginal and urinary tract infections (UTIs)
• Acute infectious diarrhea
• Antibiotic-associated diarrhea
• Certain complications of ulcerative colitis

We also know the gut microbiome interacts with other systems including the brain, nervous system, immune system, and endocrine system. Other research is looking at the efficacy of using probiotics to help treat chronic pain, mental clarity, inflammation, and metabolism.

But they don’t help with everything. While many people wonder about taking probiotics to restore good bacteria after an antibiotic, the science is mixed: Probiotics can help prevent some antibiotic side effects like diarrhea, but some research shows they may actually delay the recovery of natural gut flora after antibiotics.

Not all microbes are alike, and different probiotics may be better or worse for your body and your circumstances. In some situations, probiotics can be unsafe and should only be used under direct medical supervision, if at all. There are documented cases of probiotic organisms causing serious bloodstream infections in:

• People who are immunocompromised (such as those undergoing chemotherapy, using biologics, transplant medications, or who have advanced HIV)
• Those with central venous catheters or other indwelling catheters
• Critically ill patients (like those in an ICU)

Even in otherwise healthy people, not every gut responds well. Certain IBS subtypes and people with small intestinal bacterial overgrowth (SIBO) can feel worse on some probiotics. Supplements are not regulated by the U.S. Food and Drug Administration (FDA), so manufacturers are not legally required to prove the quality or contents of their products. This uncertainty is why experts like Dr. Goel and Medeya Tsnobiladze, ND, MS, an integrative health specialist, recommend speaking with your care team about which probiotics might be right for you before trying them.

The food-first approach

Ask experts and you’ll hear the same thing again and again: probiotics are rarely the first recommendation for gut health. “With good nutrition, the body’s colony supports itself. It does not require constant reintroduction of new microbes,” says Tsnobiladze.

Instead, most people should focus on nourishing the microbial ecosystem they already have. “Think of it as tending a garden rather than repeatedly replanting it,” Dr. Goel says.

To get your microbiome flourishing, experts recommend eating a wide variety of foods. Evidence underscoring this comes from the American Gut project, a large initiative analyzing human microbiome samples, which found that people with the most diverse microbiomes consumed more than 30 different plant-based foods each week.

Here are the three pillars to support microbial health through food:

1. Fiber. Fiber isn’t actually a nutrient for us—it’s a prebiotic food for our gut bacteria. When beneficial bacteria metabolize fiber, they produce short-chain fatty acids like butyrate, which supports the gut lining, reduces systemic inflammation, influences metabolism, and naturally stimulates GLP-1, one of the body’s own gut hormones linked with satiety, or fullness. But with so much of the modern diet coming from ultra-processed foods, only 5% of Americans meet the recommended intake of 25 to 35 grams of daily fiber.

• Fiber-rich foods: See our list of the most fiber-rich foods here. This also includes resistant starch (green banana), inulin (onions, garlic, leeks, Jerusalem artichokes), pectin (apples), and beta-glucans (oats and barley).

2. Fermented foods. A Stanford University study found that people who consumed up to six servings of fermented foods daily increased their microbiome diversity and decreased markers of inflammation. While six servings per day is unlikely to be realistic for most people, Dr. Goel recommends incorporating a bit of fermented food whenever you can. Another 2023 study showed that for every 100-gram increase in fermented foods, there were stepwise decreases in blood pressure, C-reactive protein (an inflammation marker), and waist circumference.

• Fermented foods: Yogurt, kefir, sauerkraut, kimchi, kombucha, pickles, tempeh, and miso are all good sources, even in small amounts, says Dr. Goel. Make sure to look for labels that say they contain “live and active cultures.”

3. Polyphenols. These antioxidant compounds in plant foods that contribute to their colors, flavors, astringency, and odor also nourish beneficial bacteria.

• Foods with polyphenols: Highly pigmented foods, such as blueberries, cherries, strawberries, cacao, and spinach, and herbs and spices such as cinnamon and oregano, are great sources.

For most probiotic-related benefits, it's best to incorporate the probiotic and prebiotic rich foods directly into your diet, as the beneficial microbes are more likely to colonize the GI tract, Dr. Goel says. “Fermented foods and fiber are also improving the overall quality of your diet, so it’s going to add knock-on effects,” he adds. Tsnobiladze says using oregano to reduce overgrowth or adding green banana powder to a smoothie to support the body’s microbes are examples of how food items can be used as tools in rebalancing the gut flora.

When to consider probiotics

Probiotics do have a place, and they’re best used strategically with a specific indication and time course in mind.

For specific conditions like IBS or recurrent infections, ask your health care provider for recommendations and look for strain-specific products. There are now tests that can measure the presence of bacterial families, species, and even subspecies in your stool so your clinician can make tailored probiotic recommendations. It’s best to do these tests at the recommendation of your care team rather than on your own, though, as they can navigate any results to help identify the potential causes of any symptoms.

For a severe GI condition known as recurrent Clostridium difficile infection, clinicians are using fecal microbiota transplantation, which delivers a much broader spectrum of bacteria than typical probiotics. These transplants have been proven up to 95% effective in treating C. diff infections, and the success is leading biotech companies to develop more precision-defined groups of multiple bacterial strains working in concert that they hope can treat more conditions in the future.

Tsnobiladze, the integrative health specialist, says that if you want to try a general gut reset, she recommends no more than a one-month course of probiotics once or twice a year. This should be a blend of well-studied probiotics such as Lactobacillus, Bifidobacterium, or Akkermansia, with about 10-20 billion colony forming units (CFUs) per dose, she says. Because probiotics mostly work while passing through your gut, the most important thing is to take them consistently during this reset period to allow the new good bacteria time to interact with your immune system.

It’s always best to choose brands certified by NSF or ANSI, which indicates third-party testing. And a note of caution if you do decide to try probiotics on your own: If you’ve been taking probiotics for a while and your symptoms return when you skip one day, Tsnboliadze says that means it’s the wrong probiotic. Talk with your care team for proper evaluation, as the issue may be something entirely different that needs to be diagnosed and addressed.

The bottom line

Our microbiomes are foundational to many aspects of our health, and they require consistent care—ideally through nutrition. When more help is needed, probiotics are one tool to help rebalance the community in your garden, as Dr. Goel puts it, rather than for constant supplementation. With the right approach, your ecosystem will flourish.