In a perfect world, our diet and environment would support a diverse, well-balanced, and thriving gut microbiome. But that’s not the planet most of us live in, and our guts reflect it.
Like any community, the gut microbiome is dynamic. Microbes reproduce, they eat, plus they die. A balanced diversity of species aids in preventing hostile takeovers.
Research shows, however, that our microbiomes are becoming steadily less diverse than those of our ancestors. And since the gut houses nearly 70 percent of the immune system, this shift continues to be linked to rising rates of food sensitivities, autoimmune conditions, mood disorders, and digestive issues, for example irritable bowel syndrome (IBS) and leaky gut.
Reduced contact with microbe-rich natural environments, overexposure to antibiotics and antibacterial soaps, as well as an affinity for low-fiber, high-sugar foods all rob our intestines of bacterial diversity. Lack of sleep and exercise don’t help either.
Enter probiotics. These living microorganisms — present in fermented foods, such as yogurt, kefir, kimchi, and sauerkraut, and obtainable in supplement form — can help us create and sustain a far more diverse microbiome. They support the barrier purpose of the intestinal lining and enhance nutrient absorption, which improves overall digestive health.
Probiotics can help to eliminate overzealous immune activity and the inflammation that manifests in fatigue, depression, and acne, notes functional-medicine practitioner Michael Ruscio, DNM, DC, author of Healthy Gut, Healthy You.
Not all probiotics are equally effective, though, and different people require different approaches.
We asked experts to answer common questions about probiotics, including cooking techniques in a way that works best for you.
How do probiotics work?
You might expect probiotics to simply add good bacteria to your gut, but this is not how they operate. They’re more like the gut’s enforcers.
“The concept taking probiotics is like planting a garden doesn’t seem to be the case,” explains integrative practitioner Robert Rountree, MD. Most probiotics don’t implant in the gut, he says. Instead, they create a range of antimicrobial compounds that affect other organisms, feeding “good” bacteria and eliminating the bad guys.
Ruscio concurs. “Most probiotics don’t work by forming colonies inside your gut,” he says. “They are mostly transient helpers.”
The gut’s general resistance to colonization is a good thing, he adds, because it makes us less susceptible to bad bugs. But it also means you can’t expect probiotics to stick. This is why consuming them on the routine basis is helpful.
How do I find the correct supplement for me?
“All gut microbiomes aren't created equal,” says functional-medicine nutritionist Katie Morra, MS, RD, IFMCP. “They’re like a fingerprint. Everyone has their own gut profile, just how can we all need the same probiotic blend?”
Certain probiotic strains also appear to be more beneficial for certain conditions. Fundamental essentials three main species of probiotics which are currently available in the United States:
- Lactobacillus and Bifidobacterium-based probiotics would be the best-studied. They produce lactic acid and may especially support those with IBS and depression.
L. acidophilus and B. longum are some of the most common species found in probiotic supplements. - Saccharomyces boulardii is actually a yeast, not a bacteria. Morra calls it a “yeast-fighting yeast.” Research suggests
S. boulardii may mitigate the damaging side effects of antibiotics and help keep pathogens, such as Clostridium difficile and Helicobacter pylori, in check. - Bacillus, also known as a spore-forming or soil-based organism (SBO), may help replace the bacteria that’s gone missing from your guts because of our reduced contact with soil. These include Bacillus coagulans, subtilis, and clausii. Some experts worry that SBOs may dominate other gut bacteria, particularly in people who are immune-compromised; other practitioners, like Ruscio, believe they’re not just safe but essential, citing 20 numerous studies that support their use. (For more on the safety of SBOs, see “Are soil-based probiotics safe?” below.)
Ruscio recommends a pro-biotic supplement or regimen which contains all three categories for maximum benefit, noting they each support the gut inside a slightly different way. “It’s quicker to balance the gut and find out a resolution of symptoms with the complete support provided by the 3 probiotic categories.”
To test your tolerance of all three types of probiotics, start by taking one of each type a few days apart. In the event that any single probiotic category creates constipation, diarrhea, gas, or bloating that lasts more than a few days, quit taking it and continue using the other two.
How do I identify a quality probiotic supplement?
Choosing a probiotic supplement could be daunting. “The FDA does not regulate supplements, and many times the client does not know what they are or aren't getting,” notes Morra. Still, better probiotics share some common traits:
- They contain genetically identified, well-researched strains like those listed earlier. (An internet search can reveal the level of research on any strain.)
- They’re free of all major allergens as well as artificial colors, flavors, and preservatives.
- They contain a guaranteed number of living units through the expiration date.
- They’re created using good manufacturing practices (GMP). Search for GMP certification or USP (U.S. Pharmacopeial Convention) verification around the label.
- They’re tested by an independent laboratory to verify label claims.
Some, although not all, quality probiotics need to be refrigerated. Freeze-dried capsules and soil-based probiotics generally don’t require it. If the label recommends refrigeration, make sure the seller has followed that instruction.
The quantity of colony-forming units (or CFUs) does not seem to be important, and more is not necessarily better. “If the probiotic is potent enough, you don’t need countless billions of units,” notes Rountree, adding that beneficial ranges will vary among probiotic categories.
With soil-based probiotics, for instance, 2 billion units are most likely enough to make a difference, while many Lacto-Bifido blends feature CFUs ranging from 25 billion to 50 billion, and some contain even more.
Opt for a probiotic that fits the criteria for a quality supplement over one that promises the highest number of CFUs.
Can’t I just get my probiotics from food?
To make sure, diet is a vital piece of the gut-health puzzle. “Food is a fantastic place to start,” says Ruscio. “I encourage everyone to add kimchi, sauerkraut, kefir, and kombucha to their diet. But it might be easier to get over the initial hump of rebalancing the gut’s microbiome with a well-balanced probiotic protocol.”
Our forebears didn’t use supplements, of course, but research shows each generation hosts less gut-microbial diversity compared to last, notes Martin Blaser, MD, in his book Missing Microbes. He blames the prevalence of antibiotics within our medical care and animal feed, as well as increasing rates of C-section births.
These factors imply that our microbiomes need all the help they are able to get, Rountree says. “Even if you’re lacking digestive issues, an imbalanced microbiome could be showing up as other problems like allergies or one infection after another.”
He adds that microbiome diversity has a tendency to plummet as we age (though no one really understands why), making it even more important for people over 40 to fortify their microbiomes.
Plain yogurt and sauerkraut provide good support. But many other products making probiotic claims, for example kombucha, can contain high levels of sugar. This feeds pathoenic agents the probiotics might otherwise combat, Rountree notes. Even though you stick with less-sweetened kombucha, its probiotic effect is minimal.
“Kombucha is mildly beneficial,” he observes, “but you’d need to drink gallons of it to obtain the quantities of probiotics you can get in a capsule.” (For more on selecting kombucha, see “Is Your Kombucha the Real Thing?”.)
What health conditions can probiotics help treat?
Probiotics cannot compensate for an unhealthy diet or lifestyle, but solid research suggests that they can be an effective a part of a treatment plan for a variety of illnesses:
- Irritable bowel syndrome: A meta-analysis of 20 probiotic trials found that probiotics improved IBS symptoms, including diarrhea, bloating, gas, and abdominal pain.
- Ulcerative colitis: One review of studies found that active ulcerative colitis responded well to a combination of Lacto-Bifido probiotics and an anti-inflammatory medication.
- Mood disorders: A meta–analysis of 10 numerous studies reported that probiotics improved mood in those presenting with mild to moderate depressive symptoms, while another meta-analysis concluded that probiotics were associated with a significant decrease in -depression for people under 60.
The effect of probiotics on anxiety symptoms is less decisive; in a single review, about half of the studies examined found that probiotics eased anxiety. (For more on using probiotics to deal with mood disorders, see “Psychobiotics: Using Gut Bacteria to deal with Mental Illness”.)
- Leaky gut syndrome: A randomized, double-blind, placebo-controlled trial of Lactobacillus to deal with children who had acute gastroenteritis noted the probiotic helped rebuild intestinal integrity after infection. Another study of a soil-based probiotic found it reduced symptoms associated with leaky gut in adults.
- Microbiome imbalances: Evidence shows that some probiotics are as effective as antifungal drugs in preventing the overgrowth of candida along with other fungi in premature infants and may help reduce bacterial overgrowth in patients with small intestine bacterial overgrowth, or SIBO.
In addition, there is limited but encouraging evidence that probiotics can address numerous issues: sleep, lactose intolerance, autoimmunity, atopic dermatitis, allergies, blood pressure, and cholesterol.
Should I take a probiotic while taking antibiotics?
Yes, says Rountree: “There’s no doubt that you should take probiotics while on antibiotics.” Although it may seem counterintuitive to ingest bacteria while going for a bacteria-killing agent, remember that probiotics are “friendly” microorganisms that benefit the gut environment as they go through.
“Probiotics can be synergistic with antibiotics, particularly in clearing out infection with H. pylori,” observes Ruscio. “There is also fewer adverse effects from antibiotics when they’re coadministered with probiotics.”
S. boulardii can be particularly useful. Because it’s a yeast and never a bacteria, it’s not impacted by antibiotics. It can also help battle the overgrowth of Candida albicans — a common side effect of antibiotic treatment. Lacto-Bifido blends might help reduce antibiotic-associated diarrhea as well, especially if taken within a few hours of an antibiotic dose.
Should I get my stool tested before selecting a probiotic supplement?
This is another area where there’s a lack of consensus. Morra and Rountree see some value in stool testing to identify specific microbial deficiencies or overgrowth, but Ruscio encourages individuals to forgo it.
He believes such testing may eventually become more useful as data accumulates, but he suggests people save their money and simply embark on a well-rounded probiotic protocol.
“Selecting a probiotic doesn’t have to be as confusing because it looks,” he explains. “The web makes you think you need to patch together your symptoms and figure out exactly what’s causing them. But imbalances in the gut can be easily resolved having a quality probiotic, especially when using all three categories together.”
You should notice a positive effect within one to two weeks of starting a well-rounded probiotic protocol, he states. If you don’t, you may need to layer in additional support, such as a low-FODMAP diet (more on that later).
Are soil-based probiotics safe?
As suggested by its name, soil-based Bacillus organisms are found in the dirt. Some experts warn that SBOs can compete with our resident gut bacteria and become pathogenic. But studies suggest that, for most people, specific, well-researched categories of soil-based probiotics are harmless.
“The security of all probiotics has been well documented, given you’re utilizing a formula that’s been tested to ensure it meets its label claims,” says Ruscio.
“Customer awareness around soil-based probiotics is in its infancy, and just like any supplement, the efficacy and safety factors are controversial,” says Morra, adding that they uses SBOs in her clinical practice and hasn’t observed any negative effects.
But it’s a risky approach for people with compromised immunity, she adds. The spore-forming nature of SBOs means they may proliferate and become pathogenic.
For people in reasonably good health, studied strains of soil-based probiotics should be well tolerated. As with any probiotic, discontinue its use if you experience negative reactions, like bloating, gas, or constipation, that last longer than a few days.
Who should avoid probiotics?
Though probiotics are usually safe, those who are critically ill and have a compromised immune system should avoid them. When the immune system is weakened, introducing new bacteria may trigger infections.
Providers disagree about whether individuals with SIBO should take probiotics. Morra advises these patients to avoid them: “If you have SIBO and take probiotics, you’re potentially just adding fuel to the fire.”
Still, Rountree and Ruscio take a different view, noting that a number of studies suggest probiotics are beneficial for treating SIBO. Ruscio says one study showed probiotics to become more effective than an antibiotic in combating digestive symptoms in people with the condition.
“Probiotics can actually be antibacterial,” he explains. “And probiotics don’t colonize, that is probably why they don’t increase bacteria in the small intestine.”
He suspects probiotics may contend with SIBO bacteria for food, helping starve them, which stimulates intestinal motility, which can help sweep the hostile bugs away.
What are prebiotics?
Some produce, including sunchokes, apples, bananas, leeks, onions, and garlic, includes a kind of soluble fiber that’s fermented by bacteria in the gut, helping the bacteria to grow. This fiber serves as a prebiotic, or fertilizer for healthy bacteria.
“Prebiotics are the food sources for probiotics to allow them to flourish in the gut,” explains Morra. (For more on how they work, see “Why Prebiotics Are as Important as Probiotics”.)
Before you fill your grocery cart with leeks, however, a word of caution: Those struggling with an imbalanced microbiome may be responsive to FODMAPs (fermentable oligo-, di-, and monosaccharides and polyols). These are short-chain carbohydrates present in many vegetables and fruits, and they can cause uncomfortable digestive symptoms, including bloating and gas. The more severe your symptoms, the larger your chance of reacting negatively to increased fiber and prebiotics in your diet.
A low-FODMAP diet combined with probiotics can help clean out bad bacteria in your gut which are feasting on FODMAPs and allow beneficial bacteria to replace them. Then, after a couple of months, you are able to reexpand your diet. (For more on a low-FODMAP diet, see “Can An Elimination or Low-FODMAP Diet Treat IBS?”.)
“Ultimately, the aim is to expand the diet as broadly as possible,” notes Ruscio. “Probiotics can be helpful in getting you to that point.”