In a perfect world, our diet and environment would support a diverse, well-balanced, and thriving gut microbiome. But that’s not the world most of us live in, and our guts reflect it.
Like any community, the gut microbiome is dynamic. Microbes reproduce, they eat, and they die. A balanced diversity of species helps prevent 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 has been linked to rising rates of food sensitivities, autoimmune conditions, mood disorders, and digestive issues, such as irritable bowel syndrome (IBS) and leaky gut.
Reduced exposure to microbe-rich natural environments, overexposure to antibiotics and antibacterial soaps, and 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 — found in fermented foods, such as yogurt, kefir, kimchi, and sauerkraut, and available in supplement form — can help us create and sustain a more diverse microbiome. They support the barrier function of the intestinal lining and enhance nutrient absorption, which improves overall digestive health.
Probiotics can reduce 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 how to use them 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 notion that 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 in 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 a routine basis is helpful.
How do I find the right supplement for me?
“All gut microbiomes are not created equal,” says functional-medicine nutritionist Katie Morra, MS, RD, IFMCP. “They’re like a fingerprint. Everyone has their own gut profile, so how can we all need the same probiotic blend?”
Certain probiotic strains also seem to be more beneficial for certain conditions. These are the three main species of probiotics that are currently available in the United States:
- Lactobacillus and Bifidobacterium-based probiotics are the best-studied. They produce lactic acid and can especially support those with IBS and depression.
L. acidophilus and B. longum are among 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 harmful 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 our 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, especially in people who are immune-compromised; other practitioners, like Ruscio, believe they’re not just safe but essential, citing 20 clinical trials 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 that contains all three categories for maximum benefit, noting that they each support the gut in a slightly different way. “It’s much easier to balance the gut and see a resolution of symptoms with the complete support provided by all three probiotic categories.”
To test your tolerance of all three types of probiotics, start by taking one of each type a few days apart. If you find that any single probiotic category creates constipation, diarrhea, gas, or bloating that lasts longer than a few days, quit taking it and continue taking the other two.
How do I identify a quality probiotic supplement?
Choosing a probiotic supplement can be daunting. “The FDA does not regulate supplements, and many times the customer does not know what they are or are not 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 made with good manufacturing practices (GMP). Look for GMP certification or USP (U.S. Pharmacopeial Convention) verification on the label.
- They’re tested by an independent laboratory to verify label claims.
Some, but 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, be sure the seller has followed that instruction.
The number of colony-forming units (or CFUs) does not appear to be important, and more is not necessarily better. “If the probiotic is potent enough, you don’t need hundreds of billions of units,” notes Rountree, adding that beneficial ranges will vary among probiotic categories.
With soil-based probiotics, for instance, 2 billion units are probably 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 meets 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 be 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 than the last, notes Martin Blaser, MD, in his book Missing Microbes. He blames the prevalence of antibiotics in our medical care and animal feed, as well as increasing rates of C-section births.
These factors mean that our microbiomes need all the help they can get, Rountree says. “Even if you’re not having digestive issues, an imbalanced microbiome could be showing up as other problems like allergies or recurring infections.”
He adds that microbiome diversity tends 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, such as kombucha, can contain high levels of sugar. This feeds bad bacteria the probiotics might otherwise combat, Rountree notes. Even if you stick with less-sweetened kombucha, its probiotic effect is minimal.
“Kombucha is mildly beneficial,” he observes, “but you’d have to drink gallons of it to get 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 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 clinical trials 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 reduction in -depression for people under 60.
The effect of probiotics on anxiety symptoms is less decisive; in one review, about half of the studies examined found that probiotics eased anxiety. (For more on using probiotics to treat mood disorders, see “Psychobiotics: Using Gut Bacteria to Treat Mental Illness”.)
- Leaky gut syndrome: A randomized, double-blind, placebo-controlled trial of Lactobacillus to treat children who had acute gastroenteritis noted that 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 suggests that some probiotics are as effective as antifungal drugs in preventing the overgrowth of candida and other fungi in premature infants and can 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 question that you should take probiotics while on antibiotics.” While it may seem counterintuitive to ingest bacteria while taking a bacteria-killing agent, remember that probiotics are “friendly” microorganisms that benefit the gut environment as they pass through.
“Probiotics can be synergistic with antibiotics, especially in clearing out infection with H. pylori,” observes Ruscio. “You also get fewer adverse effects from antibiotics when they’re coadministered with probiotics.”
S. boulardii can be particularly useful. Because it’s a yeast and not a bacteria, it’s not affected by antibiotics. It can also help fend off the overgrowth of Candida albicans — a common side effect of antibiotic treatment. Lacto-Bifido blends can help reduce antibiotic-associated diarrhea as well, particularly if taken within a few hours of an antibiotic dose.
Should I get my stool tested before choosing 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 people 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.
“Choosing a probiotic doesn’t have to be as confusing as it looks,” he explains. “The internet makes you think you need to piece together your symptoms and figure out exactly what’s causing them. But imbalances in the gut can be easily resolved with 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 says. 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 the name suggests, 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 safety of all probiotics has been well documented, given you’re using 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 is controversial,” says Morra, adding that she 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 generally safe, those who are critically ill or have a compromised immune system should avoid them. When the immune system is weakened, introducing new bacteria may trigger infections.
Providers disagree about whether those 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 be 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, which is probably why they don’t increase bacteria in the small intestine.”
He suspects probiotics may compete with SIBO bacteria for food, helping starve them, and stimulating intestinal motility, which can help sweep the hostile bugs away.
What are prebiotics?
Some produce, including sunchokes, apples, bananas, leeks, onions, and garlic, contains 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 so they can 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 suffering from an imbalanced microbiome may be sensitive to FODMAPs (fermentable oligo-, di-, and monosaccharides and polyols). These are short-chain carbohydrates found in many vegetables and fruits, and they can cause uncomfortable digestive symptoms, including bloating and gas. The more severe your symptoms, the higher your chance of reacting negatively to increased fiber and prebiotics in your diet.
A low-FODMAP diet combined with probiotics can help clear out bad bacteria in your gut that are feasting on FODMAPs and allow beneficial bacteria to replace them. Then, after a couple of months, you can reexpand your diet. (For more on a low-FODMAP diet, see “Can An Elimination or Low-FODMAP Diet Treat IBS?”.)
“Ultimately, the goal is to expand the diet as broadly as possible,” notes Ruscio. “Probiotics can be helpful in getting you to that point.”
This originally appeared as “The Probiotics Puzzle” in the April 2020 print issue of Experience Life.