Probiotics: What Actually Works (And What's Expensive Yogurt)

Series: Microbiome Revolution | Part: 4 of 8 Primary Tag: FRONTIER SCIENCE Keywords: probiotics, prebiotics, Lactobacillus, Bifidobacterium, gut health, supplement industry

The probiotic industry is worth approximately $70 billion globally. That's more than the GDP of Luxembourg. Every supermarket sells yogurt promising to transform your gut health. Every pharmacy stocks capsules containing "50 billion live cultures." Instagram influencers hold up supplements claiming to fix everything from bloating to depression.

Here's the uncomfortable question: how much of this actually works?

The answer is more complicated—and more interesting—than either the industry or its critics want you to believe. Some probiotics do remarkable things for specific conditions. Others are essentially expensive placebos with fancy strain names. And the difference between the two isn't captured by anything on the label.

This is a story about what we actually know, what we don't, and how to think clearly about a market that has outrun its science.

What "Probiotic" Actually Means

The official definition, from the World Health Organization: probiotics are "live microorganisms which, when administered in adequate amounts, confer a health benefit on the host."

Every word matters.

Live microorganisms: Dead bacteria don't count. If the manufacturing, shipping, or storage process kills the bacteria before you ingest them, you're swallowing corpses. Many commercial products have been tested and found to contain far fewer viable organisms than claimed, or organisms that die in stomach acid before reaching the intestines.

Adequate amounts: There's no universal "adequate amount." Different strains require different doses for different effects. A dose that works for one condition might be useless for another. Most commercial products are dosed based on marketing ("50 billion sounds bigger than 10 billion!") rather than clinical evidence.

Confer a health benefit: This is the crux. Not all bacteria that survive transit through your digestive system actually do anything beneficial. And benefits are often strain-specific—Lactobacillus rhamnosus GG might help with something that Lactobacillus rhamnosus from a different source doesn't.

The marketing industry treats "probiotic" as a magic word. The science treats it as a hypothesis that needs to be tested for each specific strain in each specific context.

The Strain Specificity Problem

Here's something that should bother you about most probiotic products: they list genus and species (Lactobacillus acidophilus, Bifidobacterium lactis) but not strain.

This matters because strain differences within a species can be enormous. It's like saying "we added some dogs" without specifying whether you mean Chihuahuas or Great Danes. Technically the same species. Very different animals.

Lactobacillus rhamnosus GG (LGG) is one of the most studied probiotic strains in the world. Decades of research support its use for preventing antibiotic-associated diarrhea, treating acute infectious diarrhea in children, and possibly reducing the duration of respiratory infections. This research is specific to LGG—a strain identified by the scientists Sherwood Gorbach and Barry Goldin (the "GG" stands for their initials).

Generic "Lactobacillus rhamnosus" from a different source might share many characteristics with LGG, or it might not. The surface proteins, the metabolites produced, the ability to adhere to intestinal cells, the interaction with the immune system—any of these might differ between strains. A product claiming benefits based on LGG research but using a different, uncharacterized L. rhamnosus strain is making an extrapolation that may or may not be valid.

The supplement industry largely ignores this problem. Clinical researchers obsess over it.

What Actually Has Evidence

Let's be specific. What probiotics, at what doses, for what conditions, have actual randomized controlled trial support?

Antibiotic-associated diarrhea: This is probably the strongest evidence base. Multiple meta-analyses confirm that certain probiotics reduce the risk of diarrhea during antibiotic treatment. Saccharomyces boulardii (a yeast, interestingly, not a bacterium) has particularly strong evidence. LGG works too. The effect is real and clinically meaningful—number needed to treat around 10-13, meaning you prevent one case of diarrhea for every 10-13 people who take probiotics with antibiotics.

Acute infectious diarrhea in children: LGG and Saccharomyces boulardii both reduce duration of diarrhea by about a day in children with acute gastroenteritis. Not a cure, but meaningful for a miserable condition.

Irritable bowel syndrome: This is messier. Some trials show benefit for specific strains; many show nothing. The most consistent finding is that Bifidobacterium infantis 35624 (branded as Alflorex in some markets) reduces overall IBS symptom severity. Multistrain products sometimes help, but the evidence is inconsistent. Given how heterogeneous IBS is, this variability makes sense—IBS is probably multiple conditions with similar symptoms.

Necrotizing enterocolitis in preterm infants: This is a life-threatening condition where parts of the intestine die. Probiotic supplementation reduces risk by about 50% in preterm infants. The evidence is strong enough that many NICUs have adopted routine probiotic use. The stakes are high and the intervention is cheap.

Ulcerative colitis maintenance: VSL#3 (now branded as Visbiome in some regions), a high-dose multistrain product, has shown benefit in maintaining remission of ulcerative colitis and treating pouchitis (inflammation after surgical removal of the colon). This requires prescription-strength doses—hundreds of billions of organisms per day.

H. pylori eradication: Adding certain probiotics to standard antibiotic therapy for H. pylori slightly improves eradication rates and reduces antibiotic side effects. Not dramatic, but real.

Constipation: Some evidence for Bifidobacterium lactis strains, though effect sizes are modest.

Eczema prevention in high-risk infants: Maternal and infant supplementation with specific strains may reduce eczema risk. Evidence is enough to drive clinical practice in some countries.

For most other claimed benefits—immune boosting, mood improvement, weight loss, general "gut health"—the evidence ranges from weak to nonexistent. That doesn't mean effects don't exist; it means we haven't proven them in rigorous trials.

Why Most Products Are Garbage

The gap between what the science supports and what the market sells is vast.

Survival problem: Many organisms in commercial probiotics die before they reach your intestines. Stomach acid is brutal. Bile isn't friendly. Some strains are acid-resistant; others aren't. Some manufacturers use enteric coating or microencapsulation to protect organisms; most don't. Without survival data for the specific product, you're taking it on faith that anything is arriving alive.

Colonization problem: Even if organisms arrive alive, they usually don't stick around. Your resident microbiome has had years to establish itself. Incoming probiotics are usually passengers, not settlers. They might have effects during transit, but they rarely become permanent residents. This isn't necessarily bad—transient effects can still be therapeutic—but it does mean "rebuilding your microbiome" with probiotics is mostly fantasy.

Standardization problem: The supplement industry is poorly regulated compared to pharmaceuticals. "50 billion CFU" on the label might mean 50 billion at time of manufacture, which could be 5 billion by the time you buy it. Shelf stability varies wildly. Some products contain strains other than what's listed, or contaminants, or nothing viable at all.

The wrong question problem: Most people take probiotics hoping for vague "gut health." But the science is condition-specific. Taking a generic probiotic for general wellness is like taking a random antibiotic hoping it helps. It might. It probably doesn't. You'd need to know what you're treating and what strain addresses it.

A genuinely science-based probiotic regimen would involve: identifying a specific condition with proven probiotic treatment, finding a product containing the specific strain(s) shown effective at the dose tested in trials, confirming the product delivers viable organisms at the claimed dose, and taking it for the duration that showed benefit in research. This is not how most people use probiotics.

The Prebiotics Distinction

Prebiotics are different from probiotics. They're not live organisms—they're food for organisms.

Specifically, prebiotics are non-digestible carbohydrates (mostly fibers) that selectively feed beneficial bacteria already in your gut. Instead of importing new bacteria, you're cultivating the ones you have.

The classic prebiotic fibers are inulin and fructooligosaccharides (FOS), found naturally in garlic, onions, leeks, asparagus, chicory root, and Jerusalem artichokes. Galactooligosaccharides (GOS) are another category. These compounds pass through your small intestine undigested and reach your colon, where bacteria ferment them.

The fermentation produces short-chain fatty acids—particularly butyrate, propionate, and acetate. These molecules have profound effects: butyrate is the primary fuel for colonocytes (the cells lining your colon), reduces inflammation, strengthens the gut barrier, and may influence brain function through the gut-brain axis.

Prebiotic supplementation reliably shifts microbiome composition toward increased Bifidobacteria and Lactobacilli. Whether this produces clinical benefits depends on the context. Evidence supports prebiotic use for improving mineral absorption (especially calcium), reducing constipation, and possibly supporting immune function.

The practical prebiotic advice is simpler than probiotics: eat a diverse range of plant foods. Fiber diversity feeds bacterial diversity. You don't need supplements if your diet includes vegetables, legumes, whole grains, and fruits. The modern Western diet is fiber-impoverished, which is probably a bigger problem than any specific probiotic deficiency.

The Food vs. Supplement Question

Fermented foods—yogurt, kefir, sauerkraut, kimchi, miso, kombucha—contain live bacteria. Are they probiotics?

Technically, they're only probiotics if they meet the definition: live organisms in adequate amounts conferring health benefits. Most fermented foods haven't been tested rigorously enough to make that claim. They contain bacteria, but whether those bacteria survive digestion in therapeutic numbers and produce measurable health effects is often unknown.

That said, fermented food consumption is consistently associated with health benefits in observational studies. A Stanford trial found that a high-fermented-food diet increased microbiome diversity and reduced inflammatory markers more than a high-fiber diet. Traditional diets rich in fermented foods (Japanese, Korean, Eastern European) tend to come with better health outcomes.

The bacteria in fermented foods are different from those in most supplements. Yogurt contains Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus—the strains that actually make yogurt—plus sometimes added probiotics like LGG or Bifidobacterium. Sauerkraut and kimchi contain Lactobacillus plantarum, Leuconostoc mesenteroides, and other lactic acid bacteria created during vegetable fermentation.

Whether food-based bacteria are better than supplements is unclear. They might benefit from the food matrix—yogurt's proteins and fats might protect bacteria from stomach acid better than a gelatin capsule. They come with actual nutrients, not just bacteria. And they're certainly cheaper than supplements.

The honest answer: we don't know enough to definitively say which is better. Fermented foods have traditional use and emerging science behind them. Supplements have more strain-specific research but worse quality control. Eating both probably doesn't hurt.

The Personalization Problem

One of the most frustrating findings in probiotic research is the high variability in individual response.

Some people respond dramatically to a given probiotic; others show no effect at all. This isn't noise—it's signal. Individual microbiome composition, immune system calibration, genetics, diet, and other factors all influence whether a given bacterial intervention will work.

A 2018 study from the Weizmann Institute in Israel tracked what happened when healthy people took a standard probiotic supplement. The bacteria colonized some people's guts and had measurable effects on gene expression. In others, the bacteria passed through without establishing at all. And—counterintuitively—after antibiotic treatment, probiotic supplementation actually delayed microbiome recovery compared to no intervention in some individuals. The probiotics occupied niches that would have been recolonized by the person's original bacteria.

This finding was heretical to the "probiotics are always good" narrative. It suggested that for some people in some situations, probiotics might actually interfere with natural recovery processes.

The implication is uncomfortable: probiotic recommendations probably can't be universal. What helps one person might not help another, and what helps in one context might hurt in a different one. We don't yet have the tools to predict who will respond to what.

How to Think About This

If you're currently taking probiotics, here's a reasonable framework:

If you have a specific condition with probiotic evidence, find the specific strain(s) shown effective in trials and take them at the tested dose. This is rational, evidence-based probiotic use.

If you're taking antibiotics, adding Saccharomyces boulardii or LGG is supported by evidence and probably worth doing. Start with the antibiotic, continue for a few days after.

If you're taking generic probiotics for vague "gut health", you're probably wasting money. That doesn't mean you're definitely getting zero benefit—absence of evidence isn't evidence of absence—but you're making an expensive bet with limited supporting data.

If fermented foods are easy to add to your diet, do it. The cost-benefit is favorable. You get food, possible microbiome benefits, and traditional dietary patterns that correlate with health.

If you're taking probiotics and feeling better, the question is whether it's the probiotic or placebo effect. This is genuinely hard to determine. Placebos are powerful, especially for GI symptoms. One approach: stop for a few weeks and see what happens. If symptoms return, maybe the probiotic is doing something. If nothing changes, you've found your answer.

The meta-principle: be specific about what you're trying to achieve, find evidence relevant to that specific goal, and be skeptical of products that promise everything.

The Future of Targeted Microbial Therapy

The probiotic industry as it exists today is a placeholder. It's what happens when a genuine scientific insight (microbes matter for health) gets commercialized before the science matures.

The future probably looks different. Instead of generic "gut health" products, we'll have therapies targeting specific conditions with strains engineered or selected for those conditions. Instead of one-size-fits-all doses, we'll have microbiome testing that identifies individual deficiencies and matches them with appropriate interventions. Instead of hoping organisms survive transit, we'll have delivery systems that ensure they arrive where they're needed.

We're already seeing glimpses. Seres Therapeutics, Finch Therapeutics, and other companies are developing defined bacterial consortia—specific combinations of strains designed to treat specific diseases. These aren't supplements; they're drugs that have to go through clinical trials. The FDA approved the first such products for C. diff prevention in 2022-2023.

Live biotherapeutic products (LBPs) is the emerging regulatory category. These are biological drugs made of living microorganisms. Unlike supplements, they'll require proof of efficacy and safety. Unlike fecal transplants, they'll be standardized and characterized.

The supplement aisle probiotics probably aren't going away. The regulatory bar for supplements is low, and the profit margins are high. But serious microbial medicine is moving toward something more rigorous. Eventually, the distinction between "supplements with bacteria" and "actual microbiome therapy" will be unmistakable.

The Coherence Perspective

From a coherence lens, the probiotic question is about whether you can shift a complex system by adding components from outside.

The answer is: sometimes, sort of, temporarily. You can nudge a system with external inputs. But systems have their own attractor dynamics. Your microbiome has settled into a particular configuration shaped by your diet, your genetics, your immune system, your environment, your history. Dropping in some outside bacteria rarely shifts the attractor permanently.

This is why diet matters more than supplements in the long run. Diet changes the selection pressure. It rewards certain bacteria and starves others. Over time, it can shift the entire landscape, not just add temporary visitors.

The coherence framing also explains why FMT works better than probiotics for many conditions. FMT isn't adding a few strains—it's transplanting an entire ecosystem with its own coherence. It has enough internal structure to resist being absorbed into the recipient's existing attractor. A capsule of ten bacterial strains can't do that.

The humbling implication: microbiome modulation is harder than it looks. You're not programming a machine; you're trying to shift the dynamics of a complex adaptive system. Sometimes that works. Often, the system just shrugs off your intervention and returns to its default.

Further Reading

- Hill, C. et al. (2014). "Expert consensus document: The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic." Nature Reviews Gastroenterology & Hepatology. - Suez, J. et al. (2018). "Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT." Cell. - Cryan, J.F. et al. (2019). "The Microbiota-Gut-Brain Axis." Physiological Reviews. - Sanders, M.E. (2019). "Probiotics and prebiotics in intestinal health and disease: from biology to the clinic." Nature Reviews Gastroenterology & Hepatology. - Sonnenburg, J. & Sonnenburg, E. (2016). The Good Gut. Penguin.

This is Part 4 of the Microbiome Revolution series, exploring how trillions of bacteria shape your body and mind. Next: "Your Microbiome Is Your Immune System's Teacher."