Probiotics, Prebiotics and Fermented Foods: What the Evidence Supports
Level 2, Intermediate
In brief
Probiotics are live microorganisms that confer a health benefit in adequate amounts; prebiotics are substrates selectively used by host microbes; fermented foods are produced through microbial growth, and not all contain live organisms. Evidence for probiotics is strain and indication specific: supportive for preventing antibiotic associated diarrhoea and some other uses, negative or mixed for many others. Fermented foods and fibre rich diets are the most broadly useful ways to support the microbiome.
The probiotic market is large and growing, and many patients take a probiotic in the belief that it supports digestion and immunity generally. Fermented foods have undergone a revival, from kombucha to kimchi. Prebiotic fibres are added to everything from breakfast cereals to protein bars. For practitioners, the task is to distinguish the uses supported by evidence from the much larger number of claims that are not, and to recognise that probiotics, prebiotics and fermented foods are different things with different evidence bases.
Definitions that matter
International scientific consensus panels have provided definitions that help clarify discussion.
| Term | Definition | Examples |
|---|---|---|
| Probiotics | Live microorganisms that, when administered in adequate amounts, confer a health benefit on the host | Specific strains of Lactobacillus, Bifidobacterium, Saccharomyces boulardii and others, with evidence for a defined benefit |
| Prebiotics | Substrates selectively utilised by host microorganisms conferring a health benefit | Inulin, fructooligosaccharides, galactooligosaccharides, some resistant starches |
| Synbiotics | Mixtures of live microorganisms and substrates that together confer a benefit | Combined products |
| Postbiotics | Preparations of inanimate microorganisms or their components that confer a benefit | Heat killed bacteria and some microbial products |
| Fermented foods | Foods made through desired microbial growth and enzymatic conversions of food components | Yoghurt, kefir, sauerkraut, kimchi, miso, tempeh, kombucha, sourdough |
2 implications follow. Not every fermented food contains live microbes at the point of eating; bread, beer and many pasteurised or shelf stable products do not. And not every product containing live microbes qualifies as a probiotic; the term implies evidence of a health benefit for that strain.
Why strain matters
Probiotic effects are specific to the strain, dose and indication. 2 strains of the same species can have different effects, and a strain that helps one condition may not help another. Evidence for “probiotics” in general is therefore close to meaningless; the relevant question is whether a particular product, at a particular dose, has evidence for the particular use.
Where the evidence supports probiotics
| Use | Evidence picture |
|---|---|
| Preventing antibiotic associated diarrhoea | Systematic reviews show a moderate protective effect in children and adults for some strains, including Saccharomyces boulardii and certain Lactobacillus strains |
| Preventing Clostridioides difficile infection in adults taking antibiotics | Gastroenterology guidance makes a conditional recommendation for specific strains and combinations |
| Preventing necrotising enterocolitis in preterm infants | Evidence of benefit for specific combinations, in neonatal settings under specialist guidance |
| Pouchitis after surgery for ulcerative colitis | A specific multi strain product has evidence for maintaining remission |
| Helicobacter pylori eradication | Some strains may reduce side effects of eradication therapy |
Where the evidence is mixed or negative
Acute gastroenteritis in children. 2 large randomised trials, in North America, found that probiotic products did not improve outcomes in children with acute gastroenteritis presenting to emergency departments, contradicting earlier smaller studies.
Irritable bowel syndrome. Some trials show benefit, but results vary widely between products, and guideline recommendations differ. A time limited trial of a specific product may be reasonable.
Inflammatory bowel disease. Apart from pouchitis, evidence for probiotics in Crohn disease and most ulcerative colitis settings is limited.
General wellness and immunity. Evidence that probiotics improve general health, prevent illness or boost immunity in healthy adults is weak.
After antibiotics. A study found that a probiotic given after antibiotic treatment delayed the return of the native microbiome compared with no intervention or an autologous faecal transplant, a reminder that intuition about restoring the gut can be misleading.
Safety and quality
Probiotics are generally safe in healthy people. However, they can cause bloodstream infections in people who are severely immunocompromised, critically ill, or have central venous catheters, and fungaemia has been reported with Saccharomyces boulardii in such settings. Their use in these groups should be guided by specialists.
Product quality varies. Analyses of commercial products have found discrepancies between labelled and actual contents, including different strains or lower counts than stated. Products with strain level identification, evidence for the intended use and credible quality controls are preferable.
Prebiotics
Prebiotics such as inulin and galactooligosaccharides reliably increase certain beneficial bacteria, particularly bifidobacteria, and some have evidence for effects such as improved stool frequency. Clinical benefits in many other areas remain under investigation. Because prebiotics are fermentable, they commonly cause gas and bloating, and can worsen symptoms in irritable bowel syndrome. Food sources, such as onions, garlic, leeks, asparagus, bananas, legumes and whole grains, provide prebiotic fibres alongside other nutrients.
Fermented foods
Fermented foods have long histories in almost every cuisine. A randomised study found that a diet high in fermented foods for 10 weeks increased gut microbiome diversity and reduced several inflammatory markers in healthy adults. Fermented dairy consumption is associated with some favourable health outcomes in observational studies. Fermented foods offer a food based way to increase microbial exposure, with the practical cautions that some are high in salt, unpasteurised products may carry infection risk in pregnancy and immune suppression, and people with histamine sensitivity may react to some aged or fermented foods.
A practical approach
- Start with diet. A fibre rich, varied diet with fermented foods is the most broadly supported way to support the microbiome.
- Use probiotics for specific indications, choosing strains and doses with evidence for that use.
- Set a trial period and review. If a probiotic does not help after a few weeks, stop it.
- Avoid probiotics in high risk groups without specialist advice.
- Introduce prebiotics gradually, especially in people prone to bloating.
- Choose quality products with strain level labelling.
- Question automatic use after antibiotics, other than for preventing antibiotic associated diarrhoea where evidence supports it.
An illustrative case
A 45 year old man takes a daily multi strain probiotic for general gut health and has recently been prescribed a course of broad spectrum antibiotics for a dental infection. He also has mild bloating, which has worsened since he started a prebiotic fibre powder.
The practitioner suggests stopping the prebiotic powder, which is likely contributing to the bloating, and replacing it with gradual increases in fibre from food. For the antibiotic course, a specific probiotic with evidence for preventing antibiotic associated diarrhoea is recommended for its duration and shortly afterwards. The general probiotic, for which there is no clear indication, is paused. He adds yoghurt and a fermented vegetable dish he enjoys to his diet. His bloating settles and he completes his antibiotics without diarrhoea.
Specific, not general
Probiotics, prebiotics and fermented foods are not interchangeable, and none is a general remedy. Used precisely, for defined purposes with evidence, probiotics can prevent specific problems. Used broadly, they are an expense with uncertain return. For most people, the best microbial therapy remains a varied, fibre rich diet that includes fermented foods.
Questions about probiotics
Do probiotics work?
Are all fermented foods probiotic?
Should everyone take probiotics after antibiotics?
References
- Hill C, Guarner F, Reid G, et al. The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nature Reviews Gastroenterology and Hepatology. 2014;11(8).
- Gibson GR, Hutkins R, Sanders ME, et al. The International Scientific Association for Probiotics and Prebiotics consensus statement on the definition and scope of prebiotics. Nature Reviews Gastroenterology and Hepatology. 2017;14(8).
- Su GL, Ko CW, Bercik P, et al. AGA clinical practice guidelines on the role of probiotics in the management of gastrointestinal disorders. Gastroenterology. 2020;159(2).
- Freedman SB, et al. Multicenter trial of a combination probiotic for children with gastroenteritis. New England Journal of Medicine. 2018;379(21).
- Suez J, Zmora N, et al. Post antibiotic gut mucosal microbiome reconstitution is impaired by probiotics and improved by autologous FMT. Cell. 2018;174(6).
- Wastyk HC, Fragiadakis GK, Perelman D, et al. Gut microbiota targeted diets modulate human immune status. Cell. 2021;184(16).
Continue your learning
Recommending microbial therapies with precision
Choosing microbial therapies for specific indications, rather than as general remedies, is part of the Gut Dysfunction module in IIFM’s 6 month Functional Medicine and Clinical Nutrition program.
This article is for the education of healthcare professionals. It is not a substitute for individual medical advice, diagnosis or treatment, and does not change any practitioner’s scope of practice. Regulation and guidelines differ between countries.