Prebiotic foods and supplements have received a lot of attention recently for their ability to change the composition of our gut microbiome. This is because prebiotics feed beneficial gut bacteria (i.e. probiotics).
Healthier diets rich in vegetables and other high fiber plant foods tend to be naturally rich in prebiotics and also generally good for gastrointestinal function.
But prebiotic foods can be friend or foe for your health, often depending on what sort of shape your gut flora is in when you consume them.
In this article, we’ll discuss the benefits of prebiotic foods and supplements, including digestive health benefits, but also look at the potential downsides and when it pays to consume prebiotics more cautiously.
What Are Prebiotic Foods?
Prebiotic foods mostly belong to a specific subgroup of carbohydrates, which also count as dietary fiber.
Fiber can’t be broken down by the small intestine. It therefore enters the large intestine intact and undigested.
Prebiotic fibers are a preferred food for gut bacteria — including beneficial bacteria, such as Bifidobacteria and Lactobacilli. Gut bacteria ferment these prebiotic fibers and are able to thrive and multiply as a result.
Mucus production to maintain a healthy intestinal barrier
Protection against inflammation
Some prebiotics names you might come across include:
These can either be sold in concentrated form as supplements, or consumed in more modest amounts from prebiotic foods. Some of the biggest sources of prebiotics in our diet are:
Onions and garlic
Beans and pulses such as red kidney beans, butter beans, and soybeans
Whole wheat products
Prebiotics and Health
Though prebiotics aren’t as well researched as probiotics yet, there are some promising potential wellness and health benefits from using prebiotic supplements. These include:
Improved colon function: A systematic review/meta-analysis (SR/MA) of nine randomised controlled trials (RCTs) found that the prebiotic resistant starch increased stool bulk and butyrate production in healthy adults [4 Trusted SourcePubMedGo to source]. Systematic reviews and meta-analyses are considered the highest standard of scientific assessment available.
Easing of chronic constipation: A meta-analysis of randomised clinical trials found that inulin (a type of prebiotic) supplements improved stool frequency, consistency, and transit time through the digestive system. However, they did not improve pain or bloating [5 Trusted SourcePubMedGo to source].
Mood-lifting potential: An RCT found that inulin intake was helpful at improving mood in some obese subjects, though strength of response depended on the individual’s gut microbiome makeup at the beginning on the study [6 Trusted SourcePubMedGo to source].
Hunger curbing: An SR/MA of RCTs concluded that inulin-type prebiotics may help reduce ghrelin (the so-called “hunger hormone”) in overweight or obese people [7 Trusted SourcePubMedGo to source]. However, they did not appear to help with weight loss or weight management [8 Trusted SourcePubMedGo to source].
Help reduce blood triglycerides (linked with heart disease)
Increase HDL (good) cholesterol
Reduce elevated liver enzymes
Improve fasting insulin and reduce insulin resistance
Prebiotics Aren’t a Panacea
While much of the research into prebiotics indicates they have a role in overall health, they aren’t universally helpful. For example, prebiotic foods and supplement don’t appear to help with the following conditions:
Eczema: An SR/MA comparing probiotics, prebiotics, and synbiotics (a combination of the two) for their effects on infant eczema found that probiotics and synbiotics reduced the incidence of eczema, but prebiotics alone had no effect [14 Trusted SourcePubMedGo to source].
Irritable bowel syndrome (IBS): A collection of SR/MAs have found little to no evidence that prebiotics are a beneficial treatment for IBS [15 Trusted SourcePubMedGo to source, 16 Trusted SourcePubMedGo to source, 17 Trusted SourcePubMedGo to source]. One of these compared the effects of probiotics, prebiotics, and synbiotics on IBS symptoms. It found that multi-strain probiotics with Bifidobacterium species had the greatest positive effect on overall IBS symptoms. Synbiotics helped with urgency, abdominal pain, and flatulence, but prebiotics alone didn’t clearly benefit IBS.
More Prebiotics Aren’t Always Better
If you imagine the bacteria in your gut as flowers in a garden, prebiotic foods and supplements can be considered the fertilizer that helps them to grow. But just as you wouldn’t indiscriminately dump bags of fertilizer on your soil, more prebiotics aren’t necessarily better when it comes to gut health.
The main concern is that if you have an overgrowth of microorganisms or an imbalance in your gut microbiome, prebiotics may not only feed the healthy microbes but the problematic ones.
Research suggests that prebiotics don’t just selectively encourage the growth of good bacteria and that byproducts produced by healthier bacterial strains can cross-feed a wider variety of bacteria. Some of these bacteria may be detrimental to gut health [18 Trusted SourcePubMedGo to source].
For people who have a sensitive gut, too many prebiotics may also cause a flare up of symptoms because of their fermentable nature. Most prebiotic foods are also FODMAPs, where the “f” stands for “fermentable” carbs that can create uncomfortable gas, bloating, and diarrhea for people with IBS .
A Double-Edged Sword
In fact a number of studies point to prebiotics having mixed effects, particularly if you have a sensitive gut. For example:
A 2017 randomized controlled trial (RCT) involving people with IBS found that prebiotics correlated with increased good bacteria in the gut. However, it also correlated with increased nausea, vomiting, headache, belching, and flatulence [20 Trusted SourcePubMedGo to source].
A 2018 RCT that compared a standard, Mediterranean-style diet plus prebiotic with a low FODMAP diet plus placebo in people with IBS found [21 Trusted SourcePubMedGo to source]:
Both regimes were largely effective at reducing gut symptoms. However, flatulence and rumbling remained in the prebiotic group.
However those who took prebiotics had an increase in beneficial bifidobacteria that wasn’t seen in the low FODMAP group.
Prebiotics caused a flare of symptoms for some patients, but this went away after 7-10 days.
Prebiotic Supplements Caution
As helpful as they can be, prebiotics aren’t always right for everybody, particularly in the cases of high-dose supplements and people struggling with poor gut health.
The approach that I find works best for my patients is for them to stay away from prebiotic supplements altogether in the first stages of a gut healing program, when the gut is still very sensitive. Later on, when gut health is more robust, prebiotics may actually play a beneficial role. However, it’s still better to start with small steps.
If you are in a good place to try a prebiotic supplement, start with a low dosage and build up slowly. Research suggests that galacto-oligosaccharides may be better tolerated and have somewhat higher effectiveness at lower doses, so this could be your supplement of choice when starting out [22 Trusted SourcePubMedGo to source].
However careful you are when taking prebiotic supplements, be prepared for 7–10 days when your gut symptoms may flare a little before settling down again [21 Trusted SourcePubMedGo to source].
Getting Prebiotics From Your Diet
More isn’t necessarily better. There’s a lot to be said for getting a more modest dose of prebiotics naturally from your food.
While there is no official recommended intake of prebiotics, 5 grams is often considered a good target intake of FOS and GOS (measured as combined fructo-oligosaccharides, and galacto-oligosaccharides) in the daily diet, in healthy individuals with no significant gut issues. A 3.5-gram daily dose is regarded as the minimum that can bring benefits [23 Trusted SourcePubMedGo to source].
Reliable analyses of the amount of prebiotics in foods are few and far between, but the table below shows some prebiotic food sources and their combined fructo-oligosaccharides,(FOS) and galacto-oligosaccharides (GOS) contents .
Combined GOS and FOS per 100g (3.5 oz)
Combined GOS and FOS per Serving
0.26g (2 slices)
Whole wheat bread
0.47g (2 slices)
Canned butter beans
0.78g (½ cup)
0.48g (½ cup)
Boiled red kidney beans
2.4g (½ cup)
0.4g (½ cup)
0.79g (3 oz serving)
0.37g (3 oz serving)
0.38g (3 oz serving)
0.26g (3 oz serving)
(*Some of the best prebiotic food sources are not included in this table — e.g.under-ripe bananas, Jerusalem artichokes, leeks, chicory root, dandelion greens and soy beans.)
As you can see, it’s quite possible to get effective amounts of probiotics from your diet alone. This may be the most balanced solution for gut microbiota benefits for most people whose gut health isn’t in very poor shape.
Determining Your Optimal Prebiotic Intake
Given that most prebiotics are also FODMAPs — a proven contributor to IBS symptoms — you may need to watch your dietary intake when you have a more sensitive gut.
In fact, finding your ideal intake of carbohydrates and prebiotics is one of the four pillars of healthy eating for gut healing that I focus on in Healthy Gut, Healthy You:
Your tolerance level for prebiotics and fermentable carbohydrates is specific to you and can change over time. For example, as your gut heals from a condition like SIBO, you might find that you can enjoy more healthy carbohydrates and prebiotics than you were /previously able to.
By experimenting a little with different diets, you can usually find the prebiotic level that suits you.
A key principle here is not to cut out more healthy carbohydrates and high fiber foods than absolutely necessary. So this means starting with the least restrictive diet (highest prebiotic content) and only moving onto a stricter elimination diet if you don’t start seeing resolution of gut symptoms within a couple of weeks.
In increasing order of restrictiveness (and decreasing order of prebiotic content) some recommended diets are:
The general idea is you would start with a whole food diet and only move on a paleo and then a low FODMAP diet if your symptoms don’t get better.
That said, there are no real hard and fast rules here. For example, the low FODMAP diet is the most proven for IBS [25 Trusted SourcePubMedGo to source]. You might want to try this first if you have been diagnosed with this condition.
Probiotics to Boost Gut Health
May people ask if someone with a sensitive gut should avoid probiotics. The answer, according to research, is no. Probiotics don’t have the same issues as prebiotics and will almost always help.
Scientific studies show a wide variety of benefits from taking probiotics, including:
For most patients with gut issues such as IBS, SIBO and inflammatory bowel conditions, diet changes and use of a multistrain probiotic can start to produce symptom relief within a couple of weeks.
The Bottom Line
Prebiotic foods and supplements have some proven benefits to offer, but changing your diet and using probiotics are better first-line options when you are trying to recover from gut-related health issues. In fact, when you are most symptomatic, you may need to cut down drastically on prebiotics, even those found in healthy foods.
As your gut health improves, you can work on discovering the right amount of prebiotics for you. The key is discovering the amount that benefits your gut microbiome without causing significant bloating, gas or diarrhea — this tolerance may change over time.
Lewis K, Lutgendorff F, Phan V, Söderholm JD, Sherman PM, McKay DM. Enhanced translocation of bacteria across metabolically stressed epithelia is reduced by butyrate. Inflamm Bowel Dis. 2010 Jul;16(7):1138–48. DOI: 10.1002/ibd.21177. PMID: 20024905. Trusted SourcePubMedGo to source
Peng L, Li Z-R, Green RS, Holzman IR, Lin J. Butyrate enhances the intestinal barrier by facilitating tight junction assembly via activation of AMP-activated protein kinase in Caco-2 cell monolayers. J Nutr. 2009 Sep;139(9):1619–25. DOI: 10.3945/jn.109.104638. PMID: 19625695. PMCID: PMC2728689. Trusted SourcePubMedGo to source
Gaudier E, Rival M, Buisine MP, Robineau I, Hoebler C. Butyrate enemas upregulate Muc genes expression but decrease adherent mucus thickness in mice colon. Physiol Res. 2009;58(1):111–9. DOI: 10.33549/physiolres.931271. PMID: 18198997. Trusted SourcePubMedGo to source
Shen D, Bai H, Li Z, Yu Y, Zhang H, Chen L. Positive effects of resistant starch supplementation on bowel function in healthy adults: a systematic review and meta-analysis of randomized controlled trials. Int J Food Sci Nutr. 2017 Mar;68(2):149–57. DOI: 10.1080/09637486.2016.1226275. PMID: 27593182. Trusted SourcePubMedGo to source
Collado Yurrita L, San Mauro Martín I, Ciudad-Cabañas MJ, Calle-Purón ME, Hernández Cabria M. Effectiveness of inulin intake on indicators of chronic constipation; a meta-analysis of controlled randomized clinical trials. Nutr Hosp. 2014 Aug 1;30(2):244–52. DOI: 10.3305/nh.2014.30.2.7565. PMID: 25208775. Trusted SourcePubMedGo to source
Leyrolle Q, Cserjesi R, D G H Mulders M, Zamariola G, Hiel S, Gianfrancesco MA, et al. Prebiotic effect on mood in obese patients is determined by the initial gut microbiota composition: A randomized, controlled trial. Brain Behav Immun. 2021 May;94:289–98. DOI: 10.1016/j.bbi.2021.01.014. PMID: 33515740. Trusted SourcePubMedGo to source
da Silva Borges D, Fernandes R, Thives Mello A, da Silva Fontoura E, Soares Dos Santos AR, Santos de Moraes Trindade EB. Prebiotics may reduce serum concentrations of C-reactive protein and ghrelin in overweight and obese adults: a systematic review and meta-analysis. Nutr Rev. 2020 Mar 1;78(3):235–48. DOI: 10.1093/nutrit/nuz045. PMID: 31504857. Trusted SourcePubMedGo to source
Qu H, Song L, Zhang Y, Gao Z-Y, Shi D-Z. The Effect of Prebiotic Products on Decreasing Adiposity Parameters in Overweight and Obese Individuals: A Systematic Review and Meta- Analysis. Curr Med Chem. 2021;28(2):419–31. DOI: 10.2174/0929867327666191230110128. PMID: 31886746. Trusted SourcePubMedGo to source
Beserra BTS, Fernandes R, do Rosario VA, Mocellin MC, Kuntz MGF, Trindade EBSM. A systematic review and meta-analysis of the prebiotics and synbiotics effects on glycaemia, insulin concentrations and lipid parameters in adult patients with overweight or obesity. Clin Nutr. 2015 Oct;34(5):845–58. DOI: 10.1016/j.clnu.2014.10.004. PMID: 25456608. Trusted SourcePubMedGo to source
Stachowska E, Portincasa P, Jamioł-Milc D, Maciejewska-Markiewicz D, Skonieczna-Żydecka K. The Relationship between Prebiotic Supplementation and Anthropometric and Biochemical Parameters in Patients with NAFLD-A Systematic Review and Meta-Analysis of Randomized Controlled Trials. Nutrients. 2020 Nov 11;12(11). DOI: 10.3390/nu12113460. PMID: 33187278. PMCID: PMC7698299. Trusted SourcePubMedGo to source
Berding K, Long-Smith CM, Carbia C, Bastiaanssen TFS, van de Wouw M, Wiley N, et al. A specific dietary fibre supplementation improves cognitive performance-an exploratory randomised, placebo-controlled, crossover study. Psychopharmacology (Berl). 2021 Jan;238(1):149–63. DOI: 10.1007/s00213-020-05665-y. PMID: 32951067. Trusted SourcePubMedGo to source
Marx W, Scholey A, Firth J, D’Cunha NM, Lane M, Hockey M, et al. Prebiotics, probiotics, fermented foods and cognitive outcomes: A meta-analysis of randomized controlled trials. Neurosci Biobehav Rev. 2020 Nov;118:472–84. DOI: 10.1016/j.neubiorev.2020.07.036. PMID: 32860802. Trusted SourcePubMedGo to source
Capitão LP, Baião R, Baek HK, Kappelmann N, Sharman R, Harvey C-J, et al. Prebiotic supplementation does not affect reading and cognitive performance in children: A randomised placebo-controlled study. J Psychopharmacol (Oxford). 2020 Jan;34(1):148–52. DOI: 10.1177/0269881119862534. PMID: 31342840. Trusted SourcePubMedGo to source
Dang D, Zhou W, Lun ZJ, Mu X, Wang DX, Wu H. Meta-analysis of probiotics and/or prebiotics for the prevention of eczema. J Int Med Res. 2013 Oct;41(5):1426–36. DOI: 10.1177/0300060513493692. PMID: 23908398. Trusted SourcePubMedGo to source
Ford AC, Harris LA, Lacy BE, Quigley EMM, Moayyedi P. Systematic review with meta-analysis: the efficacy of prebiotics, probiotics, synbiotics and antibiotics in irritable bowel syndrome. Aliment Pharmacol Ther. 2018 Nov;48(10):1044–60. DOI: 10.1111/apt.15001. PMID: 30294792. Trusted SourcePubMedGo to source
Ooi SL, Correa D, Pak SC. Probiotics, prebiotics, and low FODMAP diet for irritable bowel syndrome – What is the current evidence? Complement Ther Med. 2019 Apr;43:73–80. DOI: 10.1016/j.ctim.2019.01.010. PMID: 30935559. Trusted SourcePubMedGo to source
Asha MZ, Khalil SFH. Efficacy and Safety of Probiotics, Prebiotics and Synbiotics in the Treatment of Irritable Bowel Syndrome: A systematic review and meta-analysis. Sultan Qaboos Univ Med J. 2020 Feb;20(1):e13–24. DOI: 10.18295/squmj.2020.20.01.003. PMID: 32190365. PMCID: PMC7065695. Trusted SourcePubMedGo to source
Scott KP, Gratz SW, Sheridan PO, Flint HJ, Duncan SH. The influence of diet on the gut microbiota. Pharmacol Res. 2013 Mar;69(1):52–60. DOI: 10.1016/j.phrs.2012.10.020. PMID: 23147033. Trusted SourcePubMedGo to source
Hustoft TN, Hausken T, Ystad SO, Valeur J, Brokstad K, Hatlebakk JG, et al. Effects of varying dietary content of fermentable short-chain carbohydrates on symptoms, fecal microenvironment, and cytokine profiles in patients with irritable bowel syndrome. Neurogastroenterol Motil. 2017 Apr;29(4). DOI: 10.1111/nmo.12969. PMID: 27747984. Trusted SourcePubMedGo to source
Huaman J-W, Mego M, Manichanh C, Cañellas N, Cañueto D, Segurola H, et al. Effects of prebiotics vs a diet low in fodmaps in patients with functional gut disorders. Gastroenterology. 2018 Oct;155(4):1004–7. DOI: 10.1053/j.gastro.2018.06.045. PMID: 29964041. Trusted SourcePubMedGo to source
Wilson B, Whelan K. Prebiotic inulin-type fructans and galacto-oligosaccharides: definition, specificity, function, and application in gastrointestinal disorders. J Gastroenterol Hepatol. 2017 Mar;32 Suppl 1:64–8. DOI: 10.1111/jgh.13700. PMID: 28244671. Trusted SourcePubMedGo to source
Whelan K. Mechanisms and effectiveness of prebiotics in modifying the gastrointestinal microbiota for the management of digestive disorders. Proc Nutr Soc. 2013 Aug;72(3):288–98. DOI: 10.1017/S0029665113001262. PMID: 23680358. Trusted SourcePubMedGo to source
Lockyer S, Stanner S. Prebiotics – an added benefit of some fibre types. Nutr Bull. 2019 Mar;44(1):74–91. DOI: 10.1111/nbu.12366.
Krogsgaard LR, Lyngesen M, Bytzer P. Systematic review: quality of trials on the symptomatic effects of the low FODMAP diet for irritable bowel syndrome. Aliment Pharmacol Ther. 2017 Jun;45(12):1506–13. DOI: 10.1111/apt.14065. PMID: 28440580. Trusted SourcePubMedGo to source
Toribio-Mateas M. Harnessing the power of microbiome assessment tools as part of neuroprotective nutrition and lifestyle medicine interventions. Microorganisms. 2018 Apr 25;6(2). DOI: 10.3390/microorganisms6020035. PMID: 29693607. PMCID: PMC6027349. Trusted SourcePubMedGo to source
Stenman LK, Lehtinen MJ, Meland N, Christensen JE, Yeung N, Saarinen MT, et al. Probiotic With or Without Fiber Controls Body Fat Mass, Associated With Serum Zonulin, in Overweight and Obese Adults-Randomized Controlled Trial. EBioMedicine. 2016 Nov;13:190–200. DOI: 10.1016/j.ebiom.2016.10.036. PMID: 27810310. PMCID: PMC5264483. Trusted SourcePubMedGo to source
Leblhuber F, Steiner K, Schuetz B, Fuchs D, Gostner JM. Probiotic Supplementation in Patients with Alzheimer’s Dementia – An Explorative Intervention Study. Curr Alzheimer Res. 2018;15(12):1106–13. DOI: 10.2174/1389200219666180813144834. PMID: 30101706. PMCID: PMC6340155. Trusted SourcePubMedGo to source
Mujagic Z, de Vos P, Boekschoten MV, Govers C, Pieters H-JHM, de Wit NJW, et al. The effects of Lactobacillus plantarum on small intestinal barrier function and mucosal gene transcription; a randomized double-blind placebo controlled trial. Sci Rep. 2017 Jan 3;7:40128. DOI: 10.1038/srep40128. PMID: 28045137. PMCID: PMC5206730. Trusted SourcePubMedGo to source
Sindhu KNC, Sowmyanarayanan TV, Paul A, Babji S, Ajjampur SSR, Priyadarshini S, et al. Immune response and intestinal permeability in children with acute gastroenteritis treated with Lactobacillus rhamnosus GG: a randomized, double-blind, placebo-controlled trial. Clin Infect Dis. 2014 Apr;58(8):1107–15. DOI: 10.1093/cid/ciu065. PMID: 24501384. PMCID: PMC3967829. Trusted SourcePubMedGo to source
Lamprecht M, Bogner S, Schippinger G, Steinbauer K, Fankhauser F, Hallstroem S, et al. Probiotic supplementation affects markers of intestinal barrier, oxidation, and inflammation in trained men; a randomized, double-blinded, placebo-controlled trial. J Int Soc Sports Nutr. 2012 Sep 20;9(1):45. DOI: 10.1186/1550-2783-9-45. PMID: 22992437. PMCID: PMC3465223. Trusted SourcePubMedGo to source
Zhong C, Qu C, Wang B, Liang S, Zeng B. Probiotics for Preventing and Treating Small Intestinal Bacterial Overgrowth: A Meta-Analysis and Systematic Review of Current Evidence. J Clin Gastroenterol. 2017 Apr;51(4):300–11. DOI: 10.1097/MCG.0000000000000814. PMID: 28267052. Trusted SourcePubMedGo to source
Hedin C, Whelan K, Lindsay JO. Evidence for the use of probiotics and prebiotics in inflammatory bowel disease: a review of clinical trials. Proc Nutr Soc. 2007 Aug;66(3):307–15. DOI: 10.1017/S0029665107005563. PMID: 17637082. Trusted SourcePubMedGo to source
Yuan F, Ni H, Asche CV, Kim M, Walayat S, Ren J. Efficacy of Bifidobacterium infantis 35624 in patients with irritable bowel syndrome: a meta-analysis. Curr Med Res Opin. 2017 Jul;33(7):1191–7. DOI: 10.1080/03007995.2017.1292230. PMID: 28166427. Trusted SourcePubMedGo to source
Tiequn B, Guanqun C, Shuo Z. Therapeutic effects of Lactobacillus in treating irritable bowel syndrome: a meta-analysis. Intern Med. 2015;54(3):243–9. DOI: 10.2169/internalmedicine.54.2710. PMID: 25748731. Trusted SourcePubMedGo to source
McFarland LV, Dublin S. Meta-analysis of probiotics for the treatment of irritable bowel syndrome. World J Gastroenterol. 2008 May 7;14(17):2650–61. DOI: 10.3748/wjg.14.2650. PMID: 18461650. PMCID: PMC2709042. Trusted SourcePubMedGo to source
Hoveyda N, Heneghan C, Mahtani KR, Perera R, Roberts N, Glasziou P. A systematic review and meta-analysis: probiotics in the treatment of irritable bowel syndrome. BMC Gastroenterol. 2009 Feb 16;9:15. DOI: 10.1186/1471-230X-9-15. PMID: 19220890. PMCID: PMC2656520. Trusted SourcePubMedGo to source
I care about answering your questions and sharing my knowledge with you. Leave a comment or connect with me on social media asking any health question you may have and I just might incorporate it into our next listener questions podcast episode just for you!
Transform your health
Every product is science-based, validated by real-world use, and personally vetted by Dr. Ruscio, DNM, DC.