Can Prebiotic Supplements Boost Your Gut Health?

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Can Prebiotic Supplements Boost Your Gut Health?

How to Decide if Prebiotic Supplements Are Right for You 

Key Takeaways:

  • Prebiotics are specific dietary fibers that feed your gut bacteria.
  • Prebiotic supplements have some documented health benefits, including improved colon function and metabolic health.
  • However, consuming too many prebiotics can exacerbate gut symptoms in people with IBS and other sensitive gut conditions.
  • You’ll need to find your own tolerance level for prebiotic supplements and introduce them in the later stages of a gut healing program.

Prebiotics can be easily confused with probiotics. But though they are both involved in promoting a healthy microbiome they act in quite different ways. 

When you take probiotics you are consuming healthy bacteria such as Lactobacillus acidophilus or Bifidobacteria species directly. However when you take prebiotic supplements you are providing food to help pre-existing gut microorganisms to grow. 

Prebiotic supplements can be of help for gut health but need more careful evaluation as their effects can be more variable. For example, for those with SIBO, IBS, or other gut imbalances, prebiotics may actually exacerbate symptoms. In this article we’ll help you to decide whether they are right for you. 

What Are Prebiotic Supplements?

There’s not a total consensus on the definition of a prebiotic but the International Scientific Association of Probiotics and Prebiotics (ISAPP) states that it is:

“A substrate [nutrient source] that is selectively utilized by host microorganisms conferring a health benefit”. 

Prebiotics belong to a specific family of carbohydrates that are indigestible by digestive enzymes but fermentable by gut bacteria in the digestive tract. They also count as soluble fiber in your diet, and you will often see them referred to as prebiotic fibers too. 

Prebiotic powders or prebiotic supplements will usually include one of the following prebiotic fibers:

  • Fructo-oligosaccharides or FOS (oligofructose): Made of glucose and a string of 10-20 fructose molecules
  • Inulin: The “big brother” of FOS, comprising glucose and a chain of 20–100 fructose molecules
  • Galacto-oligosaccharides: Made of glucose and a chain of galactose molecules (galactose is another natural sugar)
  • Resistant starch: Starch that is chemically resistant to digestion

Despite their chemical-sounding, tongue-twister names, all of the above prebiotic fibers occur naturally in healthy foods [1]. For example onions, leeks, garlic, under ripe bananas, Jerusalem artichokes, wheat, asparagus, soybeans, and oats are all sources. 

Prebiotic supplements include higher levels of prebiotics than you will generally get from diet. Dried chicory root is the source of most of the inulin or FOS that you see listed on prebiotic supplements. 

How Can Prebiotics Help Health?

When friendly probiotic bacteria ferment prebiotics, they produce short-chain fatty acids (SCFAs) as a by-product. Some of the general and digestive health benefits of SCFAs are thought to include:

  • Reducing inflammation [2]
  • Improving the health of the lining and immune system of the gut [2]
  • Facilitating the microbiota gut-brain “crosstalk” that affects your response to anxiety and stress [3]

However, this is only what we know about the mechanistic actions of prebiotics, and the exact outcomes you might get from taking prebiotic supplements aren’t clear. The effect will likely vary based on the type and dosage of the prebiotic supplement you take and the composition of your own gut flora when you start taking them.

The Science of Prebiotic Supplements

Though prebiotics aren’t as well researched as probiotics yet, there are an increasing number of studies to go on. Here is what the science indicates prebiotics can and can’t do to improve health in various situations:

Gut Health

 Prebiotic EffectivenessResearch Overview
Poor motility and constipationGoodA meta-analysis of randomized clinical trials (high standard of evidence) found that inulin supplements improve stool frequency, consistency, and transit time in people with chronic constipation [4]. Prebiotic resistant starch also increased stool bulk in healthy individuals [5].
Irritable bowel syndrome (IBS)PoorA collection of systematic reviews/ meta-analyses (SRs/MAs) have found little to no evidence that prebiotics are a beneficial treatment for IBS [6, 7, 8].
Inflammatory bowel diseaseUncertainA 2019 SR/MA of 18 randomized clinical trials (RCTs) involving ulcerative colitis patients found the evidence for using prebiotics to treat ulcerative colitis was insufficient to make any conclusions [9].

Mental Health

 Prebiotic EffectivenessResearch Overview
Cognitive functionMixedAlthough one small study found evidence of improved cognitive flexibility and sustained attention after taking prebiotics [10], a larger SR/MA and an RCT found evidence that prebiotics don’t significantly benefit cognition in adults or children [11, 12].
Mood disordersUncertainOne RCT found that inulin intake was helpful at improving mood in some obese subjects, though strength of response was dependent on the individual’s gut microbiome makeup at the beginning of the study [13].

Metabolic Health and Weight Management

 Prebiotic EffectivenessResearch Overview
Metabolic healthGoodThere’s good evidence that prebiotics can , help reduce blood triglycerides (linked with heart disease), increase HDL (good) cholesterol, improve fasting insulin and reduce insulin resistance  [14, 15].
Weight lossMixedA 2021 SR/MA of 12 RCTs found that, compared to placebo, prebiotics reduced inflammatory markers, but they did not reduce body mass index (BMI), body weight, or fat mass [16]. However an earlier SR/MA did indicate modest benefit for BMI [14]. Prebiotics may also increase the feeling of fullness [17] and reduce ghrelin (the so-called “hunger hormone”) in overweight or obese people [18].

Downsides of Prebiotic Supplements

Though prebiotic fiber supplements can have benefits, they also come with potential downsides. 

These can depend on your existing gut issues and the type or dosage of prebiotic supplements you use. 

The main issue is that most prebiotics are also FODMAPs — fermentable carbohydrates that can cause uncomfortable symptoms for people with IBS and SIBO (small intestinal bacterial overgrowth) [19].

A 2017 randomized controlled trial (RCT) involving people with IBS found that prebiotic supplementation correlated with increased beneficial bacteria. However, it also correlated with increased nausea, vomiting, headache, belching, and flatulence [20]. This is important to note, because while increasing beneficial gut bacteria sounds good, the way you actually feel is what really matters. 

A second problem is that prebiotic supplements, when used in large or inappropriate amounts, may feed gut bacteria in general, including possibly some bad bacteria, not just the good types [21]. A good analogy is to think of taking prebiotic supplements as putting fertilizer on a garden — some may be good but too much could harm the soil and cause weeds to grow.

In short, if the bacteria in your gut are overgrown or imbalanced, the benefits of prebiotics may be limited and your symptoms could actually be exacerbated. 

Clinical Takeaway 

Can Prebiotic Supplements Boost Your Gut Health? - Prebiotic%20Pros%20and%20Cons 16x9 Landscape L

So, what we know is that though prebiotics can definitely have benefits, they may also cause discomfort in some situations. 

Experience with many patients and their symptoms leads me to recommend avoiding prebiotic supplements at the start of your gut healing journey when your gut is still highly sensitive. This is especially the case for people with IBS or SIBO. 

After your symptoms have improved, it’s fine to carefully introduce prebiotic supplements. If the time is right for your microbiome to accept and benefit from prebiotics, any side effects should be minor and short-lived.

For example, one study found prebiotics caused a 7-10 day flare of symptoms for some people before the benefits kicked in [22].

Getting Your Dosage Right

Can Prebiotic Supplements Boost Your Gut Health? - Find%20Balance%20with%20Prebiotics Landscape L

In order to achieve benefits and avoid side effects, a modest dosage of prebiotics is generally best. Around 3-5 grams per day is useful [23], but going over that dose may lead to more side effects.

Improving Your Gut Health With Diet 

Rather than jumping straight to prebiotics to try and improve your microbiome, the better and more fundamental place to start is with diet.  

Any improvement in your diet that involves cutting down on highly processed foods, and introducing more whole foods, such as lean protein, whole grain, and lots of vegetables will start nudging your health in the right direction.

But when your gut is especially sensitive, you’ll need to pay particular attention to finding the ideal balance of carbohydrates and prebiotics that works for you (this is one of the four pillars of a gut-healthy diet, below):

Four Principles of a Healthy Diet infographic by Dr. Ruscio

Determining the right amount of carbohydrates and prebiotics for you is such an important dietary principle because everyone’s individual tolerance level of prebiotics and fermentable carbohydrates is a bit different and can change over time. In the early stages, you may not only need to avoid prebiotic supplements but also go easy on food sources of fermentable carbs and prebiotic fibers.

Depending on your level of sensitivity, you may do well on a standard whole food / Mediterranean-style diet, or a paleo-style diet (veggies, lean protein, limited grains).

However a stricter low-FODMAP diet (very low from most fermentable carbs) could be the elimination diet for you if your IBS /SIBO symptoms are more troublesome. 


Below is a summary of common low FODMAP foods and high FODMAP foods (you can also find a list of handy FODMAP snacks here). Cutting out FODMAPs can be very effective at reducing IBS and SIBO symptoms.

FODMAP Food List infographic by Dr. Ruscio

Let’s say you’ve taken all known high FODMAP foods out of your diet for 2-3 weeks and your symptoms have improved. When you reintroduce these foods, do so one by one to test for reactions. You will probably be able to keep on eating some FODMAPs (up to your own personal tolerance level), while keeping the foods that you continue to have a problem with out of your diet for the longer term. 

Boosting Your Microbiome With Probiotics

Whereas prebiotics taken too early in your gut healing program might cause problems, research shows that probiotics (both food and supplements) are a safe and effective option, pretty much from the beginning.

Probiotic-rich foods you can try adding to your diet include kefir, kimchi, and sauerkraut. However, it’s also a good idea to use a multistrain probiotic supplement for faster symptom relief.  

Scientific studies show a wide variety of benefits from taking probiotics, including:

  • A more rapid recovery from imbalances in your gut microbiome [24]
  • A healthier immune function in your gut [25, 26]
  • Reduced gut inflammation [27]
  • Reduced incidence of leaky gut [28, 29, 30]
  • Benefits for SIBO, inflammatory bowel disease (IBD), and IBS [31, 32, 33, 34]

Once diet changes and probiotics have done their work to establish a healthier microbe balance in your gut you could then consider prebiotic supplements to maintain that healthy balance. 

Choosing a Prebiotic Supplement 

The FDA does not regulate prebiotic supplements (or any kind of supplement). If you decide to choose a prebiotic supplement, it’s therefore especially important to take the usual precautionary measures. These may include choosing a reputable brand with high-quality manufacturing processes and checking the ingredients and dosage are suitable for you. It’s a good sign if the product has been tested in independent clinical trials too.

Different prebiotics types and dosages can have different effects in different people, so it’s difficult to give concrete recommendations on what might work for you.


  • Some research suggests that galacto-oligosaccharides may be favorable for a sensitive gut, as they produce a beneficial effect at lower doses and may boost beneficial bifidobacteria more selectively.
  • Another study found a type of resistant starch prebiotic was less likely to produce noticeable bloating and gas because fermentation of this prebiotic took place further down the bowel.

In practice, though, these preliminary studies are difficult to interpret. Some trial and error will be needed to find the best type and dosage of prebiotic supplement for you and your own, highly individual, microbiome.

Piecing It All Together

Prebiotics can boost levels of existing good bacteria, benefiting gut health. But they may also come with increased symptoms, such as gas, bloating and diarrhea for those with sensitive digestive systems or gut imbalances.

Whether you will benefit from prebiotic supplements is very individual, and some trial and error might be needed to help find what is the best probiotic supplement (and dosage) for you. 

The best advice for most patients with gut health issues is to only introduce prebiotics after you have taken initial steps to improve your gut’s resilience with diet and probiotics. 

For a more comprehensive approach to ridding yourself of gut health issues check out my eight-step gut healing program in Healthy Gut, Healthy You. Or, for a personal health consultation, click here

➕ References
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