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Are Prebiotic Foods Helpful or Harmful to Your Gut Flora?

Written by Dr. Ruscio on September 3, 2021

Written by Dr. Ruscio on September 3, 2021 — Reviewed by Aimee Gallo

Dr. Michael Ruscio is a DC, Naturopathic Practitioner, researcher, and clinician. He serves as an Adjunct Professor at the University of Bridgeport and has published numerous papers in scientific journals as well as the book Healthy Gut, Healthy You. He also founded the Ruscio Institute of Functional Health, where he helps patients with a wide range of GI conditions and serves as the Head of Research.

Your Guide to Prebiotic Foods and Supplements 

• About Prebiotic Foods|
• Prebiotics and Health|
• More Prebiotics Aren’t Better|
• Prebiotics From Diet|
• Probiotic Intake|
• Probiotics to Boost Gut Health|
• Recommended Products|

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. 

In turn, good bacteria produce short chain fatty acids (SCFAs) that can benefit gut health. For example, SCFAs have been linked with [1, 2, 3]:

• Preventing leaky gut
• Mucus production to maintain a healthy intestinal barrier
• Protection against inflammation 

Some prebiotics names you might come across include:

• Galacto-oligosaccharide (GOS)
• Fructo-oligosaccharide (FOS) 
• Inulin 
• Resistant starch

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
• Leeks
• Asparagus
• Broccoli
• Bananas 
• Jerusalem artichokes
• Chicory root
• Dandelion greens
• 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]. 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].
• 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].
• 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]. However, they did not appear to help with weight loss or weight management [8].
• Metabolic and cholesterol-lowering effects: Research reviews have found good evidence that prebiotics can [9, 10]:
  • 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:

• Cognitive function: Although one small study found evidence of improved cognitive flexibility and sustained attention after taking prebiotics [11], a larger SR/MA and an RCT found evidence that prebiotics don’t significantly benefit cognition in adults or children [12, 13].
• 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].
• Irritable bowel syndrome (IBS): A collection of SR/MAs have found little to no evidence that prebiotics are a beneficial treatment for IBS [15, 16, 17]. 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].

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 [19].

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].
• 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]:
  • 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].

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].

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].

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 [24].

(*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: 

• A whole food / Mediterranean-style diet (veggies, fruit, whole grains, lean proteins)
• A paleo-style diet (veggies, lean protein, limited grains)
• A low FODMAP diet (free from most fermentable carbs)

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]. 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:

• A more rapid recovery from imbalances in your gut microbiome [26]
• A healthier immune function in your gut [27, 28]
• Reduced gut inflammation [29]
• Reduced incidence of leaky gut [30, 31, 32]
• Benefits for SIBO, Crohn’s, ulcerative colitis, and IBS [33, 34, 35, 36, 37, 38]

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.

You can read more about my eight-step to heal your gut in my book Healthy Gut, Healthy You. Or, visit our clinic’s website to book a personal, in-person or telehealth consultation.