Prebiotics. Part 2: When Fermentable Substrates Aren’t Digested Properly

gastrointestinal_upsetIn the first part of the series of posts on prebiotics I made it clear that even though only some types of carbohydrates such as inulin, oligofructose and resistant starch are officially labeled as prebiotics, a lot of fermentable substrates found in vegetables, fruits and other whole foods actually work as prebiotics since they stimulate the growth and/or activity of bacteria in the digestive system in ways claimed to be beneficial to health. However, there are some health conditions that reduce the beneficial effects of these fermentable substrates. The most common disorders associated with adverse symptoms from the consumption of prebiotics are simplified/dysfunctional gut flora and/or Small Intestinal Bacterial Overgrowth.

Simplified/dysfunctional gut flora

Healthy gut flora consists of hundreds of different species of bacteria, and enzymes produced by dozens of different bacterial species in the colon break down fermentable substrates into energy we can use. Antibiotics, western diets, bottle-feeding and other factors promote a simplified gut flora with less bacterial diversity. A simplified gut flora is associated with partial digestion of fermentable substrates, and symptoms of food intolerance such as gas, bloating, and constipation. If new species of bacteria are introduced in the gut, adverse symptoms go away.

Example: Lactose intolerance
Lactose intolerance is one example where gut flora lack the necessary enzymes to digest lactose, and gastrointestinal symptoms occur following the consumption of dairy products with lactose. Ingesting probiotic bacteria with lactose digesting enzymes while at the same time consuming small amounts of lactose, will slowly alleviate symptoms of lactose intolerance as the new bacteria get a chance to grow in the gut and transfer their genes to the bacteria on the lining of the gut.

When gut flora have the necessary lactose digesting enzymes, lactose functions as a fermentable substrate.

Adaptation phase

While gastrointestinal symptoms such as gas, bloating, diarrhea and constipation following the consumption of fermentable substrates often indicate a simplified gut flora, it could also be that an adaptation phase is all that is needed to tolerate the foods in question without trouble. Even when the necessary bacteria and enzymes are present in the gut, it usually takes time for gut flora to adapt to increased intake of fermentable substrates.

For example when most people increase their intake of a prebiotic like Fructooligosaccharides (FOS), they experience intestinal gas and other unwanted gastrointestinal symptoms. FOS is primarily fermented by bifodobacteria in the colon, and when these bacteria slowly start growing from the increased intake of FOS; gastrointestinal symptoms should subside. This is also the reason why it’s recommended to start with a small dose of prebiotic supplements.

Small Intestinal Bacterial Overgrowth

In comparison to the large intestine, the small intestine contains relatively low amounts of microorganisms. In cases of Small Intestinal Bacterial Overgrowth (SIBO) abnormally large numbers of commensal bacteria are present in the small intestine. SIBO is characterized by elevated use of fermentable substrates in the small intestine, and this upper gut fermentation further increases the overall bacterial load in the small intestine. Bacterial fermentation in other parts of the digestive system than the colon is one of the reasons why patients with SIBO experience gastrointestinal discomfort and pain.

The specific carbohydrate diet and the low FODMAP diet

The main purpose of both the specific carbohydrate diet and the low FODMAP diet is to reduce the consumption of fermentable carbohydrates. Since we know that fermentable carbohydrates aren’t broken down properly in cases of simplified/dysfunctional gut flora and/or small intestinal bacterial overgrowth, it’s no surprise that “all” studies show that removing foods that contain these carbohydrates from the diet will reduce symptoms of Irritable bowel syndrome (IBS), SIBO, inflammatory bowel disease (IBD) etc. (1, 2, 3, 4)

In the next posts on prebiotics I’ll look into the optimal sources and intake of fermentable substrates, and whether removing fermentable carbohydrates from the diet is the right approach when treating gastrointestinal disorders such as SIBO, IBS and IBD…

All posts in the series on prebiotics

Part 1: What are prebiotics?
Part 2: When fermentable substrates aren’t digested properly
Part 3: Good health with no plant-based foods in the diet


  1. […] 1: What are prebiotics? Part 2: When fermentable substrates aren’t digested properly Part 3: Good health with no plant-based foods in the […]

  2. […] How following mainstream advice to eat 6-8 servings of vegetables a day could hurt your gut Vegetables (as well as some fruits) are often high in insoluble fiber. Vegetables that are high in insoluble fiber include: Another helpful tip is to reduce the variety of vegetables you eat at any given meal. Make them yourself. P.S. Prebiotics. Part 2: When Fermentable Substrates Aren’t Digested Properly. […]


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