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Diet vs. prebiotics

In the second of a four-part CME series titled, "The Microbiome and Digestive Health: A Look at Prebiotics," Liping Zhao, PhD, and Yan Y. Lam, PhD, cover diet vs. prebiotics. This educational activity is supported by an educational grant from GlaxoSmithKline.


Liping Zhao, PhD

Eveleigh-Fenton Chair of Applied Microbiology and Professor, Department of Biochemistry and Microbiology

Rutgers, The State University of New Jersey

Yan Y. Lam, PhD

Assistant Research Professor, Department of Biochemistry and Microbiology

Rutgers, The State University of New Jersey

Prebiotics are “healthy foods,” which can selectively promote beneficial microbes in the human host. Many people tie this term to a group of widely used oligosaccharide products, e.g., inulin, fructo-oligosaccharides (FOS) and galacto-oligosaccharides (GOS). However, many of our everyday food are also rich sources of naturally occurring prebiotics. The history and definition of prebiotics was previously covered in part 1 of this series, “Prebiotics 101.”

1. Can dietary fibers be considered prebiotics?

Dietary fibers are a wide range of complex carbohydrates that are resistant to human digestion but can become energy sources for gut bacteria. When gut bacteria ferment dietary fibers, they release potentially beneficial bioactive compounds including short-chain fatty acids (SCFAs) and hydrogen gas. To the bacteria, these compounds are metabolic by-products, but to humans, they provide many important healthy functions. Molecular hydrogen can help scavenge hydroxyl radicals, thus serving an antioxidant function. SCFAs are signaling molecules that regulate gut homeostasis, energy metabolism and immune response. Thus, dietary fibers and SCFA-producing bacteria constitute one of the best studied examples of human-microbe symbiosis.

In a recent randomized controlled trial,1 patients with type 2 diabetes received either usual care or a large amount of diverse dietary fibers from whole grains, traditional Chinese medicinal foods and oligosaccharide prebiotic products. The high-fiber diet selectively promoted a group of bacteria that produce acetate and butyrate. When these bacteria became predominant, they produced SCFAs that stimulated the gut hormone-insulin secretion cascade to improve glucose regulation. They also suppressed the growth of many detrimental bacteria including those that produce indole, hydrogen sulfide and endotoxin, possibly by acidifying the gut environment, producing antimicrobials and exerting a competitive exclusion effect. Akin to tall trees in a closed forest, this select group of beneficial bacteria is the “foundation guild” for a healthy gut microbiota and keeps the pathogenic bacteria at bay. In this study, the dietary fibers behaved as prebiotics by selectively promoting beneficial bacteria that contributed a measurable benefit to host health.

2. Are all dietary fibers prebiotics?

Dietary fibers need to be fermentable to be considered prebiotics. Some dietary fibers, e.g., cellulose, are not fermentable by the human gut bacteria. Fibers in grains tend to be more fermentable as compared to those in vegetable and fruits. This may explain why only the intake of cereal fiber, not fibers from vegetables or fruits, has been associated with lower colorectal cancer-specific mortality after the cancer diagnosis.2

Whether dietary fibers can function as prebiotics may also differ from one individual to another. Depending on the carbohydrate-active enzymes that the gut bacteria encode, people with different gut microbiota compositions showed different fermentation pattern to the same dietary fiber.3 Interestingly, when an easy-to-ferment prebiotic is mixed with a hard-to-ferment fiber, the latter may become more readily fermentable possibly due to a cross-feeding effect.?4 More work is needed to understand how we may target SCFA producers with the right combination of prebiotics to promote our health in a personalized and precise way.

3. Are there any differences in effectiveness between prebiotics in food vs. manufactured prebiotics?

A major difference between prebiotics in food and those manufactured is the physicochemical structure, and therefore their fermentability as well as bioavailability in the different segments of the gut. Manufactured prebiotics can be easily fermentable by many gut bacteria and may exert adverse effects. For example, fermentation by gas-producing bacteria in the small intestine may lead to gastrointestinal symptoms like bloating, flatulence, diarrhea or abdominal pain. Prebiotics may be exploited by potentially harmful bacteria when administered to individuals with a disrupted gut microbial community with low diversity due to the lack of beneficial bacteria which can outcompete and suppress the pathogens.5 There is a need for further clinical studies to support the role of prebiotics, including naturally-occurring and manufactured prebiotics, in conditions associated with disrupted gut microbiota.

Prebiotics in foods, on the other hand, are much more complex in structure. Physically, they are embedded in the food matrix and interwoven with each other as well as with other components such as proteins. All these features make prebiotics in foods less accessible and may increase their specificity to the beneficial bacteria, as seen by only a select group of bacteria being promoted by the high-fiber diet in the example above.

Talking points to use with your patients

    • Dietary fibers are generally considered as prebiotics because many of them can promote the growth of a select group of beneficial gut bacteria. Akin to tall trees in a closed forest, this group of bacteria may structure a healthy gut microbiota and keep pathogens at bay.
    • Dietary fibers in grains are more fermentable and therefore may be more effective prebiotics than dietary fibers found in fruits and vegetables. However, fruits and vegetables have other potential health benefits beyond fiber and are important components of a balanced diet.
    • There is currently little clinical data to support the use of commercial prebiotics in the adult population, but ongoing clinical studies will help shed light on their usefulness.
    • As we strive to develop the next generation of prebiotics, we need to consider the cross-feeding interactions among gut microbial members as well as attempt to mimic the complexity found in dietary sources.


1. Zhao, L., Zhang, F., Ding, X. et al, Gut bacteria selectively promoted by dietary fibers alleviate type 2 diabetes. Science. 2018;359(6380):1151-6.

2. Song, M., Wu, K., Meyerhardt, J.A. et al, Fiber Intake and Survival After Colorectal Cancer Diagnosis. JAMA Oncol. 2018;4(1):71-9.

3. Chen, T., Long, W., Zhang, C. et al, Fiber-utilizing capacity varies in Prevotella- versus Bacteroides-dominated gut microbiota. Sci Rep. 2017;7(1):2594.

4. Hamaker, B.R., Tuncil, Y.E. A perspective on the complexity of dietary fiber structures and their potential effect on the gut microbiota. J Mol Biol. 2014;426(23):3838-50.

5. Singh, V., Yeoh, B.S., Chassaing, B. et al, Dysregulated Microbial Fermentation of Soluble Fiber Induces Cholestatic Liver Cancer. Cell. 2018;175(3):679-94 e22.

CME Information

The AGA Institute is accredited by the Accreditation Council for Continuing Medical Education (ACCME) to provide continuing medical education for physicians. The AGA Institute designates this enduring activity for a maximum of 0.25 AMA PRA Category 1 Credits™.

Physicians should claim only the credit commensurate with the extent of their participation in the activity.

In accordance with the ACCME’s Standards for Commercial Support of Continuing Medical Education, all faculty and planning partners must disclose any financial relationship(s) or other relationship(s) held within the past 12 months. The AGA Institute implements a mechanism to identify and resolve all conflicts of interest prior to delivering the educational activity to learners.

To claim your CME credits for this activity, please visit AGA University.

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