Enhancing the Microbiome Through Diet, Sleep, and Exercise

David A. Johnson, MD


March 16, 2016

Strategies for Altering the Microbiome

The gut microbiome, a dynamic feature of the gastrointestinal system, has the potential to dramatically influence health outcomes. Through complex interactions with the host immune system and signaling pathways, the gut microbiome can significantly influence the pathogenesis of disease states such as cancer, metabolic syndrome, inflammatory bowel disease, and nonalcoholic fatty liver disease.

Recent technological advances have vastly improved not only our understanding of the gut microbiome but also potential mechanisms through which we may confer health benefits by altering it. As what one eats partially determines the gut flora, there are very likely significant dietary effects on the gut microbiome and a likely interaction across a broad spectrum of systemic diseases. Furthermore, emerging data on factors such as sleep and exercise underline their potential role in affecting the microbiome. This review summarizes our current understanding of how microbiome health may be affected by these lifestyle factors.

Dietary Considerations

A wide range of dietary carbohydrates, including prebiotic food ingredients, fermentable fibers, and milk oligosaccharides, have been shown to produce significant changes in the intestinal microbiota. These shifts in the microbial community are often characterized by increased levels of bifidobacteria and lactobacilli. A more recent study revealed that species of Faecalibacterium, Akkermansia, and other less well studied members may also be enriched.[1]

Investigations of clinical outcomes associated with dietary modification of the gut microbiota have shown systemic as well as specific health benefits.[1] Both prebiotic oligosaccharides comprised of a linear arrangement of simple sugars as well as fiber-rich foods containing complex carbohydrates have been clinically studied with variable benefit. However, inconsistency of response across study participants can make the outcome of dietary interventions less predictable and limit the value of making specific recommendations to individual patients.


Nondigestible food ingredients, prebiotics can beneficially affect the host by selectively stimulating the growth and/or activity of one or more bacteria in the colon. They do so via selectively fermented ingredients that can change the composition and/or activity in the gastrointestinal microflora. In order for a food to be classified as a prebiotic, it must resist gastric acidity, hydrolysis by mammalian enzymes, and absorption in the upper gastrointestinal tract, so that it is able to be fermented by the gut microbiota into short-chain fatty acids (including acetate, propionate, and butyrate) that can be used for energy. Thus, prebiotics not only can cause shifts in the microbiota by supporting growth of a particular intestinal microbiome but also serve as substrates for production of biologically active metabolites. The primary prebiotics are the inulin-type fructans oligofructose and fructo-oligosaccharides, yet there are a number of others, including the galactan galacto-oligosaccharide. Fermentation of prebiotic carbohydrates yields butyrate and other short-chain fatty acids as well as other end products that lower the local pH, stimulate mucin production by colonocytes, and induce immunomodulatory cytokines, all of which may have potential disease modulation effects.

Prebiotic fibers are often natural constituents of a variety of foods, especially whole grains, fruits, root vegetables, and legumes. Although some foods contain appreciable concentrations of these prebiotics, they are probably found too infrequently in most Western diets to contribute much fermentable fiber to the colon. Prebiotic fiber products such as psyllium have been commonly used to supplement where needed. As a practical strategy, consumption of fermentable fiber or combinations of prebiotics may enrich for a larger and more diverse population of gut microbes and should be a standard recommendation for most disease states.


In order for a live micro-organism to be classified as a probiotic, it must satisfy the following criteria: (1) exert a beneficial effect on the host; (2) be nonpathogenic and nontoxic; (3) contain a large number of viable cells; (4) be capable of survival and metabolism within the gut; (5) remain viable during storage and use; (6) have good sensory properties; and (7) be isolated from the same species as the intended host.

Probiotics have long been used as therapeutic agents for improving gastrointestinal health. Although several microbial taxa or genera have been suggested as being beneficial to the host, there is still no actual definition of what constitutes a healthy gut microbiome to a specific patient. Most available information concerns Bifidobacterium and Lactobacillus spp; consequently, most commercially available products generally contain bacteria from one or both of these species.

Probiotics have been shown to provide a number of health benefits and can potentially be used to alter the gut microbiome and thereby treat certain gastrointestinal conditions. Within the gastrointestinal tract, probiotics play a number of functional roles, including maintaining the intestinal barrier integrity, regulating mucin secretion, controlling immunoglobulin A secretion, and producing antimicrobial peptides, which influence cytokine production. In clinical trials, probiotics have shown beneficial effects in nonalcoholic fatty liver disease and ulcerative colitis, but a favorable effect has not been consistently demonstrated to date. The combined physiologic and clinical data strongly support the continued research of probiotics as a potential therapy for manipulating the gut microbiome.

Artificial Sweeteners

Introduced over a century ago, artificial sweeteners were designed to enhance taste without the effects of caloric intake, theoretically benefiting health by weight reduction and enhanced glycemic control. These agents are commonly used in a broad array of foods, beverages, and candy designed for diabetics and those actively dieting. However, recent information shows that these formulations drive the development of glucose intolerance through induction of compositional and functional alterations to the intestinal microbiota, which in fact promote glucose intolerance.[2] These agents may therefore have directly contributed to enhancing the very obesity epidemic they were intended to combat.


Comments on Medscape are moderated and should be professional in tone and on topic. You must declare any conflicts of interest related to your comments and responses. Please see our Commenting Guide for further information. We reserve the right to remove posts at our sole discretion.