Enhancing the Microbiome Through Diet, Sleep, and Exercise

David A. Johnson, MD


March 16, 2016

Additional Lifestyle Factors


Similar to other organ systems, the gastrointestinal tract operates on a 24-hour circadian schedule that anticipates and prepares for changes in the physical environment associated with day and night. These circadian rhythms regulate a number of gastrointestinal functions, ranging from gastric acid production to small intestinal nutrient absorption to colonic motility. These rhythms are also strong regulators of immunologic processes and the gut microbiome (abundance, speciation, and function), which fluctuates in accordance with their influence. This occurs via bidirectional communication between the central nervous system and an immune system and is mediated by shared signals (neurotransmitters, hormones, and cytokines [the brain-gut axis]) and direct innervations of the immune system by the autonomic nervous system.

Prolonged sleep curtailment and the accompanying stress response invoke a persistent unspecific production of proinflammatory cytokines, which results in a low-grade chronic inflammatory state. Epidemiologic studies have established the best amount of sleep to target as approximately 7 hours. This is the range that best correlates with lower prevalence of cardiovascular disease.

Recent attention has also focused on the sleep disruption-related upregulation of provocative cytokines, such as tumor necrosis factor alpha in patients with inflammatory bowel disease, which can increase the risk of inducing a disease flare or perpetuating disease activity.[3]


There has long been a connection between exercise and gut symptomatology. Exercise and fitness modulate vagal tone, which is an integral component of the brain-gut microbiome axis. With exercise contraction of skeletal muscle, there is an innate immunity enhancement created by the release of muscle-related anti-inflammatory cytokines or myokines. Additionally, there is an associated reduction of toll-like receptors (involved in many inflammatory and cancer pathways) on monocytes and macrophages. Exercise and the gut microbiome share many immunometabolic and physiologic processes that are well established in cardiovascular health and other areas beyond the gut.

Although there is an intuitive role for exercise in the prevention and treatment of gastrointestinal conditions such as irritable bowel syndrome, nonalcoholic fatty liver disease, and obesity, among others, the recommendation to include exercise and fitness is not yet standard for specific disease state management.

As the microbiota has an established role in the development and homeostasis of the gastrointestinal tract, the potential impact of exercise and fitness on the gut microbiota has attracted recent attention. However, more research is required to quantify the anti-inflammatory and metabolic effects of moderate exercise and to weigh these against the potential hazards of excessive exercise.[4]


The effects of prebiotics, probiotics, and even antibiotics on the gut microbiome will continue to remain a mainstay of investigation and will hopefully advance our knowledge of the intricacies of the gut microbiome while improving clinical outcomes. Supplemental focus on exercise and sleep function will likely have an added beneficial effect. My prediction is that enhancing our disease management protocols will require us soon to all be in the "gut microbiome business." This will likely be directed toward "dysbiosis" management using multiple approaches, often in combination.

Exciting work from the Weizmann Institute in Israel highlights the need to develop new nutritional strategies tailored to the individual patient, whereby unique diet and exercise protocols are used to correct the microbiome.[5] In taking such an approach, we may no longer rely on empiricism or published clinical trial data but instead more accurately address each patient's needs in order to restore microbiome balance.


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