Viruses, bacteria, fungi, and protozoa are the microorganisms that naturally live in the digestive tract. Sleep affects gut health and vice versa. A healthy gut microbiota consists of all kinds of microorganisms that produce thousands of compounds and coexist harmoniously. A healthy diet and lifestyle are the biggest factors influencing bacteria variety, and maintaining a varied diet preserves microbiota diversity. Everybody’s gut microbiome is different; the more diverse the gut microbiome, the healthier sleep will be. The Injury Medical Chiropractic and Functional Medicine Clinic Team can develop a personalized nutritional plan to improve gut health and sleep patterns.

Sleep Affects Gut Health: EP's Functional Chiropractic Clinic

Sleep Affects Gut Health

Not having a diverse gut microbiome has been linked to autoimmune diseases, Parkinson’s disease, and mental health issues like anxiety and depression. Not getting healthy sleep is associated with many diseases and disorders, including:

  • Gastrointestinal disorders
  • Infections
  • Diabetes
  • Cardiovascular disease
  • Neurological disorders
  • Anxiety
  • Depression
  • Cancer

Changes in sleep patterns influence the central nervous system and the immune system, which affect different organ systems. For example, studies have shown some gastrointestinal disorders, like irritable bowel syndrome – IBS could be associated with increased REM sleep or the fourth part of the sleep cycle when vivid dreaming occurs. In Crohn’s disease or ulcerative colitis, long-term immune response activation can result in poor sleep, insufficient quality sleep, or other sleep problems. The deepest stages of sleep are when the brain and gut communicate to repair the body, restore nutrients, and remove and release toxins.

Sleep Cycle

During sleep, the immune system produces proteins called cytokines that perform functions during the inflammatory response, either by increasing or blocking inflammation, depending on the body’s needs. Cytokines help promote sleep, fight infection, or stop inflammation in chronic inflammatory diseases like Crohn’s disease or ulcerative colitis.

  • Insufficient sleep significantly alters cytokine production, and infection-fighting cells decrease in numbers when sleep deprived, making it harder for the body to fight infections and lessening protection. This increases the inflammatory response and keeps the immune system on.
  • Chronic or long-term immune response activation can result in sleep disturbances or disorders.
  • Some disorders include small intestinal bacterial overgrowth and inflammation caused by microbiome abnormalities or dysbiosis.
  • The gut barrier function begins to malfunction, leading to bacteria and pathogens leaking into blood circulation/leaky gut, triggering immune responses.

Ways to Improve Sleep

One of the main ways to improve sleep quality and gut microbiome health is to practice healthy sleep hygiene. According to the National Sleep Foundation, individuals should:

Nap Smart

  • Naps can be a great way to refresh the mind and body and replenish energy levels during the day.
  • Naps don’t make up for little sleep at night.
  • Keep naps to 20-30 minutes for optimal benefits without disrupting nighttime sleep.

Optimal Sleep Environment

  • Comfortable ergonomic mattress and pillows.
  • Blackout curtains.
  • Temperature between 60 and 67 degrees.

Quit Electronics Before Bed

  • The bright lights from phones and screens can make it difficult to fall asleep fully.
  • Use an alarm clock with a soft night light and keep the bedroom tech-free.

Create Sleep Routine

  • Take a warm shower, read a book, or do light stretches.
  • Create a wind-down routine to relax before bed to signal the body that it’s time for sleep.

Avoid Caffeine and Alcohol Before Bed

  • These substances make it harder for the mind and body to fall or stay asleep.

Food As Medicine


Chabé, Magali et al. “Gut Protozoa: Friends or Foes of the Human Gut Microbiota?.” Trends in parasitology vol. 33,12 (2017): 925-934. doi:10.1016/

Deng, Feilong, et al. “The gut microbiome of healthy long-living people.” Aging vol. 11,2 (2019): 289-290. doi:10.18632/aging.101771

Gut Bacteria Research: Physicians’ Committee for Responsible Medicine. (2019). “Gut Bacteria: Optimize Gut Health With a Plant-Based Diet,”

Ianiro, Gianluca, et al. “How the gut parasitome affects human health.” Therapeutic advances in gastroenterology vol. 15 17562848221091524. 30 Apr. 2022, doi:10.1177/17562848221091524

Lozupone, Catherine A et al. “Diversity, stability and resilience of the human gut microbiota.” Nature vol. 489,7415 (2012): 220-30. doi:10.1038/nature11550

Sleep and Gut Microbiome Study: PLoS One. (2019). “Gut microbiome diversity is associated with sleep physiology in humans.

Sleep Hygiene Information: National Sleep Foundation. (2019). “Sleep Hygiene.”

Vaishnavi, C. “Translocation of gut flora and its role in sepsis.” Indian journal of medical microbiology vol. 31,4 (2013): 334-42. doi:10.4103/0255-0857.118870


Professional Scope of Practice *

The information herein on "Sleep Affects Gut Health: EP Health Coach Clinic" is not intended to replace a one-on-one relationship with a qualified health care professional or licensed physician and is not medical advice. We encourage you to make healthcare decisions based on your research and partnership with a qualified healthcare professional.

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Our information scope is limited to Chiropractic, musculoskeletal, physical medicines, wellness, contributing etiological viscerosomatic disturbances within clinical presentations, associated somatovisceral reflex clinical dynamics, subluxation complexes, sensitive health issues, and/or functional medicine articles, topics, and discussions.

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Dr. Alex Jimenez DC, MSACP, RN*, CCST, IFMCP*, CIFM*, ATN*


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