A Healthy Gut Can Help with Sleep

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Research has shown that keeping out gut microbiome healthy may be beneficial to our immune systems, waistlines, and risk for chronic disease. Our gut microbiome may even impact our sleep!

A new study from Japan, conducted on mice, included a control group and experimental group. The experimental group was given a concoction of antibiotics for 4 weeks that depleted their intestinal bacteria. Researchers evaluated the differences in intestinal contents between these mice and control mice. Both sets of mice ate the same diet.

Metabolites are bits and pieces of broken-down food from digestion. The metabolites of each group were compared. The researchers found over 200 metabolite differences between the mouse groups. Roughly 60 normal metabolites were gone in the microbiota-depleted animals. Some differed in the amount and some had more or less than the control mice. 

The researchers then investigated what the function of the metabolites was by using a metabolome set enrichment analysis. They discovered that the biological pathways most impacted by the antibiotic treatment were those needed to make neurotransmitters -- the compounds that brain cells use to communicate to each other. One example was the tryptophan-serotonin pathway. It was nearly completely shut down, giving the microbiota-depleted mice more tryptophan than the control group, but almost no serotonin. This indicates that without these gut microbes, the mice couldn’t make any serotonin from the tryptophan they ate. Scientists also discovered that the mice had vitamin B6 deficiencies, which would increase production of serotonin and dopamine. 

In addition, the research team evaluated how the mice slept by examining their brain activity in EEGs. They saw that, compared to control mice, those that were microbiota-depleted had more REM and non-REM sleep at night, when mice are normally active and less non-REM sleep in the daytime, when mice should normally be sleeping. The microbiota-depleted mice had sleep/wake cycles that were switched more frequently than the cycles of the control mice.

One of the scientists, Professor Yanagisawa, believes that the sleep abnormalities were the result of lack of serotonin, though the exact reason still needs to be evaluated. The team discovered that wiping out the gut microbiome eliminated gut serotonin and they recognize that serotonin levels in the brain can impact sleep/wake cycles. Yanagisawa states that “changing which microbes are in the gut by altering diet has the potential to help those who have trouble sleeping."

While more research is needed in this area, here are some tips for good gut health and sleep hygiene:

  • Limit use of antibiotics unless absolutely necessary.
  • Eat a variety of plant-based foods high in fiber including fruit, vegetables, whole grains, nuts, seeds, beans, and lentils.
  • Drink plenty of water to stay hydrated and keep bowels regular.
  • Limit processed sugar and high-fat foods, which may impact the gut microbiome.
  • Go easy on alcohol. It impacts the gut microbiome too.
  • Reduce caffeine intake to prevent insomnia. Avoid caffeine after 2 PM.
  • Step away from your screens (TV, phones, tablets) at least 3 hours before bed. Blue light from those screens keeps your brain awake.
  • Avoid long naps during the day as they may throw off your sleep cycle.
  • Establish a bedtime routine and go to bed around the same time each night.
  • Exercise regularly to tucker yourself out.

Lisa Andrews, MEd, RD, LD



  1. Yukino Ogawa, Chika Miyoshi, Nozomu Obana, Kaho Yajima, Noriko Hotta-Hirashima, Aya Ikkyu, Satomi Kanno, Tomoyoshi Soga, Shinji Fukuda, Masashi Yanagisawa. Gut microbiota depletion by chronic antibiotic treatment alters the sleep/wake architecture and sleep EEG power spectra in miceScientific Reports, 2020; 10 (1) DOI: 10.1038/s41598-020-76562-9
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