Problems Sleeping? Look to Your Gut

How the bacteria in your gut manipulate your sleep patterns.

Posted Jun 06, 2019

You and your microbes, still awake.
Source: patat/iStock

Your gut is linked to your brain in surprising ways, and you may be losing sleep over it. Research into the gut-brain axis reveals that, amazingly, microbes in your gut can affect your mood—and along with that, your sleep patterns. Sleep disorders and depression are common among people with gut problems like irritable bowel syndrome (IBS), Crohn's disease or ulcerative colitis. This association goes both ways: your gut can affect—or be affected by—your mood and sleep patterns.

The idea that your brain can affect your gut seems to imply that you could treat gut problems with psychiatry, which is nutty. Except that it seems to work. Research suggests that cognitive behavioral therapy, which is aimed at the mind, can ease symptoms of IBS—including sleeplessness.[1] What an unexpected way to treat gut problems! Problems with sleep, mood and gut turn out to be inextricably bound together.

Microbes can secrete dozens of human neuroactive chemicals, which gives them a disturbing amount of power over our brain. They can send messages slowly through the endocrine system, somewhat faster through the immune system, and at lightning speed through the vagus nerve. A well-balanced microbiota is a wonderfully silent partner, but a poorly balanced one will end up with a few dominant "bully" species that can make a lot of fuss.

These top dogs, without counterbalancing microbes, tend to act as disease-causing pathogens. When they don’t get what they want, they can release neurotoxins like ammonia that affect sleep, stress, and brain function in general.[2]

The Cycles of Life

All living things have chemical reactions that cycle over and over again. Some, like the Krebs cycle you vaguely remember from high school, are fast, converting glucose to energy at a madcap pace. Others, like the circadian cycle, take 24 hours. The name circadian means "about a day," and even bacteria display these leisurely daily oscillations.

It affects us from early on. Without circadian rhythms, we might just be blobs. Dr. Ann Kiessling of the Bedford Research Institute, which investigates stem cell therapies, says:

"Stem cells may especially need circadian signals to differentiate into specific cell types, such as neurons or bone marrow. The first evidence of circadian oscillator proteins is at the late 2-cell stage in mice, when at least 10% of stem cells are expressing circadian oscillator proteins, but not synchronized. Then as the cells differentiate, they start to synchronize. We don't know what triggers that, but differentiation and synchronization seem to be coupled."

Each cell in your body runs a tiny version of the circadian clock and needs to cooperate with all its neighbors, so it's important for them to continuously synch up. In animals, the brain controls this daily cycle with a sleepy-time chemical called melatonin, which builds up when it gets dark at night to make you sleepy and drops in the morning to wake you up.

This internal clock wants to synchronize with daylight, explaining why traveling across time zones, artificial lights, and cloudy climates all mess with your rhythms. When your body's rhythm is disrupted, your microbiota also gets disrupted, which can boost the numbers of poor team players like Candida at the expense of beneficial bacteria like Lactobacillus and Bifidobacteria.[3] That helps to explain why shift workers have higher rates of gut issues, sleep problems and depression.

You can mess up your daily rhythm by simply keeping your lights on in the evening. It's not a small effect: Evening light can delay the release of melatonin by up to two hours.

Rodent Studies

A study by Rob Knight and colleagues in 2017 looked at what stress does to sleep and gut health in rats. Rats that were stressed by tail shocks had disruptions in their sleep patterns. Their gut microbiota also changed: it lost diversity. A few species dominated their gut microbes, and that loss of balance was unhealthy. When they gave the rats a prebiotic, their gut microbiota became more diverse and contained more probiotic and psychobiotic species like Lactobacillus rhamnosus. They also slept better. They had better REM and non-REM sleep.[4]

A healthy microbiota produces butyrate, a short-chain fatty acid that is the preferred fuel for the cells lining the gut. That maintains the proper permeability to absorb nutrients and yet keep out microbes. Studies with both mice and rats show that butyrate improves sleep.[5]

You may not be getting tail shocks, but your boss may be kicking your butt all day. That, too, can mess up your sleep.

What Can You Do?

  • Don't eat late at night. It screws up your microbial circadian clocks, which are trying to wind down for the night. It can also encourage gastric reflux.
  • Eat more fiber. Fast foods are delicious, but most of them have sacrificed the fiber for the flavor. Fiber supports beneficial bacteria that produce healing and nurturing chemicals. Fibrous foods include artichokes, asparagus, onions, beans, leafy greens and most non-starchy veggies.
  • Try a prebiotic supplement. Although the supplement industry is poorly regulated, many prebiotics have been shown to work in human subjects. They have tongue-tangling names like fructo-oligosaccharide and galacto-oligosaccharide. Mercifully, these are typically shortened to acronyms like FOS and GOS.
  • Eat a wide variety of foods. A repetitive diet with just a few food groups will not help you maintain a diverse—ergo healthy—microbiota.
  • For dessert, try strawberries or cherries, which contain melatonin and may encourage drowsiness.
  • Adjust your lights. We keep them on until late at night, and it tricks your body into thinking it's still daylight. Blue light is especially potent for keeping you alert when you should be settling down for the night. In the morning, try to get as much sunshine as possible. That ensures your circadian clock gets started for the day and makes bedtime come earlier.
  • Stay young. As you age, your melatonin levels fall. Fortunately, you can buy melatonin supplements, which have been shown to help people over 55 to fall asleep faster and sleep longer. Take it about an hour before sleep. Melatonin also increases healthy diversity in your gut microbes.[6] It's a good idea to talk to your doctor if you are considering melatonin for long-term use.

Your microbiota responds to your own biological clock, and your own biological clock responds to your microbiota. Feedback loops like this are found throughout all of biology and they can be nasty. However, by improving your microbiota and synching it to normal cycles, you can start to sleep better. That, in turn, will further balance your microbiota, turning a vicious cycle into a virtuous one. Before you know it, you could be snoozing like a baby.


[1] Kinsinger, Sarah W. “Cognitive-Behavioral Therapy for Patients with Irritable Bowel Syndrome: Current Insights.” Psychology Research and Behavior Management 10 (July 19, 2017): 231–37.

[2] Galland, Leo. “The Gut Microbiome and the Brain.” Journal of Medicinal Food 17, no. 12 (December 1, 2014): 1261–72.

[3] Li, Yuanyuan, Yanli Hao, Fang Fan, and Bin Zhang. “The Role of Microbiome in Insomnia, Circadian Disturbance and Depression.” Frontiers in Psychiatry 9 (December 5, 2018).

[4] Thompson, Robert S., Rachel Roller, Agnieszka Mika, Benjamin N. Greenwood, Rob Knight, Maciej Chichlowski, Brian M. Berg, and Monika Fleshner. “Dietary Prebiotics and Bioactive Milk Fractions Improve NREM Sleep, Enhance REM Sleep Rebound and Attenuate the Stress-Induced Decrease in Diurnal Temperature and Gut Microbial Alpha Diversity.” Frontiers in Behavioral Neuroscience 10 (January 10, 2017).

[5] Szentirmai, Éva, Nicklaus S. Millican, Ashley R. Massie, and Levente Kapás. “Butyrate, a Metabolite of Intestinal Bacteria, Enhances Sleep.” Scientific Reports 9, no. 1 (May 7, 2019): 7035.

[6] Yin, Jie, Yuying Li, Hui Han, Shuai Chen, Jing Gao, Gang Liu, Xin Wu, et al. “Melatonin Reprogramming of Gut Microbiota Improves Lipid Dysmetabolism in High-Fat Diet-Fed Mice.” Journal of Pineal Research 65, no. 4 (November 2018): e12524.