How Sleep and Gut Microbes Team Up to Create Health or Disease

Increasingly, research is revealing a sleep-gut-brain triangle that offers easy ways to improve health.

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The mechanisms of sleep remain somewhat of a mystery. We do know, however, that sleep is the key to growth, development, and the process of removing toxins from our brains.

Yet good sleep doesn’t come easily to everyone. For a variety of reasons, falling and staying asleep night after night can be difficult for some adults and children.

Research into the gut microbiome may offer insight as to why. Sleep and the gut microbiome—bacteria, fungi, and other microorganisms in the colon—are linked in a bi-directional cause-and-effect relationship. Having healthy gut microbes can help us rest more deeply and longer, while an unhealthy microbiome is associated with poor sleep.

The sleep-gut link means a variety of health woes could be tackled from either side. This could be particularly important for colicky babies with trouble adopting better sleep habits or anyone who needs a fresh take on improving sleep.

Valuable Microbes

Our gut microbiome begins to form from microbes passed along to us from our mothers. Babies are coated with bacteria and other microbes through vaginal delivery. Breastfeeding is also beneficial for infant microbiome development.

Moms can also expose babies to pathogens or an imbalance of good-to-bad bugs. Babies might also have microbiome deficiencies. Two common causes of deficiencies are cesarean delivery and early antibiotic exposure.

A study of 162 healthy infants published in Progress in Neurobiology confirmed the existence of a sleep-gut link and that it is involved with a baby’s motor and personal-social development. The timing of when a baby first rolls over, crawls, walks, smiles, recognizes faces, and copies behavior is all affected by the link between sleep and gut microbes. In other words, poor sleep perturbs the gut microbiome, thus raising the risk of developmental delays.

“The most significant associations between sleep habits, gut microbiota, and behavioral outcomes were found at 3 months of age, potentially identifying an early sensitive period for later functionality of sleep rhythm and gut microbial balance,” the authors wrote, noting that helping renormalize gut microbes or sleep patterns could help prevent developmental delays and disorders.

“As many adult diseases root in early childhood, leveraging protective factors of adequate sleep and age-appropriate gut microbiota in infancy could constitute a health-promoting factor across the entire human lifespan,” they wrote.

Early Bedtime Begets Better Gut Health

Children with better sleep patterns enjoy better overall well-being, though other healthy activities can help facilitate better sleep schedules, according to experts.

Children with a consistent sleep schedule, particularly with an early bedtime, tended to have healthier gut flora in a study published in Nature in October. The study examined the gut flora of 88 children, along with sleep diaries kept by parents.

Those who went to bed before 9:30 p.m. had significant differences in gut bacteria species, including more diverse and beneficial microbes that have been correlated with health. One such bacterium, Akkermansia muciniphila (A. muciniphila), had an indirect role in helping the body remove damaged cells and improve cognition.

A. muciniphila may also boost immunity and improve symptoms associated with obesity, diabetes, inflammatory bowel disease, cancer, and neuropsychiatric conditions. These conditions can make sleep even more challenging.

Overall, 57 percent of children between the ages of 3 and 17 aren’t going to sleep at a consistent bedtime, according to data collected by the National Survey of Children’s Health. Racial and ethnic minorities are particularly affected.

Childhood sleep problems can be addressed with nutrition, exercise, acupressure, and cognitive-behavioral therapy, according to the authors of the Nature study. They said they hope their insight can lead to new drugs for kids with sleep disorders.

Nervous System Role

Children who go to sleep early also tend to have better-regulated autonomic nervous systems, which are associated with a healthier microbiome, Dr. Armen Nikogosian, internist and functional medicine specialist, told The Epoch Times.

Our autonomic nervous system keeps our bodies humming even during sleep, regulating bodily processes such as heart rate, blood pressure, breathing, and digestion. Autonomic nervous system disorders can be caused by bacteria, viruses, medications, underlying diseases, and genetics.

The autonomic nervous system has two components: the sympathetic division, which prepares the body to face stressful emergencies, and the parasympathetic division, which restores homeostasis with a resting heart rate and slower breathing. Our nervous system should mainly operate in the parasympathetic.

“It makes total sense to me,” Nikogosian said of the sleep-gut link. He added that a child or adult with better parasympathetic tone would have “calmer, more focused, more restful sleep.”

He said, “I could see those sorts of patients going to bed earlier.”

Balancing the Gut

It can be a bit tricky, however, to contend with fussy babies who can’t seem to fall asleep. This was the case with Cheryl Sew Hoy’s firstborn, who also struggled with a number of conditions.

“The first sign was sleep issues. She was never able to nap more than 30 minutes,” Sew Hoy told The Epoch Times. “She was also very colicky, cried a lot, and then at 6 months when she started eating solids, she got eczema.”

Common in infants, eczema often appears as dry, bumpy, itchy patches of skin and can be linked to allergies. Sew Hoy’s daughter went on to have a sesame allergy and eventually developed gluten and dairy intolerances.

She thought these issues were likely connected to her daughter’s gut microbiome. When Sew Hoy found out her baby was in a breech position and might need to be delivered by C-section, she spent hours studying the effect it might have.

Surgically born babies don’t receive as many beneficial bacteria, including Bifidobacterium and Bacteroides, as vaginally born infants. That can make C-section babies more vulnerable to disease, according to research.

However, it was a few years before Sew Hoy discovered she could test her daughter’s stool to see what microbes she was missing. Restoring those improved her allergies.

An award-winning entrepreneur, Sew Hoy went on to launch Tiny Health, a business aimed at boosting a child’s microbial health in the first 1,000 days. The company offers gut and vaginal microbiome testing, which can ensure women are passing along the right microbes to their babies, along with coaching to correct any imbalances in moms and children.

Tiny Health has worked with more than 30,000 families since 2022. Company (not peer-reviewed) data show that about 30 percent of babies born vaginally have a microbiome signature that is comparable to that of a C-section baby, Sew Hoy said.

Addressing Sleep Habits

Addressing sleep habits early in life can also be beneficial. Dr. Sally Ibrahim, sleep specialist and associate professor at Case Western Reserve University School of Medicine, told The Epoch Times that more children are showing up in her office.

Often, sleep isn’t the only problem kids are facing. Many of her young patients have been diagnosed with autism, attention deficit hyperactivity disorder, or mood disorders.

“Into adulthood they continue to have trouble with sleep disturbances of all sorts,” she said.

There are practices, Ibrahim said, that can help foster better sleep:

• Keep a Sleep Diary: Take notes about your sleep, including what time you go to bed, any issues you have falling asleep, and what times you wake up. Look for trends that might indicate a better time to go to bed or circumstances that reveal when you are more likely to have problems or get a better night of rest. Parents can also keep a diary for their children.
• Examine Your Diet: Avoid eating right before bed, and consider giving up caffeine as a family. Caffeine can cause nighttime restlessness.
• Adopt a Bedtime Routine: A “short and sweet” routine cues the body for bedtime—something essential for children and adults alike. Include teeth hygiene, dressing in pajamas, a book, and dim light, and be consistent.
• Cultivate Better Screen Habits: Turn off all screens at least an hour before bed, and don’t take them into the bedroom. That said, Ibrahim acknowledged that such a drastic move could mean “having a war on your hands” for some parents. A good compromise might be to use screens strictly for an app that is calming, passive, or even sleep-related.

“If nothing else, regularity is super key,” she said. “Parents will say, ‘I just let everything go on the weekend.’ You can’t do that. If you really want to help with sleep problems, you have to be consistent about it—even on the weekends. It’s so important.”