Understanding Gut Health: The Connection between Gut and Brain

It’s no surprise that people experience more depression and anxiety when their inflammatory bowel disease (IBD) flares up. The gut and brain are in constant communication through the vagus nerve, immune system, and countless chemical messengers. When the gut is inflamed, that inflammation can spread systemically and reach the brain. The immune system in the gut (GALT) talks directly with brain immune cells (microglia), while the gut microbiome produces most of the body’s neurotransmitters—the same ones that regulate mood and focus. In Dr. Rachel’s practice, many clients notice their mental health symptoms worsen during IBD flares, or even with gut inflammation that doesn’t yet meet diagnostic criteria but is linked to dysbiosis. This is particularly concerning when considering that the circadian rhythm can also influence gut health and overall well-being. When the inflammation is resolved at the root, other issues often fade away too. Because 70% of the immune system sits in the gut, a leaky intestinal barrier allows bacterial fragments, food particles, and toxins like LPS to leak into the bloodstream—triggering immune activation throughout the body and brain. Mitochondrial dysfunction, metabolic imbalance, and environmental toxins all contribute to this process. That’s why Dr. Rachel takes a root-cause approach, repairing the gut lining, restoring mitochondrial health, and rebalancing the microbiome—to help the body heal from the inside out.

You’ve been told that gut health primarily revolves around probiotics and fiber. You’ve been led to believe that digestion hinges solely on your diet (or perhaps that diet doesn't matter at all). You’ve also been informed that constipation and IBS are merely “functional disorders” that you must manage. 

What if you’ve been misled? 

Because here's the real story: Your gut operates on a circadian rhythm, and if you disrupt this rhythm, you disrupt your gut health. 

Let’s unpack the truth. 

Your Gut Is Not Random — It’s Rhythmic 

Your gut follows a strict 24-hour rhythm. Daytime equals activity, movement, and digestion. Nighttime means rest and minimal motility. This rhythm is governed by two systems: the central clock in your brain (the suprachiasmatic nucleus or SCN), which resets with light, and peripheral clocks in your gut lining, which reset through food and metabolism. 

These two clocks need to operate in harmony. When they don’t, digestive chaos ensues. 

What Happens When the Rhythm Breaks? 

When your circadian rhythm is thrown off—due to shift work, jet lag, excessive blue light at night, or irregular eating patterns—your gut suffers. 

Here’s what goes wrong: 

- Constipation: Your colon fails to wake up properly in the morning. 

- IBS: Your bowel contractions lose their natural flow, leading to hypersensitivity and unpredictability in your gut. 

- Heartburn at night: Your esophagus loses tone while you sleep. 

- Slower digestion: Small intestine motility diminishes after dark. 

- Diarrhea & frequent bathroom trips: Increased gut motility. 

In essence, your gut becomes confused about when to move and when to rest. 

Result? Bloating, pain, irregular bowel movements, and inflammation, all of which can contribute to conditions like inflammatory bowel disease. 

This Is Not Just "Bad Luck" or "Aging" 

Research indicates that genetic variants in circadian clock genes, such as CLOCK, BMAL1, PER, and CRY, can slow down gut motility. Melatonin—the hormone that regulates your sleep—also plays a crucial role in gut movement. Remarkably, you produce 400 times more melatonin in your gut than in your brain. When your circadian clock is disrupted, melatonin production decreases, and your gut pays the price. 

This is biology, not just bad luck. 

How to Restore Your Gut’s Rhythm 

Here’s the good news: You can reset the clock and get your gut back in sync. The key is to work with your circadian biology, not against it. 

Here’s how: 

- Avoid excessive blue light from constant screen use. 

- Get natural light in the morning and throughout the day. 

- Avoid eating late at night—the gut is meant to rest and repair overnight. 

Stop viewing gut problems as random or merely “functional.” They are rhythm disorders that impact your mitochondrial health as well. 

Duboc, H., Coffin, B., & Siproudhis, L. (2020). Disruption of Circadian Rhythms and Gut Motility: An Overview of Underlying Mechanisms and Associated Pathologies. Journal of Clinical Gastroenterology, 54(5), 405–414. https://doi.org/10.1097/MCG.0000000000001333