When you hear the word “serotonin,” you probably think of mood, happiness, or antidepressants. But here’s something surprising: about 90% of all the serotonin in your body is made in the gut, not the brain.

That doesn’t mean your gut makes you happy in the same way your brain does—but it does mean your digestive system plays a huge role in your emotional and physical well-being. And your gut microbiome—the trillions of bacteria living in your intestines—has a major say in how much serotonin your body actually produces.

Today, we’re exploring how serotonin really works, what role your microbiome plays, and why taking care of your gut may be one of the best things you can do for your mental health.

Last week I talked about how the gut and the brain communicate, and how it’s a 2 way street. But I didn’t get into the details of how serotonin ends up in your gut. Let’s do that now.

What Serotonin Does in the Gut

Serotonin isn’t just a “feel-good” chemical. In the gut, it’s actually a regulatory signal produced mostly by specialized intestinal cells called enterochromaffin cells.

In your digestive system, serotonin helps:

• Control gut motility — how quickly food moves through the intestines
• Regulate enzyme secretion and fluid balance
• Signal discomfort or fullness to the brain
• Coordinate communication between the gut and the nervous system

So while gut serotonin doesn’t directly control mood—it affects digestion, inflammation, and communication with the brain, all of which influence how you feel.

Does the Microbiome Make Serotonin?

This is where things get really interesting.

The gut microbiome itself produces only a small amount of serotonin directly—probably less than 5% of your body’s total serotonin. Certain bacteria, including Candida, Streptococcus, Escherichia, and Enterococcus, can make a little serotonin on their own.

But the bigger role of the microbiome is that it acts like a control system for serotonin production. Gut bacteria send chemical signals to your intestinal cells, essentially telling them how much serotonin to make.

A landmark study from Caltech in 2015 found that mice raised without any gut bacteria produced about 60% less serotonin in their intestines than normal mice. When healthy bacteria were reintroduced, serotonin production returned to normal levels.

So even though bacteria aren’t producing most of the serotonin themselves, they’re responsible for turning on your body’s serotonin factory.

The Gut-Brain Serotonin Connection

Serotonin produced in the gut cannot cross the blood-brain barrier, so it doesn’t directly raise serotonin levels in the brain. But it still communicates with the brain in other powerful ways—especially through the vagus nerve, which connects the two systems.

Through this communication, gut serotonin can influence:

• Stress sensitivity
• Appetite and cravings
• Mood regulation
• Anxiety and sleep cycles

An imbalanced microbiome—called dysbiosis—can disrupt this signaling. The result can be poor digestion, inflammation, and mood changes such as anxiety or brain fog.

In other words, your gut doesn’t produce happiness directly—but it helps determine how your brain experiences it.

What Affects Serotonin Production in the Gut

Several factors influence how well your gut produces and regulates serotonin:

1. Microbiome health: Dysbiosis—too many harmful microbes or too few beneficial ones—can interfere with serotonin signaling.
2. Diet: Fiber-rich foods and prebiotics feed the bacteria that support serotonin regulation. Fermented foods can also help maintain balance.
3. Inflammation: Chronic inflammation in the gut can reduce serotonin synthesis.
4. Lifestyle: Poor sleep, chronic stress, and lack of exercise all affect serotonin indirectly by changing the gut environment.

Supporting Gut and Brain Health Together

If you want to support both your digestion and your mental health, start by optimizing your gut environment.

Here’s how:

• Identify and address underlying gut imbalances in the microbiome. This one is huge, and I see it make a ton of difference in a lot of patients in how they feel.
• Eat a diverse diet rich in plants, fiber, and fermented foods to nurture the right microbes.
• Manage stress with breathwork, meditation, yoga, or sound healing to keep the gut-brain axis calm.
• Get consistent sleep and movement, which enhance both gut motility and serotonin signaling.

When you care for your gut, you’re also supporting your brain’s resilience, clarity, and stability.

Serotonin may be known as the “happiness molecule,” but most of it is made right inside your gut. Your microbiome helps control how much you produce, how it’s released, and how well your brain receives the message.

So if you want better digestion, calmer moods, and clearer thinking, don’t just focus on the brain—start with the gut. Because when your gut is healthy, your entire nervous system works better.

And if you need help doing that, give us a call at the IBS Treatment Center. Distance is not an obstacle. We’ve been working with patients all over the world via telemedicine since 2005, and we can help you too.

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