Your Mood and Your Microbiome: What a Dietitian Wants You to Know About the Gut-Brain Axis

Have you ever had a ‘gut feeling’, like your stomach reacts to stress before your brain has fully caught up, or noticed that when life gets stressful, your digestion seems to follow? This link is known as the gut-brain axis, and understanding how it functions can explain the connections between what you eat, how you digest, and how you feel day to day.

How the Gut and Brain Communicate

The gut-brain axis is the term researchers use to describe the bidirectional communication system between your brain and your digestive tract, connecting the central nervous system with the enteric nervous system, which is sometimes called the gut’s “second brain”. It works in both directions through a combination of the nervous system, the immune system, and various hormones.

One of the most important pathways in this system is the vagus nerve, which is one of the longest nerves in the body, running from the brainstem all the way down to the colon. Approximately 80% of the signals traveling through the vagus nerve move upward, from the gut to the brain, not the other way around. So in many ways, your gut does a significant amount of reporting to your brain about what’s happening inside your body, including relaying information about inflammation, bacterial balance, gut movement, and even emotional state and response to stress.

This connection explains why emotional stress can directly trigger physical gut symptoms and why ongoing digestive issues can affect mood, focus, and overall mental wellbeing. They’re not two separate problems that happen to show up at the same time; they’re intricately connected.

The Role of Serotonin

Serotonin is often thought of as a mood chemical, and while it does help regulate mood, it also controls gut motility, or how quickly or slowly food moves through your digestive tract. Your gut produces roughly 90% of your body’s serotonin, not your brain. The serotonin your gut produces communicates with the brain through the vagus nerve, which explains why digestive symptoms and mood shifts so often show up together.

Your gut also produces other neurotransmitters and their precursors, including GABA, which plays a role in feelings of calm and anxiety regulation, and dopamine, with research suggesting that the intestines produce much of it as well. The bacteria living throughout your gut influence this production process, which is one of the reasons that the balance of your microbiome has such a wide-reaching effect on how you feel day to day.

This also helps explain why some people with IBS see improvement with SSRIs, even though doctors typically prescribe those medications for mood disorders. It’s not that their symptoms are “just” anxiety, it’s that serotonin is biologically active in both places, and researchers have been increasingly documenting that physiological overlap.

How Your Gut Microbiome Affects Your Mental Health

Your gut microbiome is the collection of trillions of bacteria, fungi, and other microorganisms living in your digestive tract, and their influence on your health extends well beyond digestion. When the microbiome is diverse and relatively balanced, it supports immune regulation, nutrient absorption, and neurotransmitter production. When imbalanced, also known as dysbiosis, symptoms can include bloating, irregular bowel habits, low energy, difficulty concentrating, and mood changes.

How does the microbiome impact how we feel?

Short-chain fatty acid production. When beneficial bacteria in the gut ferment dietary fiber, they produce compounds called short-chain fatty acids, and butyrate is one of the most important ones. Butyrate serves as the primary fuel source for the cells lining the colon and carries anti-inflammatory effects that extend beyond the gut. Getting enough fiber from a variety of plant sources is one of the most direct ways to support this process, which is part of why fiber-rich diets consistently support better health outcomes.

The stress response. Research shows that gut bacteria influence the HPA axis, which is the hormonal system responsible for regulating cortisol response. When the microbiome falls out of balance, the stress response can become more reactive, meaning everyday stressors feel more intense than they otherwise might. This is something I see come up in practice fairly often, where clients feel like their stress tolerance has gotten worse over time, and part of what we’re often looking at together is what’s happening with digestion.

Immune regulation. Your gut houses around 70% of your immune system, and the microbiome plays a major role in training immune cells and regulating inflammation. Researchers have increasingly linked chronic low-grade inflammation, which can stem from dysbiosis, to depression and anxiety. Studies also show that people with IBS experience anxiety and depression at significantly higher rates than the general population, and that the relationship between gut dysfunction and mental health runs in both directions (PMID: 31607239)

What to Eat to Support This Connection

The food choices you make every day are one of the most direct ways to shape your microbiome and, by extension, how you feel.

Vary your fiber sources. Different strains of beneficial bacteria feed on different types of fiber, so eating a wide range of plant foods gives your microbiome more to work with. Studies associate eating 30 or more different plant foods per week with greater microbiome diversity, which sounds like a lot but adds up quickly when you count herbs, spices, nuts, and seeds alongside your regular fruits, vegetables, and whole grains.

Include fermented foods regularly. Foods like plain Greek yogurt, kefir, kimchi, sauerkraut, miso, and tempeh introduce live beneficial bacteria and studies show they increase microbiome diversity and reduce inflammatory markers over time.

Prioritize omega-3 fatty acids. Fatty fish like salmon, sardines, and mackerel are the most concentrated sources, and flaxseed, chia seeds, and walnuts offer plant-based omega-3s. Research consistently links higher omega-3 intake to reduced inflammation and better mood outcomes, making it one of the more well-researched dietary supports for the gut-brain connection.

Limit ultra-processed foods. Heavily processed foods tend to be low in fiber, which means your beneficial bacteria have less to feed on over time. Researchers have also looked at how some additives and artificial sweeteners may affect microbiome composition, though this remains an evolving area. If gut symptoms or mood are something you’re actively working on, it’s worth looking at the overall balance of processed versus whole foods in your diet, not because these foods are off limits, but because variety and fiber help strengthen the microbiome.

Alcohol affects the gut more than most people expect. Even moderate intake can alter microbiome composition and affect gut permeability. If you’re dealing with ongoing gut symptoms, it’s worth noticing whether there’s a pattern between alcohol consumption and how you feel the next day, both digestively and emotionally.

The Takeaway

Digestive symptoms affect so much more than digestion. They can impact confidence, appetite, food choices, and overall quality of life, and when stress is part of the picture, understanding the gut-brain axis gives us a place to start.

As a registered dietitian specializing in digestive health, I use the gut-brain axis as a framework to guide the work I do with clients, helping them understand their symptoms and identify the most practical places to start making changes. In practice, that means looking at how consistently you’re eating, how much fiber and variety is in your diet, how you’re managing stress, whether you’re sleeping, and whether your diet is giving your microbiome what it needs to function well. When clients start making changes in these areas, it’s really common for both gut symptoms and mood to shift together, because they were connected all along.

If you’re noticing that your digestion and your mental health seem to influence each other, or if your digestive symptoms are affecting your mood or anxiety, let’s work together. You can schedule an appointment [here].

This post is for educational purposes only and does not replace individualized medical or nutrition advice.