The Gut-Brain Connection

How Your Microbiome Shapes Your Mood, Mind, and More

We’ve all heard the phrase “trust your gut,” but what if your gut is doing more than giving you intuitive nudges? What if it's actually influencing your mood, your ability to focus, your sleep, and even how anxious or calm you feel?

That’s the concept behind the gut-brain connection and this connection is way more powerful, nuanced, and science-backed than most of us were ever taught. That’s exactly why we’re diving into it today.

Once you understand what’s really happening between your digestive system and your brain, you start to connect the dots between symptoms that might’ve felt completely unrelated. Why your digestion changes when you’re stressed. Why your mood dips when your gut is off. Why anxiety can flare when you eat certain foods. And even why you might feel foggy, irritable, or exhausted when your gut lining is compromised.

There’s a lot going on behind the scenes and the more you know, the more empowered you’ll feel to support your brain and your gut.

So What Exactly Is the Gut Microbiome?

Your gut microbiome is like a vast rainforest: it’s diverse, dynamic, and deeply influential. It’s made up of trillions of bacteria, fungi, viruses, and other microbes that live throughout your digestive tract. Most of them are hanging out in your colon, doing way more than just helping you break down food.

A healthy gut microbiome does more than just digest your food. It helps produce vitamins, metabolize hormones, regulate your immune system, keep inflammation in check, and communicate key messages & signals with your brain. These microbes are constantly sending out messages using neurotransmitters, hormones, and short-chain fatty acids. When your gut microbiome is balanced, those messages support a calm and steady mood with predictable patterns. But when your gut is off? That messaging system can start to send some pretty chaotic signals.

So if you’ve ever thought your anxiety, brain fog, or low energy were just “in your head” and you have digestive symptoms, then there’s a good chance your gut has actually been playing a major role all along.

The Gut-Brain Axis: Your Internal Highway

The gut and the brain are constantly talking to each other and this two-way communication system is what we call the gut-brain axis. It involves your central nervous system (your brain and spinal cord), your enteric nervous system (which lives in your gut), your immune system, and your endocrine system (hormones).

One of the key messengers in this axis is the vagus nerve. It’s a long nerve that runs from your brainstem all the way down to your gut. When it’s working well, the vagus nerve sends calming, regulating signals back and forth to tell your brain to stimulate rest & digestion (known as the parasympathetic state). This is why I often recommend belly breathing before meals to optimize digestion and reduce bloating, because taking deep breathes into the diaphragm stimulates this nerve to put you in rest and digest.

But that’s just one piece of the puzzle — the vagus nerve isn’t doing all the heavy lifting alone. The microbes in your gut also produce metabolites like short-chain fatty acids (butyrate is a big one) and neurotransmitters like serotonin and GABA that influence your mood, cognition, and stress response.

To put it simply: your gut is constantly checking in with your brain and vice versa. And if either one is inflamed, stressed out, or out of balance, the other tends to feel it too.

The Microbes That Shape Your Mind

Certain bacteria in your microbiome play a significant role in regulating mood, cognition, and even behavior.

Lactobacillus and Bifidobacterium species are two genera of bacteria that help produce GABA, a calming neurotransmitter that can reduce feelings of anxiety and help you sleep more soundly. Some strains of Bifidobacterium also support tryptophan metabolism which is a precursor to serotonin (aka your happy hormone).

Then there’s Faecalibacterium prausnitzii, a butyrate-producing bacterium that plays a huge role in calming gut inflammation. Butyrate doesn’t just support gut health — it’s also been linked to improved cognitive function, better memory, and even protection against neurodegenerative diseases.

Akkermansia muciniphila is another one I love to see on gut testing results. This is what I consider a keystone species and can reveal a lot about the status of someone’s gut microbiome. Its presence is associated with improved metabolic and cognitive health. Low levels of Akkermansia, on the other hand, are often seen in people with obesity, insulin resistance, and mood disorders.

How the Brain Talks Back

The gut-brain axis isn’t just a one-way street. Your thoughts, emotions, and stress levels profoundly impact your gut.

Ever lost your appetite before a big event? Or felt the urge to run to the bathroom when you were nervous? Or eaten something in a stress hurried state that left you with stomach pain and bloating? That’s your brain talking directly to your gut.

Just as we talked about the parasympathetic state earlier, the opposite of that is the sympathetic state known as “fight or flight” mode. When you’re in sympathetic mode, your brain triggers the release of cortisol and other stress hormones that slow down blood flow to your digestive system, reduces stomach acid production, changes gut motility, and reduces absorption of nutrients during digestion.

When all of these digestive shifts are happening on a physiological level, it can manifest as bloating, constipation, diarrhea, nausea, or even food sensitivities. In my clinical practice, there’s rarely a time that I don’t address the nervous system & HPA axis when working with digestive health patients because the two systems are so intricately connected with one another.

Over time, chronic stress can even reshape your microbiome leading to a reduction of beneficial bacteria and making it easier for less helpful microbes to take over. This is why I always say that regulating your nervous system is just as important as what you eat when it comes to gut health. A stressed out mind almost always creates a stressed out gut.

Your Gut Makes Neurotransmitters Too!

Here’s something most of us were never taught: your gut isn’t just digesting food, it’s also manufacturing some of the same neurotransmitters your brain uses to regulate mood, energy, motivation, and even sleep.

This might surprise you, but 90 and 95% of your serotonin is actually made in your gut and not your brain! Serotonin plays a key role in regulating mood, appetite, sleep, and even how you process pain. While most of that serotonin stays in the gut to regulate motility (how things move through your intestines), it still has systemic effects. It influences how you process stress, how your immune system behaves, and how balanced or off you feel emotionally. Low gut serotonin production is one reason why gut issues and mood issues often show up hand in hand.

Melatonin is another big one. We typically think of melatonin as the hormone that helps us fall asleep at night (which it does) but interestingly, the gut produces 400x more melatonin than the pineal gland in your brain. Gut-derived melatonin helps regulate not just your circadian rhythm, but also gut motility, inflammation, and intestinal permeability. It’s one of the reasons why digestion tends to follow a rhythm and why irregular meal times, travel, or poor sleep can totally throw off your digestion. It’s all connected!

Your gut also plays a role in dopamine production. Dopamine is your “reward” neurotransmitter associated with motivation, pleasure, focus, and drive. While most of the dopamine your gut produces doesn’t cross into the brain, it still influences the way your nervous system operates and how your gut communicates with your brain. For example, low dopamine activity in the gut can slow digestion and impact mood and attention.

And then there’s GABA, short for gamma-aminobutyric acid. This is a calming neurotransmitter that helps downregulate the nervous system and reduce anxiety. Certain strains of Lactobacillus and Bifidobacterium actually produce GABA in the gut. This is where specific probiotics can have a powerful impact on the gut-brain axis, especially in people struggling with anxious thoughts or an overactive stress response.

All of this reinforces a simple but powerful truth: your mental health doesn’t start and end in your brain. It’s deeply influenced by what’s happening in your gut microbiome and how well that internal environment supports the production and signaling of your neurotransmitters.

So when someone tells me they feel “off”, unfocused, emotionally flat, or overly reactive, we don’t just look at stress or hormones. We look at the gut too because more often than not, it’s playing a bigger role than they realized.

When the Microbiome Goes Rogue

Let’s talk about what happens when the gut becomes home to microbes that don’t have your best interest at heart.

Your microbiome is meant to be a balanced ecosystem, with friendly bacteria keeping the less than helpful organisms in check. But when that balance gets disrupted (think: antibiotics, food poisoning, stress, poor diet, certain medications, or even travel), it opens the door for opportunistic microbes to overgrow.

Let’s start with candida. Candida albicans is a type of yeast that naturally lives in the gut, mouth, skin, and vaginal tract. In small amounts it’s harmless and part of a healthy microbiome. But when it goes into overgrowth it can start causing problems. Candida overgrowth is one of the most common fungal imbalances I see in practice and it’s been linked to symptoms like anxiety, fatigue, brain fog, sugar cravings, bloating, gas, recurrent yeast infections, and skin rashes. Anxiety is one of the biggest symptoms I see with it, thanks to the neurotoxic byproducts it releases (like acetaldehyde) which can interfere with your brain chemistry and even your detox pathways!

Then there’s everyones favorite critters: parasites. These are often dismissed as only being an issue if you’ve traveled somewhere tropical but you’d be surprised how many people have low-grade, chronic parasitic infections picked up from food or water. Two common ones I see in practice are Blastocystis hominis and Dientamoeba fragilis. They can be cause symptoms ranging from bloating, nausea, loose stools, stomach pain, irritability, sleep disturbances, and mood changes like anxiety. They can also trigger an immune responses, inflame the gut lining, and disrupt the balance of your microbiome, making it harder for beneficial bacteria to thrive.

Another big player here is SIBO, short for “Small Intestinal Bacterial Overgrowth”. This happens when bacteria that are supposed to live in your large intestine migrate into the small intestine where they don’t belong. Once there, they start fermenting carbohydrates and fibers way too early in the digestive process which can lead to an array of symptoms such as gas, bloating, reflux, abdominal pain, constipation or diarrhea, nutrient deficiencies, brain fog, mood changes, and fatigue. There are different types of SIBO depending on what gases are being produced: hydrogen, methane, or hydrogen sulfide and each can present differently in symptoms. For example, methane dominant SIBO is often linked to constipation, irritability, and a general sense of heaviness and fogginess (both mentally and physically).

But even beyond the more well known disruptors like candida and parasites, there’s a whole class of bacteria we call opportunistic microbes. These are bacteria that can be present in low amounts in a healthy gut but if the balance tips they can go into overgrowth and create problems. Some key species I see on stool testing include Klebsiella, Pseudomonas, Enterococcus, Staphylococcus spp, or Streptococcus spp. These bacteria can produce inflammatory compounds, interfere with nutrient absorption, and trigger immune responses that affect not just your gut but your mood, memory, and stress. Some produce byproducts like lipopolysaccharides (LPS) which are known to create systemic inflammation and have been associated with both depression and neurodegenerative diseases.

I see this all the time in patients who come in with both digestive complaints and emotional or cognitive symptoms. The gut isn’t just inflamed — it’s literally sending distress signals to the brain. When these microbial imbalances are identified and addressed, I often hear things like “I didn’t even realize how much brain fog I was dealing with”!

What Happens with Leaky Gut

Leaky gut, or increased intestinal permeability, is what happens when the tight junctions in your gut lining break down. Tight junctions are like these tiny seals between the cells that line your gut. Their main purpose is to keep substances out of the bloodstream by controlling what passes through the gut lining. These seals can start to breakdown under a variety of circumstances that negatively impact the gut: chronic stress, poor diet, food poisoning, medications like NSAIDs or antibiotics, or imbalances in the gut microbiome. When there’s increased intestinal permeability, the damaged gut lining can allow food particles, bacteria, toxins, and immune triggers to leak into the bloodstream which leads to systemic inflammation.

This systemic inflammation stemming from the gut can also impact the brain by weakening the blood-brain barrier, which is supposed to protect your brain from harmful substances. When this barrier becomes “leaky” too, neuroinflammation can set in leading to brain fog, memory issues, mood swings, low energy, and even symptoms associated with anxiety or depression.

Given the nature of the gut microbiome and it’s influence on the gut lining, I seldom treat a patient with digestive concerns without also addressing the gut lining as well. The heal and seal method!

How SSRIs Affect the Gut

One question I get a lot when we’re talking about the gut-brain axis is: “how do SSRIS impact the gut?” And I want to start by saying this loud and clear: SSRIs can be incredibly helpful and in some cases absolutely necessary and life-saving medicine. I’ve successfully worked with many patients who are on them and have no intention of coming off and that’s completely valid. Sometimes medication is part of your healing journey and there’s zero shame in that. The goal of naturopathic medicine isn’t to avoid meds at all costs but to instead find what works best for you and build a support plan around it.

That said, since SSRIs (like Zoloft, Prozac, or Lexapro) work by increasing serotonin levels in the brain it makes sense that these medications can have some GI effects, especially early on. Nausea, appetite changes, or digestive shifts are pretty common during the adjustment phase.

But beyond the short term side effects, research shows that SSRIs can actually influence the gut microbiome over time. Some studies have found that they may reduce microbial diversity or shift bacterial populations in ways that promote dysbiosis, like lowering beneficial strains such as Bifidobacterium and encouraging the growth of more inflammatory species. These changes don’t just affect digestion. They can also impact immune health, neurotransmitter production, and the gut lining itself.

No, this doesn’t mean SSRIs are bad or shouldn’t be used. But it does mean that if you’re taking one, it’s a good idea to also support your gut with intentional nutrition, stress management, and maybe even targeted supplements or probiotics to keep your microbiome strong and supported.

SSRIs and gut health don’t have to be at odds. In fact, this is where a more integrative approach really shines: mental health care that honors both the brain and the gut as part of the same conversation.

Healing and Supporting the Gut-Brain Axis

When I’m working with someone on their gut health, one of my first steps is to look deeper by utilizing a comprehensive stool test. This gives us a much clearer picture of what’s actually going on in the gut: which microbes are thriving, which ones are missing, whether there’s inflammation, leaky gut markers, or signs of overgrowth like candida, parasites, or SIBO.

From there, the treatment plan becomes highly personalized. If we uncover imbalances, we’ll typically start with a targeted herbal protocol to address overgrowth, calm inflammation, and restore microbial balance. But once that groundwork is laid, I also bring in supportive tools to help repair the gut lining and strengthen the gut-brain connection.

Here are some of my go-to supplements and peptides that can make a real difference:

• BPC-157: a regenerative peptide that’s been shown to help heal the gut lining, reduce inflammation, and support overall resilience in the gut-brain axis. I’ve seen beautiful outcomes with it in patients dealing with both gut symptoms and cognitive/mood concerns.

• L-glutamine: helps repair and restore barrier function, reduce inflammation - I use this in all of my leaky gut protocols.

• Zinc carnosine: protects the mucosal lining, helps reduce inflammation, has some antioxidant benefits, and another staple in my leaky gut protocols.

• Probiotics: are hugely helpful but the strains matter. Lactobacillus rhamnosus GG, Bifidobacterium longum, and B. infantis are some of the strains I reach for when I’m supporting the gut-brain axis specifically. Spore-based probiotics like Bacillus coagulans can also support microbial diversity and calm inflammation.

• Other supportive supplements I like: magnesium (especially glycinate or threonate), omega-3s, prebiotic fibers, butyrate, and adaptogens can round out the picture.

Final Thoughts

If there’s one thing I want you to take away from this, it’s that your symptoms are never random. Whether it’s brain fog, bloating, anxiety, or fatigue — there’s usually a thread running through it and the gut-brain connection is often that common root.

You don’t need to chase down every single symptom individually. Start supporting the communication between your gut and your brain and you might be surprised by how many pieces start falling into place.