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Bayou Health | Three Common Unexpected Gut Health Issues

By Nathan Coker
In Bayou Health
Jul 30th, 2025
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BY DR. NATHAN MORRIS

As a functional medicine doctor, I often ask people the question, “How do you think your gut health is doing?” Inevitably they reply, “It’s doing fine, doc; I go to the bathroom every day.” What they don’t know is that processing our food is just one aspect of gut health, and there are many conditions that tell me that gut health is not “fine.”

Your gut is a dynamic and intelligent ecosystem that influences your immune system, hormone balance, and especially brain function. A growing body of research shows that an unhealthy gut can contribute to a wide variety of chronic symptoms—including those that show up on your skin as acne, in your joints as arthritis, or in your ability to think clearly. By understanding how the gut is involved, you can take the first step toward addressing the root cause rather than just treating symptoms on the surface of conditions like acne, arthritis, and brain fog.

We will explore how inflammation originates as a chain reaction from your gut, and how the bacteria and fungi that make up your gut microbiome significantly contribute to this inflammation by compromising the gut barrier, activating the immune system, and producing harmful byproducts.

We will explore three seemingly unrelated conditions and find the common threads that connect them and finally explore the simplistic approach available to everyone to start addressing these issues with some basic interventions.

Gut Health and Acne (The Gut-Skin Axis)
Who would think that your acne or other skin issues were connected to your digestive system? Well, surprisingly, it is intimately connected. We now know that the skin is often a mirror of internal gut health. The term “Gut-Skin Axis” describes the communication between your digestive system and your skin, which is primarily mediated through the immune system that resides in the gut, as well as the microbes and their byproducts.

When the message being communicated from the gut signals there is inflammation secondary to overgrowth of bad bacteria or fungus, a leaky gut barrier, food allergies, and most especially excess sugar intake, the skin is the messenger that there is a problem.

What we know from the research is that people with acne often have GI symptoms like diarrhea, constipation, bloating, and abdominal pain, so there is a direct correlation. People with small intestinal bacterial overgrowth (SIBO) often have a more severe form of acne called rosacea, so the correlation is there. We will next explore joint pain and the causes for it, which are very similar.

Key takeaway: A balanced gut microbiome, healthy gut lining, and reduction of inflammatory foods help reduce systemic inflammation and hormonal imbalances that contribute to acne.

Gut Health and Joint Pain (Gut-Immune Axis)
The gut houses 70% of your immune system. This 70% of your immune system performs 99% of the work determining what is good and bad that enters your body. A healthy gut trains the immune system to tolerate harmless stimuli and react only to real threats. When the gut is inflamed or leaky, immune cells can become overreactive and confused, causing the body to attack friendly, but not perfect, parts of the body like joints. The key word here is overreactive. Joint pain and arthritis are essentially caused by an overreactive immune system that results from a gut sending incorrect signals.

Certain gut bacteria can also produce inflammatory substances that spread through the bloodstream, amplifying joint inflammation. Creating a healthy microbiome is essential for stopping this production of inflammatory substances and calming down the previously mentioned overreaction.

These two factors, immune system dysfunction and disruptive bacteria, are especially important in autoimmune joint conditions like rheumatoid arthritis, but even people without an autoimmune-like condition can experience inflammation-driven joint stiffness or pain due to poor gut health, which is often called osteoarthritis. The good news is this is not an inevitable consequence of aging. You can be 80 and be joint pain-free if your gut is healthy.

Key takeaway: A healthy gut supports immune tolerance and reduces inflammation, helping to prevent or calm joint pain. Read on to find out how we create a healthy gut after we discuss brain fog.

Gut Health and Brain Fog (The Gut-Brain Axis)
The gut and brain are in constant communication through the gut-brain axis, which includes the largest nerve in the body, the vagus nerve.

The vagus nerve is telling the gut many things, including what our mood should be, how our immune system in the brain should react, and whether it should be clear-headed or foggy. When the vagus nerve from the gut is signaling there is inflammation in our GI tract or directly causing inflammation through messengers, the brain becomes lethargic, quits making feel-good neurotransmitters, and causes brain fog. The reasons the vagus nerve signals the way it does are for the same reasons we have acne and joint pain. Overgrowth of non-beneficial bacteria/fungus and a leaky gut lead to immune system overreactions. Imbalances in gut flora can also contribute to poor blood sugar regulation, which impacts brain energy and focus.

Key takeaway: A healthy gut supports clear thinking and emotional balance by regulating inflammation and producing essential brain chemicals.

What are some next steps for all these conditions?
1. Clean Up Your Diet
• Reduce sugar, refined carbs, gluten, and dairy.
• Focus on whole, fiber-rich foods: vegetables, leafy greens, legumes, and seeds.
• Add fermented foods like sauerkraut, kimchi, and kefir (if tolerated).

2. Support Your Microbiome
• Take a specific, high-quality probiotic (with Lactobacillus rhamnosus and Bifidobacterium strains) known to help with immune function and inflammation.
• Consider prebiotic fiber to feed your good gut bacteria (e.g., inulin, green banana powder, garlic).
• Make sure you have 30 grams of fiber in your diet every day (chia seeds, flaxseeds, green leafy vegetables).

3. Repair Your Gut Lining
• Supplements like colostrum, L-glutamine, and aloe vera can help rebuild gut barrier integrity.
• Bone broth and cooked vegetables can be soothing and supportive.

Conclusion:
A healthy gut is the foundation for clear skin, pain-free joints, and mental clarity, highlighting the deep interconnectedness between digestion and whole-body health. By nurturing your gut through balanced nutrition with the removal of inflammatory foods and targeted supplement support, you can unlock lasting relief from acne, joint pain, and brain fog.