How Your Gut Can Affect Pain, Mood, & Sleep
What if the root cause of your chronic pain isn’t in your joints or nerves, but deep within your gut?
In this episode, Dr. MaryK Geyer reveals the hidden influence of the microbiome on chronic pain, anxiety, and gut health. From surprising connections between gut bacteria and inflammation to why conventional medicine often misses the mark, this conversation will shift how you think about your symptoms.
Don’t miss this eye-opening discussion, your gut might be the missing piece you’ve been overlooking. Dive in now before you spend another day treating the wrong problem!
Episode Video
What if your gut, not your joints or nerves, was the root cause of your chronic pain? This isn’t science fiction. The rapidly advancing field of microbiome research is revealing how trillions of bacteria in our digestive system are deeply connected to inflammation, autoimmune activity, and even our perception of pain. If you’re dealing with fatigue, anxiety, or mysterious symptoms that don’t respond to conventional treatments, your microbiome may be trying to tell you something.
Understanding the Microbiome and Why It Matters
The human microbiome refers to the community of microorganisms living in and on the body, with a significant concentration in the gut. Far from being harmful, many of these bacteria are essential to health. They help us digest food, manufacture vitamins, regulate our immune systems, and even produce neurotransmitters like serotonin and dopamine. As research advances, the microbiome is no longer seen as a passive environment but as a dynamic participant in our body’s key functions.
In fact, up to 80% of the immune system resides in the gut. This makes gut health essential to managing inflammation, a critical factor in many chronic pain conditions. Poor gut health can increase intestinal permeability (sometimes referred to as "leaky gut"), allowing unwanted particles to enter the bloodstream and trigger an immune response. This immune activation often leads to systemic inflammation, a driver of chronic pain.
How Gut Health Influences Chronic Pain
Chronic pain patients are increasingly presenting with underlying gut issues, including IBS, IBD, and dysbiosis (a microbial imbalance). Specific strains of gut bacteria have been linked with conditions like rheumatoid arthritis and even newly diagnosed autoimmune diseases. When the gut microbiome is disrupted, it can lead to mitochondrial dysfunction and a cascade of other systemic issues that fuel persistent pain.
Doctors are now adopting integrative approaches that begin with the gut. By analyzing symptoms and using tailored testing methods, including stool tests, PCR, and even customized probiotics, doctors can assess gut health and determine the best treatment course. This often involves calming the immune system, restoring microbial balance, and supporting the gut barrier.
The Microbiome and Mental Health
The gut-brain connection is another pivotal piece of the puzzle. Known as the gut-brain axis, this bidirectional communication system allows gut bacteria to influence brain function. Since up to 90% of serotonin and around 50% of dopamine are produced in the gut, imbalances in gut bacteria can directly affect mood, sleep, and mental clarity.
It’s no coincidence that patients with gut disorders often experience anxiety, depression, and brain fog. Rather than treating these symptoms in isolation, addressing the microbiome can lead to profound mental health improvements. Functional medicine doctors are also seeing measurable effects of dietary changes and gut support on neurotransmitter production and mental wellbeing.
Microbiome Testing: When and Why It Matters
Not every patient requires a microbiome test immediately, but many benefit from one at some point in their healing journey. Experienced practitioners evaluate symptoms and use tests strategically, whether it's PCR, microscopy, or culture-based analysis. New technologies even allow for custom-formulated probiotics based on the unique bacterial profile of an individual.
These personalized treatments are especially helpful for patients with chronic or complex conditions. For example, those with mast cell activation syndrome, autoimmune disorders, or persistent bladder or vaginal infections often show gut imbalances that require targeted support. Restoring the microbiome can reduce symptom flare-ups and enhance resilience against future health issues.
Diet and the Microbiome: What to Feed Your Gut
What you eat directly impacts which gut bacteria thrive or die. Fiber, in particular, is a major player in gut health as it feeds beneficial bacteria. However, extreme or restrictive diets can sometimes do more harm than good, especially when used long-term. Therapeutic diets like low-FODMAP, AIP, or carnivore may offer short-term relief, but they should be guided by a professional.
Instead, a sustainable approach focuses on balance and relationship with food. Eating a diverse range of whole foods, reducing ultra-processed items, and including fermented foods can nurture the microbiome. Baby steps, rather than extreme overhauls, are often more successful in promoting lasting health changes.
Can Probiotics Replace Weight-Loss Medications?
GLP-1, a hormone involved in appetite regulation and blood sugar balance, is now the target of both pharmaceutical and probiotic treatments. Certain probiotic strains have shown potential to stimulate GLP-1 production, curbing cravings and supporting metabolic health. While these won't replace medications like Tirzepatide overnight, they offer a promising complementary or alternative strategy with fewer side effects.
Why the Microbiome Deserves Your Attention
Whether you're dealing with pain, fatigue, mental fog, or hormonal imbalances, your gut health could be at the center of it all. The microbiome's influence stretches far beyond digestion, affecting immunity, mood, metabolism, and inflammation. Testing, professional guidance, and intentional dietary choices can help uncover the root cause of your symptoms and put you on a path to healing.
Optimizing the microbiome isn’t just a wellness trend. It’s an evidence-backed approach to health that empowers patients with chronic pain and complex health challenges. Taking care of your gut may be the smartest investment you make in your overall wellbeing.
About Dr. MaryK Geyer
Dr. MaryK Geyer brings a powerful blend of medical expertise, real-world grit, and deep compassion to the conversation. As the founder of Empower Integrative Health, a mom of five, a former Army medic, and a global health leader, she’s spent nearly two decades transforming the way we think about wellness. With experience ranging from teaching future physicians to co-founding Naturopaths Without Borders, Dr. Geyer now focuses on helping patients get to the root of complex, chronic conditions. Her approach is refreshingly human: individualized, integrative, and fiercely committed to getting people feeling better—faster.
Want to connect with Dr. Geyer? Visit her clinic at Empower Integrative Health in Scottsdale or find her on:
Final Thoughts
The connection between the microbiome, chronic pain, and gut health isn’t just an emerging field, it’s a foundational shift in how we understand the body. Dr. MaryK Geyer’s insights challenge the outdated notion that pain is only structural or neurological. Instead, she highlights how a disrupted gut ecosystem can influence everything from joint pain to hormone balance, mood, and even immune response.
By recognizing the gut as the second brain, we open up new possibilities for healing that go beyond prescriptions and quick fixes. Whether it’s through individualized probiotics, functional testing, or strategic nutrition, optimizing gut health can be a powerful pathway to reducing inflammation, calming chronic symptoms, and reclaiming energy and clarity.
If you've been chasing symptoms and feeling like nothing is working, it might be time to look inward, literally. Addressing your gut microbiome might not just make you feel better. It could change your entire approach to wellness.
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