Irritable Bowel Syndrome: A Functional Medicine Approach to Root-Cause Healing
By Dr. Shannon O’Keefe, DC, DCBCN
Board-Certified Clinical Nutritionist with Advanced Education in Functional Medicine & Internal Diagnosis
If you're reading this, you're probably no stranger to the discomfort, frustration, and mystery of IBS—irritable bowel syndrome. Maybe you've been told it's "just stress." Maybe you’ve tried eliminating certain foods, adding fiber, or using medications that help a little—but never enough.
I want you to know that what you're experiencing is real, and you’re not alone. At O’Keefe Matz Functional Health Clinic in Saint Paul, I work with patients every week who are struggling with IBS. What I’ve found is that IBS is not the problem—it’s a symptom of something deeper going on in the body.
And that’s exactly where functional medicine shines.
What Makes IBS So Complex
IBS isn’t a single condition—it’s a collection of symptoms that can have different root causes in different people. For one person, it might be small intestinal bacterial overgrowth (SIBO). For another, chronic stress might be disrupting the gut-brain connection. And for someone else, the trigger might be food sensitivities, past infections, or hormonal changes.
This is why a one-size-fits-all approach doesn’t work. Your story is unique—and so should your treatment plan be.
How I Approach IBS Using Functional Medicine
When you come to see me, we start by getting really curious about your history. I want to know:
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When did your symptoms start?
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What was happening in your life at the time?
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Have you taken antibiotics or acid blockers?
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How’s your stress level?
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What foods make you feel better—or worse?
Then we go deeper with advanced functional and diagnostic testing to help identify what your body needs to restore balance. These may include:
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Comprehensive stool testing to assess digestion, inflammation, infections, microbiome balance, and enzyme levels
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SIBO breath testing to evaluate methane and hydrogen gas levels produced by bacterial overgrowth in the small intestine
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Food sensitivity testing (IgG/IgA) to identify delayed immune responses to specific foods
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Cortisol/adrenal stress testing (saliva or dried urine) to assess the impact of chronic stress on gut function
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Intestinal permeability testing to check for “leaky gut”
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Organic acid testing to assess microbial metabolites, detox function, and vitamin production
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Comprehensive blood work including:
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Inflammatory markers (CRP, ESR)
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Nutrient status (B12, folate, iron, vitamin D, magnesium, zinc)
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Thyroid function (TSH, Free T3, Free T4, Reverse T3, thyroid antibodies)
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Blood sugar balance (fasting glucose, insulin, HbA1c)
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Liver enzymes and gallbladder function
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CBC, CMP, and lipids to assess overall metabolic health
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All of these help us build a clear picture of what’s happening inside your body—not just in the gut, but systemically.
What Healing Looks Like
Once we identify the root causes of your IBS, I design a step-by-step plan tailored to your body’s unique needs. My approach focuses on repairing, rebalancing, and restoring your digestive system from the inside out. Your personalized plan may include:
Nutritional Therapy
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A targeted elimination or low-FODMAP diet to remove inflammatory triggers
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Gradual reintroduction strategies to identify food sensitivities
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Anti-inflammatory meal planning to support gut calm and nutrient absorption
Microbiome & Infection Support
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Herbal or prescription antimicrobial support to rebalance gut bacteria and eliminate overgrowths
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Individualized probiotic and prebiotic protocols to restore microbiome diversity and function
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Gentle antifungal or antiparasitic support, if needed, based on test findings
GI Healing Protocols
Restoring the gut lining and overall digestive function is essential in long-term IBS recovery. This involves a multi-layered process that includes:
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Supporting the repair and regeneration of the intestinal lining to help seal gaps in the gut wall
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Strengthening the mucosal barrier to protect against irritation and help regulate immune activity in the gut
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Enhancing the body's natural anti-inflammatory processes to reduce gut reactivity and calm the immune system
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Rebuilding a healthy digestive environment that promotes short-chain fatty acid production, which fuels the cells lining the colon and improves motility and regularity
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Supporting enzyme and acid production to ensure that food is properly broken down and nutrients are absorbed
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Encouraging proper bile flow and fat digestion, which are often disrupted in people with long-standing digestive issues
These therapies are gentle, personalized, and based on your specific history and lab results. Rather than suppressing symptoms, they help strengthen and restore your gut’s natural function so it can heal from within.
Nervous System & Vagal Tone Support
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Acupuncture to reduce gut sensitivity and calm the nervous system
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Frequency Specific Microcurrent (FSM) to modulate inflammation and improve vagus nerve signaling
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Breathing practices, HRV training, and gentle movement to improve stress response and gut-brain communication
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Strategies to stimulate vagal tone and restore natural motility, particularly important in IBS-C
Lifestyle & Long-Term Maintenance
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Tools to improve sleep quality and circadian rhythm regulation
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Gentle daily routines to support your body’s stress and detox pathways
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Movement practices matched to your energy and inflammation level
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Ongoing strategies to expand food variety and maintain long-term GI resilience
You Are Not Broken—You Just Haven’t Been Heard
Many of my patients tell me they felt dismissed or told their symptoms were “in their head.” That kind of invalidation only adds to the stress and isolation IBS can bring.
"Dr. O’Keefe was the first provider who truly listened to me. She didn’t just give me a handout and send me home. She took the time to understand what was happening in my body and gave me a plan that finally made sense. Within a few weeks, my bloating and urgency were dramatically reduced. I feel like I have my life back."
– Sarah T., age 36
"After 10 years of IBS-C, I thought surgery was my only option. Dr. Shannon helped me identify SIBO and underlying thyroid issues. With her care and functional testing, I saw more progress in 3 months than in the past 10 years."
– Kevin M., age 42
"The combination of acupuncture, dietary support, and FSM completely changed my relationship with my gut. I’ve never felt more supported or more hopeful about my health."
– Rachel P., age 50
Healing IBS Is Possible—But It Starts With Listening to Your Body
You don’t have to “just live with it.” Your body has an incredible ability to heal when given the right support, the right tools, and the space to recover.
If you’re struggling with IBS—whether it’s IBS-C, IBS-D, or a frustrating mix of both—I’d love to help you uncover the root causes and guide you through a personalized healing journey.
Ready to Begin?
Let’s work together to get your gut back on track—naturally and thoroughly.
Contact us today to schedule a consultation.
O’Keefe Matz Functional Health Clinic – Saint Paul, MN
Phone: 651-292-8072
Website: www.improveurhealth.com
