IBS—irritable bowel syndrome—affects roughly 1 in 10 people worldwide.
It’s what’s known as a diagnosis of exclusion, which means you only get the label after doctors rule out other conditions with similar symptoms, like Crohn’s disease, celiac disease, IBD, or even colon cancer. If nothing else shows up but the symptoms remain, the diagnosis becomes IBS.
For many patients, that’s where the conversation ends. They’re given a name for their symptoms, but not much guidance on why it’s happening or what to do next.
If this sounds familiar, you’re not alone. So many people walk away from their doctor’s office feeling abandoned, misunderstood, and left to “deal with it” as though their gut will never be the same again. But IBS is more than just a label—it’s your body trying to tell you that something deeper is going on.
At Boulder Holistic Functional Medicine in Boulder, Colorado, we go deeper. We look past the symptoms to the root cause of your IBS so we can bring your gut and body back into balance.
What is IBS?
Irritable Bowel Syndrome (IBS) is a chronic condition that affects the gut. It’s a functional gut disorder which means, most of the time, tests and scans will come back normal. Your body is still digesting and passing food, but not without a few uncomfortable, and sometimes debilitating, symptoms.
Typical symptoms of IBS include:
- Bloating and/or stomach cramps
- Irregular bowel movements
- Mucus in stool
- Relief with bowel movements
- Food sensitivities
- Bloating or pain after eating
IBS typically includes diarrhea, constipation, or a mix of the two. There are specific IBS types based on which of these present most frequently:
- IBS-C → constipation-predominant
- IBS-D → diarrhea-predominant
- IBS-M → mixed, alternating between both
As functional medicine doctors, Boulder Holistic doesn’t stop with the symptoms. We look even deeper for the root cause of your gut dysfunction.
What Causes IBS: Finding Your Root Cause
You might be asking yourself, what is irritable bowel syndrome caused by?
For years, IBS was considered either “all in your head” (a psychological issue) or “all in your gut” (a purely digestive issue). More recent studies have revealed that both are true.
IBS is really a disorder of the gut–brain connection. Your gut sends overactive messages to your brain, and your brain processes them in an overactive way. Stress, hormonal imbalances, infections, and other triggers can make this loop even worse.
The symptoms of IBS are often the gut’s way of crying out for help. But the reason behind those symptoms looks a little different for everyone.
Here are some of the most common root causes from a functional medicine perspective:
1. Post-Infectious IBS
Sometimes IBS develops after a case of food poisoning or a stomach bug. In these cases, the immune system can accidentally damage the gut’s nerve cells, leading to long-term issues with gut motility (how food moves through the intestines). This type is especially common in people with diarrhea-predominant IBS (IBS-D).
2. Gut Dysbiosis
Your gut is home to trillions of microbes (called your microbiome) that help you digest food, regulate immunity, and even influence mood. When your microbiome is thrown out of balance—most commonly by antibiotics, poor diet, or stress—it can lead to gas, bloating, inflammation, and unpredictable bowel movements.
A common but often overlooked form of dysbiosis is SIBO (small intestinal bacterial overgrowth), which is caused by an overgrowth of bad bacteria somewhere in the gut.
3. Leaky Gut (Intestinal Hyperpermeability)
Your intestines are designed to be permeable. Their job is to let useful nutrients out into the bloodstream while keeping larger more harmful things in. But if something happens to damage the intestinal lining, undigested food, toxins, and microbes can get out into the bloodstream and trigger your immune system. This “leak” triggers the immune system and may lead to inflammation, food sensitivities, and a wide range of other issues.
There are a few well-known triggers for leaky gut, including certain foods, environmental toxins, and stress.
- Inflammatory foods—such as gluten, dairy, soy, and eggs—can fuel ongoing, low-grade inflammation throughout the body.
- Environmental exposures like heavy metals, mold, and glyphosate (a commonly used herbicide) can disrupt the gut microbiome and weaken the intestinal barrier.
- Chronic stress, unresolved trauma, and poor sleep interfere with cortisol rhythms, vagus nerve signaling, and immune balance—further compromising gut health.
To heal leaky gut, you need to look internal and external to resolve all possible contributors.
4. Mast Cell Activation & Histamine Intolerance
Mast cells are part of your immune system, and when they’re overactive, they release histamine and other chemicals that irritate the gut. This can lead to diarrhea, pain, and increased gut sensitivity.
5. Gut-Brain Axis Disruption
The gut is called your “second brain” for a reason. Stress, trauma, or nervous system imbalance can disrupt the vagus nerve—the communication superhighway between your gut and your brain. When this happens, digestion and pain perception both get thrown off.
6. Genetic & Epigenetic Factors
Genetics don’t cause IBS on their own, but certain genetic variations (called SNPs, or “snips”) can make someone more vulnerable when combined with stress, diet, or environmental triggers.
Three genes in particular often show up in gut-related issues:
- MTHFR: This gene helps process folate and make methyl groups, which are crucial for detoxification, neurotransmitter balance, and regulating inflammation. Variants here can make it harder to clear toxins or calm inflammation, which can worsen IBS symptoms.
- DAO: Diamine oxidase is the main enzyme that breaks down histamine in the gut. If DAO activity is reduced, histamine can build up and contribute to food sensitivities, bloating, and diarrhea—symptoms that overlap with IBS.
- COMT: This gene helps break down stress hormones and neurotransmitters like dopamine and norepinephrine. Variants here can make someone more stress-sensitive, which directly affects the gut–brain axis and can amplify IBS flares.
Your environment, diet, stress levels, and toxin exposures can “switch on” or “switch off” how these genes are expressed. In other words, your genes aren’t necessarily good or bad, but the way you live can push them in one direction or the other.
A Functional Medicine Approach to Diagnosing IBS
Conventional medicine often stops at the label. Functional medicine goes deeper, using a root-cause approach to figure out why your gut is misfiring in the first place.
The tests we use to diagnose and treat the root cause of IBS include:
- Comprehensive stool testing → looks at your gut bacteria, parasites, inflammation levels, and digestive function.
- SIBO breath test → checks for bacterial overgrowth in the small intestine.
- Leaky gut panels (zonulin) → measure whether your gut lining is letting things through it shouldn’t.
- Mast cell and histamine markers → look for immune system overactivity.
- Food sensitivity testing → helps uncover which foods may be triggering your symptoms.
- Adrenal and cortisol rhythm testing → checks how stress is affecting your digestion.
- Heart rate variability (HRV) or vagal tone → measure how well your nervous system is communicating with your gut.
- IBS Smart test → measures levels of certain antibodies in the blood that may indicate post infectious IBS
By looking at the whole body, we can connect the dots and build a personalized plan that targets the actual causes of your IBS, not just the symptoms.
Irritable Bowel Syndrome Treatments Strategies: From Quick Fixes to Deeper Healing
Irritable Bowel Syndrome Medications (conventional tools for symptom relief as needed):
- Medications that calm cramping (antispasmodics).
- Anti-diarrheals or gentle laxatives for constipation.
- Rifaximin, a non-absorbed antibiotic often used for SIBO.
- Low-dose antidepressants that calm nerve pain in the gut.
These can bring temporary relief, but they don’t fix the root cause.
Functional & Integrative Therapies for IBS
Nutraceuticals (supplements that work like medicine):
- Digestive enzymes → help break down food more effectively.
- Herbal antimicrobials (like oregano oil, berberine, or allicin) → target bacterial overgrowth or dysbiosis.
- Probiotics (Saccharomyces boulardii and spore-based strains) → rebalance the microbiome.
- Gut-healing nutrients (L-glutamine, Tributyrin X, zinc carnosine, marshmallow root) → repair and soothe the gut lining.
- DAO enzyme or quercetin → help with histamine intolerance.
- Magnesium or binders → ease constipation and support detox.
Targeted Diets (used short term and always guided):
- Low FODMAP diet → reduces gas and bloating by removing fermentable foods.
- Low-histamine or low-oxalate diets → if food intolerances are driving symptoms
- Elemental diets → simple, pre-digested nutrition used in stubborn SIBO cases or during severe flares.
- Carnivore diet → recommended in some cases
While there is no one-size-fits-all irritable bowel syndrome diet, many people get relief by changing the way they eat. The goal with any of these diets is to heal, not restrict. Once your gut is healing, foods are slowly reintroduced so you can see how your body reacts to each one.
Peptides: The New Frontier in Gut Repair
Peptide therapy is an exciting and emerging field in functional medicine. These short chains of amino acids can heal IBS naturally by instructing your cells to repair the gut lining or balance the immune response. Some peptides are taken by mouth, while others are delivered through a simple injection.
A few of the most exciting peptides currently in use include:
1. BPC-157
Known as the “body protection compound,” BPC-157 promotes tissue repair, reduces inflammation, and supports healing of the gut lining. It has shown promise in treating ulcers, leaky gut, and post-infectious gut damage.
2. Larazotide Acetate
This peptide works to ‘seal up’ the gut lining. It’s been researched for celiac disease, but it may also support those with IBS when the gut barrier is weakened.
3. KPV (Lysine–Proline–Valine)
This naturally-occurring peptide has both anti-inflammatory and immune-modulating properties. KPV helps those with intestinal inflammation and mast cell activation. It may also help mucosal healing for those with IBS or IBD-lite.
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Peptides like BPC-157, Larazotide Acetate, and KPV are just the newest tool in the functional medicine tool box. As always, our goal isn’t just to silence your symptoms — it’s to identify the unique mix of factors driving your IBS and build a personalized plan for long-term healing.
How to Cure IBS Permanently
Despite what you might have been told, IBS isn’t a life sentence. Whether it began in your gut or not, functional medicine has the tools to revive your microbiome, heal your intestinal lining, and reset your nervous system for true and lasting relief.
Let us help you find the root cause of your IBS. Schedule a consultation with Boulder Holistic Functional Medicine and get your customized functional medicine treatment plan today!
