IBS, IBD, and Root Cause Healing: A Holistic Approach to Gut Recovery

Taking Control: Understanding the Roots of Gut Disorders

Why Symptoms Alone Aren’t the Full Story

If you’ve been diagnosed with IBS or IBD—or are living with gut issues without a formal diagnosis—you’re not alone. Digestive disorders now affect over 70 million people in the U.S. alone, and rates of chronic bloating, pain, and unpredictable bowel movements are climbing every year. Despite all the diets, supplements, and medications out there, many people still struggle to find lasting relief.

Why? Because most approaches focus on quieting the symptoms rather than understanding the why behind them.

IBS and IBD aren’t just digestive problems—they’re signs that something deeper is out of balance. Inflammation, immune dysfunction, microbiome imbalances, stress, and even poor sleep all play a role. This is where root cause healing comes in: instead of putting a patch on the symptoms, we start asking what’s driving them.

In this article, we’ll explore how IBS and IBD differ (and overlap), why your gut symptoms might be more than just a random flare-up, and how a whole-system, root cause approach can help you move from frustration to true gut resilience.

This post is part of our Gut Healing Series — a 12-part journey into the hidden roots of digestive imbalance and the natural path back to balance. From microbiome repair to herbal remedies, mindful fasting, and daily rhythms that support your gut-brain connection, each article offers practical steps rooted in science and tradition.

Explore the full series here

IBS vs. IBD: Understanding the Basics (and the Limitations of Conventional Treatment)

At first glance, IBS (Irritable Bowel Syndrome) and IBD (Inflammatory Bowel Disease) can look deceptively similar. Both involve chronic digestive discomfort—things like bloating, abdominal pain, urgency, constipation, diarrhea, or some combination of the above. But under the surface, these two conditions are very different—and those differences matter when it comes to healing.

IBS is considered a functional disorder, meaning that there’s no visible damage or structural change to the gut when examined with a colonoscopy or imaging. The gut simply doesn’t function the way it should. It’s often a diagnosis of exclusion—once serious pathology has been ruled out, IBS becomes the default label. Symptoms are real, but the cause is often unclear. Treatments typically include medications that reduce bowel spasms, fiber supplements, or antidepressants to calm the gut-brain connection. But these solutions often mask symptoms rather than address the root cause.

IBD, on the other hand, is an inflammatory disease—an umbrella term for Crohn’s disease and ulcerative colitis. Unlike IBS, IBD involves visible inflammation and damage to the digestive tract. These are autoimmune conditions, meaning the body’s own immune system mistakenly attacks healthy gut tissue. Conventional treatments rely heavily on pharmaceuticals: anti-inflammatory drugs, corticosteroids, immunosuppressants, and biologics that dampen specific immune pathways. In more severe cases, surgery to remove parts of the bowel may be recommended.

While these medications can be lifesaving and help manage flares, they rarely address why the inflammation started in the first place. Many patients continue to experience symptoms even on medication, and side effects can be significant.

In both IBS and IBD, conventional medicine often stops at symptom suppression. What’s frequently missing is a deeper exploration of the root drivers—things like chronic stress, poor sleep, gut microbiome imbalances, food sensitivities, toxin exposure, trauma, and nervous system dysregulation. This is where a functional or holistic approach can make a profound difference.

Understanding the difference between these conditions—and how they’re treated—is the first step. But healing begins when we stop asking only what is wrong and start asking why the body is reacting in the first place.

The Root Cause Mindset: Shifting How We View Gut Healing

Too often, conventional medicine trains us to see symptoms as the problem—something to suppress, silence, or override. But what if symptoms are actually signals? What if your bloating, urgency, cramping, or fatigue aren't just random annoyances, but messages from your body pointing toward deeper imbalances?

This is the heart of the root cause philosophy.

Instead of chasing symptom relief, we pause and ask: Why is this happening? What’s driving this pattern underneath the surface?

Think of your body like a boat that’s slowly taking on water. If you only bail water out of the bottom, you'll stay afloat for a little while—but the leak will keep filling it up. A root cause approach is about climbing down to find the hole, patching it, and letting the boat stabilize on its own.

For many people with IBS, IBD, or other digestive struggles, that leak may be stress, gut dysbiosis, food sensitivities, or chronic inflammation. But no two leaks look exactly the same—and that’s the power of this philosophy. It recognizes that healing is not about forcing the same protocol on everyone, but about removing the barriers to your own body’s innate ability to repair itself.

Root cause healing isn’t quick or flashy. It’s quiet. Gentle. Often slower than we’d like. But it’s also deep, lasting, and deeply empowering—because it honors the intelligence of the body and helps restore trust in your system again.

Symptoms Are Signals: What Your Gut Is Trying to Tell You

In a root cause approach, symptoms are not the enemy. They’re messengers—your body’s way of waving a red flag and asking for help. When you learn to interpret these messages instead of silencing them, healing becomes possible at a much deeper level.

Here’s what some of the most common gut symptoms are trying to tell you:

• Bloating: Often dismissed as “normal,” bloating is one of the most common signs that your digestive system is struggling. It can indicate poor stomach acid production, enzyme deficiency, small intestinal bacterial overgrowth (SIBO), or imbalanced gut flora. It may also signal that certain foods—often fermentable carbs (FODMAPs)—are feeding the wrong microbes.
• Gas and Cramping: These symptoms suggest irritation in the gut lining or fermentation from undigested food. Cramping can also be a sign of intestinal spasms triggered by stress or inflammation. It’s not just discomfort—it’s information.
• Constipation or Diarrhea: Your bowel movements are a real-time snapshot of gut health. Chronic constipation may point to sluggish motility, dehydration, magnesium deficiency, or a nervous system stuck in fight-or-flight mode. On the other end, frequent diarrhea could reflect inflammation, infection, or an inability to properly absorb nutrients.
• Fatigue: The gut plays a huge role in nutrient absorption and immune regulation. If the gut lining is inflamed or leaky, or if you're not breaking down food effectively, the body may be running on empty—despite eating plenty. Fatigue is also common in those with chronic immune activation, as seen in many IBD cases.
• Skin Flare-Ups: Conditions like eczema, acne, or rashes often have roots in the gut. When toxins or inflammatory proteins leak into the bloodstream (thanks to a compromised intestinal barrier), the skin becomes a secondary detox organ—and symptoms show up on the surface.
• Anxiety and Brain Fog: The gut-brain connection is real. Gut bacteria help produce neurotransmitters like serotonin and GABA, which regulate mood and clarity. If dysbiosis is present—or if inflammation is crossing the blood-brain barrier—mental health symptoms can appear without any clear emotional trigger.

Each of these signals holds a clue. And while it might feel overwhelming to connect the dots, the good news is: these symptoms are reversible. When we listen instead of suppress, when we explore instead of ignore, we get to the true cause—and that’s where real healing begins.

Why Conventional Treatments Often Miss the Mark

Conventional medicine has its strengths, especially in emergency care and advanced diagnostics. But when it comes to chronic gut issues like IBS and IBD, the mainstream approach often falls short — not because doctors don’t care, but because the system isn’t designed to address root causes.

Let’s look at why:

1. Symptom Management, Not System Repair

Traditional treatments for IBS and IBD typically revolve around reducing symptoms with pharmaceuticals. These may include antispasmodics, laxatives, anti-diarrheals, acid blockers, immunosuppressants, or steroids. While these drugs can provide temporary relief or reduce inflammation in acute flares, they rarely address why the gut is inflamed, imbalanced, or dysregulated in the first place.

The result? A cycle of dependence, where symptoms return as soon as the medication wears off — or new symptoms emerge from side effects.

2. Limited Testing, Limited Answers

Many people with gut symptoms are told their labs are “normal” or that “everything looks fine.” But standard tests often miss low-grade inflammation, microbiome imbalances, leaky gut, or nervous system dysregulation. Functional medicine uses more advanced and nuanced diagnostics to uncover what’s really going on — from stool testing and food sensitivity panels to cortisol mapping and nutrient levels.

Without a complete picture, it’s hard to create a complete solution.

3. Overlooking the Mind-Gut Connection

The gut-brain axis plays a powerful role in both IBS and IBD. Yet conventional care rarely integrates stress management, trauma healing, or nervous system retraining into the treatment plan. That’s a major blind spot — because even the best diet or medication won’t stick if your body is stuck in a stress response.

4. One-Size-Fits-All Protocols

Every gut is unique. What triggers symptoms in one person may not affect another. A cookie-cutter approach — a low-FODMAP handout or a single medication — doesn’t account for individual triggers, microbiome diversity, or healing timelines. Without personalization, many patients feel unheard or stuck trying the same options over and over.

5. Ignoring Nutrition and Lifestyle

Despite overwhelming evidence, diet and lifestyle changes are still considered “adjuncts” rather than primary tools in many GI clinics. Rarely are patients coached through how to actually heal their gut through real food, quality sleep, targeted herbs, and nervous system support — the very tools that can create long-term transformation.

How a Root Cause Approach Actually Works

Healing from IBS or IBD doesn’t happen through suppression—it happens through understanding, clearing, and rebuilding. A root cause approach offers a structured way to do just that. Here’s what the process typically looks like:

1. Identify Triggers and Stressors

The first step is detective work. We look closely at what’s inflaming the gut—this might include specific foods, emotional stress, sleep disruption, microbial imbalances, or even trauma stored in the nervous system. Tracking symptoms, reviewing your history, and tuning in to patterns can begin to illuminate what’s throwing your system out of balance.

2. Remove Obstacles to Healing

After identifying your personal triggers, the next essential step is to clear the path for recovery. This can involve eliminating inflammatory foods, managing chronic stress, prioritizing quality sleep, and addressing hidden infections or imbalances in the gut microbiome.

One often overlooked obstacle is the impact of medications. Long-term use of antibiotics, NSAIDs (like ibuprofen), acid blockers, and even certain psychiatric or hormonal medications can compromise the gut lining, disrupt digestion, and alter microbial diversity. While these medications can be necessary, it's important to understand how they may contribute to gut dysfunction—and to explore ways to support and protect your digestive system while using them.

Removing what hinders healing creates space for the body to restore its natural rhythm and resilience.

3. Rebuild the Gut Environment

With the path cleared, it's time to restore. We use nutrient-dense food, targeted herbal support, soothing teas, gut-repairing supplements, and lifestyle shifts to nourish the intestinal lining, balance the microbiome, and regulate the nervous system. The goal isn’t perfection—it’s creating an environment where your gut can thrive again.

4. Reconnect to the Body’s Intelligence

The final step is often the most overlooked. Healing isn’t just physical—it’s also about learning to listen to your body again. When you slow down and tune in, you’ll begin to recognize early signs of imbalance and know how to respond with care, not panic. This reconnection builds trust in your own system, turning healing into a long-term relationship—not just a short-term fix.

Herbs, Foods, and Lifestyle for Gut Recovery

When you’re healing from IBS, IBD, or chronic digestive distress, the path forward isn’t just about what you remove — it’s about what you rebuild. A root cause approach shines when it comes to supporting your body’s natural repair process through nourishment, herbal support, and daily rhythms that restore balance.

Herbs That Help Soothe and Repair

Certain herbs have a long history of calming inflammation, rebuilding the gut lining, and easing spasms or discomfort. A few of the most effective include:

• Marshmallow Root – Rich in mucilage, marshmallow coats the gut lining like a balm, soothing irritation and supporting tissue repair.
• Slippery Elm Bark – Another mucilaginous herb that relieves inflammation, calms ulcers, and promotes bowel regularity.
• Licorice Root (DGL) – Anti-inflammatory and supportive to the adrenal system, licorice helps heal the gut lining and protect against further damage.
• Chamomile – A gentle nervine that calms both the gut and the mind, easing cramping, gas, and stress-related digestive symptoms.

These herbs work best when paired with a comprehensive approach, not taken in isolation — and they can often be combined in teas, powders, or extracts designed for gut repair.

Food as Medicine

Gut-healing foods are simple, soothing, and nutrient-dense. During recovery, it helps to focus on:

• Cooked, easy-to-digest meals like soups, stews, and congee
• Non-irritating vegetables (steamed greens, carrots, squash)
• Healthy fats (olive oil, ghee, avocado) to reduce inflammation
• Gelatin-rich broths for rebuilding the gut lining
• Anti-inflammatory spices like turmeric, fennel, and ginger
• Mindful meals — slowing down, chewing well, and eating in a calm state

The emphasis here is less on restriction and more on giving your body exactly what it needs to feel safe and supported.

Lifestyle That Supports Healing

No gut protocol is complete without attention to how you live your life. Your nervous system, sleep habits, and daily pace all affect digestion. Supporting your gut often includes:

• Daily stress regulation through breathwork, walking, meditation, or time in nature
• Consistent sleep rhythms, Deep gut healing happens at night—especially between 10:00 pm and 2:00 am, when your body is wired for repair.
• Gentle movement to support circulation and motility
• Time away from screens and noise to calm the system
• Creating a rhythm around meals so your body knows when to expect nourishment

When your day supports healing, your gut doesn’t have to work alone.

Reclaiming Your Gut, Reclaiming Your Life

Living with gut issues like IBS or IBD can feel like being stuck in survival mode — constantly scanning for triggers, planning your day around the nearest bathroom, or bracing for the next flare-up. But it doesn't have to stay that way.

Your symptoms are not your identity. They're messages — signals that something deeper needs attention, not suppression. When we stop fighting the body and start listening to it, real healing begins.

The path isn’t always linear, and it certainly isn’t one-size-fits-all. But with the right support, education, and tools, you can absolutely shift from managing symptoms to rebuilding true resilience from the inside out.

If you’re ready for a more structured approach, the Laguna Gut Protocol was built for this. It walks you through the exact herbs, foods, fasting rhythms, and daily practices that support long-term gut healing — without the overwhelm.

For more articles on Gut Health and Holistic Healing visit our Healing Protocol page.

Wishing you deep healing and a happier gut,
Cole 
LagunaBeachApothecary.com