Reversing Crohn's and Colitis Naturally

Fecal microbiota transplantation (FMT) has become one of the most intriguing—and misunderstood—tools in the world of gut health. In this episode, Josh breaks down what fecal transplants actually do, where the science is strongest, and why they should not be treated as a universal “miracle cure.”

The conversation begins with the basic science behind FMT: transferring microbes from a screened donor into a recipient with the goal of restoring microbial diversity and improving the ecology of the gut microbiome. Josh explains how this relates to intestinal health, immune-system regulation, microbial metabolism, nutrient production, and the overall balance of the gut ecosystem.

A major focus is the established use of FMT for recurrent C. difficile infection, including the research discussed in the episode showing dramatically better outcomes than some conventional approaches. Josh then explores why people with Crohn’s disease, ulcerative colitis, IBS, SIBO, and other chronic gut conditions are increasingly interested in FMT—even though the episode emphasizes that applications outside recurrent C. difficile remain investigational.

The most important part of the discussion is what happens when an FMT fails. Josh identifies three major considerations: the relationship between the immune system and the microbiome, the “terrain” or environment into which the new microbiome is introduced, and what happens after the transplant. Factors discussed include chronic stress, environmental exposures, infections, diet, alcohol, processed foods, prebiotics, and other aspects of post-transplant care.

The episode also addresses the serious risks associated with DIY fecal transplants and explains why donor screening and medical oversight matter.

For anyone interested in gut health, inflammation, the microbiome, root cause, or the relationship between the immune system and chronic inflammatory disease, this episode offers a more nuanced way to think about FMT: not simply as adding “good bacteria,” but as attempting to rebuild an entire microbial ecosystem.

TOPICS DISCUSSED:

• Why FMT Is Gaining Popularity + The Central Failure Problem
• What Fecal Microbiota Transplantation Actually Is
• FMT For Recurrent C. Difficile And What The Research Shows
• FDA-Approved FMT Products And Delivery Methods
• The Microbiome, Microbial Diversity, And Immune-System Relationship
• FMT Delivery Methods: Enema, Capsules, And Colonoscopy
• DIY Fecal Transplants And Serious Safety Risks
• Why Fecal Transplants Fail: Immune System Vs. Microbiome
• The “Terrain” Problem And Post-FMT Care
• FMT For Crohn’s, Colitis, And Other Conditions: Promising But Investigational

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IBS and IBD are often confused with one another, but they are not the same condition—and understanding the difference may be one of the most important steps in making sense of chronic gut symptoms.

In this episode, Josh Dech breaks down the distinction between irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD), including Crohn’s disease and ulcerative colitis. He explains why IBS is generally considered a functional disorder, while IBD involves structural changes such as inflammation, ulceration, strictures, and tissue damage.

The conversation also explores the surprising similarities between IBS and IBD. Both can involve abdominal pain, diarrhea, constipation, urgency, bloating, dysbiosis, gut-barrier disruption, environmental triggers, stress, lifestyle factors, and medication-related aggravation. Josh also discusses why people with IBD can continue experiencing IBS-type symptoms even when their inflammatory disease is considered to be in remission.

A major focus of the episode is the relationship between IBS and SIBO—small intestinal bacterial overgrowth. Josh highlights research suggesting substantial overlap between IBS and SIBO, particularly in people experiencing mixed constipation-and-diarrhea symptoms.

From there, he introduces a provocative hypothesis: could some cases of IBD potentially develop following an earlier IBS/SIBO pattern? Josh walks through his own population-attributable-risk thought experiment and arrives at a theoretical range suggesting that a substantial percentage of IBD could potentially be connected to this progression.

Importantly, Josh emphasizes that this is a theory requiring further research—not an established conclusion.

The episode ultimately raises a bigger root-cause question: if certain forms of gut dysfunction can be identified earlier, could earlier investigation and intervention potentially change the trajectory of chronic inflammatory gut disease?

For anyone interested in gut health, the microbiome, inflammation, immune-system dysfunction, SIBO, IBS, Crohn’s disease, ulcerative colitis, or root-cause approaches to chronic illness, this episode provides a provocative framework for thinking about where inflammatory bowel disease may begin—and whether there could be opportunities to intervene earlier.

TOPICS DISCUSSED:

• IBS Vs. IBD: Fundamental Differences And Similarities
• IBS Symptoms, Diagnosis, Subtypes And Rome Criteria
• SIBO And Its Relationship To IBS
• IBD Symptoms, Inflammation And Structural Damage
• Crohn’s Disease Vs. Ulcerative Colitis
• Shared Triggers: Stress, Environment, Medications And Lifestyle
• The Gut-Brain Axis, Dysbiosis And Gut-Barrier Dysfunction
• IBS/IBD Prevalence And Diagnostic Changes
• Josh’s IBS → SIBO → IBD Population-Risk Thought Experiment

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Crohn’s disease and ulcerative colitis are often approached primarily through the lens of symptom management, medication, and surgery. But what happens when we start asking a different question: What may have contributed to the development of the disease in the first place?

In this episode, Josh Dech explores a root-cause approach to inflammatory bowel disease (IBD), challenging listeners to look beyond the label and investigate the layers that may influence gut health, inflammation, the microbiome, and immune-system regulation.

The conversation covers the relationship between diet and IBD, including the Crohn’s Disease Exclusion Diet (CDED), Ulcerative Colitis Exclusion Diet (UCED), and Specific Carbohydrate Diet (SCD). Josh also discusses research involving supplements and probiotics such as curcumin, VSL#3, vitamin D, Boswellia, TUDCA, and wormwood—while emphasizing an important distinction: something that helps manage inflammation or induce remission is not necessarily the same thing as identifying and addressing an underlying driver. 

The episode then moves deeper into the root-cause framework. Josh explains why he believes a detailed personal history can reveal important patterns involving early-life factors, antibiotics, food sensitivities, environmental exposures, stress, and microbiome disruption. Rather than automatically ordering extensive testing, he describes using history to determine which potential drivers deserve investigation first.

Several case examples illustrate this approach, including stories involving suspected mold exposure, repeated antibiotic use, structural changes to the digestive tract, and a child with severe ulcerative colitis.

For anyone interested in gut health, IBD, inflammation, the microbiome, immune-system function, and functional medicine, this episode offers a thought-provoking examination of what it means to truly look upstream.

TOPICS DISCUSSED:

• The Root-Cause Philosophy Behind Crohn’s And Colitis
• Medication, Remission, And The Distinction Between Management And Root-Cause Work
• Dietary Approaches To IBD, Including CDED, UCED, And SCD
• Supplements, Probiotics, And Evidence Around Remission
• Microbiome Disruption And Immune-System Regulation
• The Importance Of A Detailed Personal And Medical History
• Antibiotics And Other Potential Contributors To IBD Risk
• Environmental Exposures, Particularly Mold
• Case Studies Involving Patients With Crohn’s/Colitis

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Finding the root cause of Crohn’s disease, colitis, diverticulitis, IBS, and other chronic gut conditions is rarely as simple as ordering one laboratory test. In this episode, Josh Dech explains why a history-first approach can be more valuable than immediately ordering an expensive battery of functional medicine tests.

Josh walks through how he investigates the timeline leading up to chronic gut symptoms, including events that may have occurred months, years, or even decades before diagnosis. He discusses the relevance of factors such as antibiotic exposure, food poisoning, diet, environmental exposures, childhood illness, birth history, ultra-processed foods, and potential mold exposure.

From there, Josh explains how he uses targeted testing to investigate potential contributors to gut dysfunction. The conversation explores the gut microbiome, dysbiosis, environmental toxins, mold exposure, organic acids, hair tissue mineral analysis, blood work, SIBO/IMO testing, genetics, food sensitivity testing, and other specialized assessments.

A major theme throughout the episode is that more testing does not necessarily mean more answers. Josh explains why overlapping tests can provide diminishing returns and why interpreting laboratory data in the context of a person’s history is critical.

The episode also explores the relationship between the microbiome and the immune system, environmental exposures and inflammation, and why identifying potential upstream contributors may be more useful than simply treating downstream symptoms.

For anyone dealing with chronic digestive symptoms or inflammatory bowel disease and wondering where to start with root-cause investigation, this episode offers a practical framework for thinking about gut health, inflammation, microbiome health, environmental factors, and personalized testing—without automatically spending thousands of dollars on every available laboratory panel.

TOPICS DISCUSSED:

• Why A Detailed Health History Comes Before Laboratory Testing
• Identifying Events And Exposures Preceding Gut Symptoms
• Childhood, Birth History, Antibiotics, Diet, And Microbiome Development
• Gut Microbiome Testing, Dysbiosis, And The Gut Zoomer/GI Map Concept
• Environmental Toxins And Mold Exposure Testing
• Organic Acid Testing (OAT) And What It Can Reveal
• Hair Tissue Mineral Analysis (HTMA) And Mineral/Metal Patterns
• Blood Work, Immune Markers, MCAS/CIRS, And Advanced Testing
• Genetic, Hormone, Food-Sensitivity, And VCS Testing

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SIBO—small intestinal bacterial overgrowth—is often treated as though the bacteria themselves are the entire problem. But what if the overgrowth is actually a sign that something deeper in the digestive system has gone wrong?

In this episode of Reversing Crohn’s and Colitis Naturally, Josh Dech takes a root-cause approach to SIBO and explains why simply trying to eliminate excess bacteria may not be enough to create lasting improvement.

Josh breaks down what SIBO is, why the small intestine normally contains dramatically fewer microbes than the large intestine, and what can happen when bacteria migrate into an environment where they don't belong. He explores how excessive fermentation can contribute to bloating, abdominal discomfort, diarrhea, constipation, malabsorption, irritation, and intestinal dysfunction.

The conversation goes deeper into the systems responsible for keeping the gut microbiome balanced, including stomach acid, bile flow, the migrating motor complex (MMC), the ileocecal valve, secretory IgA, antimicrobial peptides, gut motility, stress, medications, parasites, and other potential contributors.

One of the most important concepts in the episode is the difference between treating the overgrowth and addressing its root cause. Josh compares killing SIBO without correcting the underlying dysfunction to putting out a fire without fixing the gas leak.

He also explains the major SIBO-related gas patterns: hydrogen, methane/intestinal methanogen overgrowth (IMO), hydrogen sulfide, and mixed presentations, including how their symptoms can differ.

The episode explores the possible relationship between food poisoning, post-infectious IBS, antibodies, gut nerves, motility, and recurrent SIBO, along with testing options such as IBS Smart, Trio-Smart, lactulose breath testing, and small-intestinal aspiration.

If you're dealing with chronic gut symptoms, IBS, Crohn's, colitis, bloating, constipation, diarrhea, or recurring digestive dysfunction, this episode offers a deeper framework for understanding how the microbiome, immune system, gut motility, and digestive environment can interact.

TOPICS DISCUSSED:

• What SIBO Is And Why Excess Bacteria In The Small Intestine Can Cause Problems
• Root Causes And Underlying Dysfunction Behind SIBO
• The Different Types Of SIBO/IMO: Hydrogen, Methane, Hydrogen Sulfide, And Mixed
• Food Poisoning, Post-Infectious IBS, Antibodies, And The Vinculin/Motility Connection
• The Migrating Motor Complex, Motility, And Intestinal Stagnation
• The Relationship Between SIBO And Crohn’s/Colitis
• Stomach Acid, Bile Flow, pH, And The Digestive Environment
• SIBO Testing And Diagnostic Options

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Josh examines the scientific criteria used to define autoimmune diseases and explains why he believes Crohn's disease and ulcerative colitis are more accurately described as immune-mediated conditions rather than classic autoimmune diseases. He discusses antibodies commonly associated with IBD, the role of the immune system, and why identifying environmental triggers may be more important than simply suppressing inflammation.

The conversation also explores genetics, explaining why inherited susceptibility is only one piece of the puzzle. Josh reviews research involving identical twins, immigrant populations, and changing disease rates across industrialized nations to argue that environment, lifestyle, and the microbiome play a significant role in disease development.

You'll also learn about common risk factors—including antibiotics, smoking, ultra-processed foods, environmental toxins, mold exposure, and nutrient deficiencies—and how each may influence gut health, inflammation, immune system function, and the intestinal microbiome.

Finally, Josh introduces his root-cause framework for restoring health through identifying triggers, replenishing deficiencies, repairing the gut lining, rebuilding the microbiome, and supporting healthy immune regulation.

Whether you're living with Crohn's disease, ulcerative colitis, or simply interested in functional medicine and root-cause healing, this episode offers a thought-provoking perspective on gut health, chronic inflammation, the microbiome, and the future of IBD treatment.

TOPICS DISCUSSED:

• Autoimmune Theory And Why It's Challenged
• Root-Cause Model Of Crohn's And Colitis
• Genetics Versus Environmental Influences
• Environmental Toxins And Modern Lifestyle
• Gut Microbiome, Microbes, And Immune Responses
• Antibiotics, Smoking, Birth Control, And Other Risk Factors
• Leaky Gut And Immune Dysregulation
• The Five R Framework For Recovery

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In this episode, IBD specialist and functional medicine consultant Josh Dech breaks down the three most well-studied dietary approaches for inflammatory bowel disease (IBD): the Crohn's Disease Exclusion Diet (CDED), the Ulcerative Colitis Exclusion Diet (UCED), and the Specific Carbohydrate Diet (SCD). Josh explains the clinical evidence behind each approach, including research demonstrating steroid-free remission rates, improved mucosal healing, and strategies for supporting the gut microbiome while reducing inflammation.

You'll also learn when an elemental diet becomes necessary—an advanced nutritional intervention used when severe inflammation makes normal eating nearly impossible—and why cleaner elemental formulas may offer advantages over conventional hospital products.

Throughout the episode, Josh challenges conventional recommendations commonly given during IBD flares, discussing why many standard hospital diets focus only on reducing digestive workload while overlooking the role of processed foods, additives, sugars, and other factors that may influence gut health and the microbiome.

Most importantly, Josh explains why dietary therapy alone is rarely the complete answer. While therapeutic diets can help reduce inflammation and induce remission, long-term recovery requires identifying and addressing the underlying root causes driving chronic immune dysfunction.

If you're looking for evidence-based nutrition strategies, a deeper understanding of gut health, microbiome balance, inflammation, immune system function, and root-cause healing for Crohn's disease or ulcerative colitis, this episode provides a practical roadmap grounded in both clinical research and functional medicine principles.

TOPICS DISCUSSED:

• CDED (Crohn's Disease Exclusion Diet)
• UCED (Ulcerative Colitis Exclusion Diet)
• Hospital Diets and Criticism of Conventional Nutrition Advice
• Elemental Diets and Severe Flare Management
• Specific Carbohydrate Diet (SCD)
• Root-Cause Healing vs. Symptom Management
• Gut Microbiome, Dysbiosis, and Bacterial Mechanisms
• Foods to Include vs. Foods to Eliminate During Flares

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Josh challenges several conventional assumptions surrounding Crohn's disease and ulcerative colitis while presenting a root-cause approach focused on identifying the underlying drivers of chronic inflammation. He discusses how toxins, microbial imbalances, nutrient deficiencies, environmental exposures, stress, and immune system dysfunction can interact to influence gut health and recovery.

Listeners will learn why healing often occurs in layers, how biofilms can temporarily release toxins as they're disrupted, why the microbiome changes throughout recovery, and how immune system shifts may produce new symptoms even when overall health is improving. Josh also explains the roles of nutrient replenishment, nervous system regulation, detoxification pathways, hormone fluctuations, and individualized treatment protocols in creating the non-linear healing patterns many people experience.

Throughout the episode, he emphasizes the importance of distinguishing between expected healing responses and signs that a protocol may need to be adjusted. Rather than chasing symptom suppression alone, Josh encourages listeners to investigate the root cause of inflammation while using data, testing, clinical history, and individualized strategies to guide treatment decisions.

If you've ever wondered why your gut health seems to improve one week and worsen the next, this episode provides a framework for understanding the complexities of healing, the microbiome, inflammation, immune system function, and the root-cause approach to long-term digestive wellness.

TOPICS DISCUSSED:

• Why healing is not linear
• Root-cause model (toxins, microbes, deficiencies)
• Immune system shifts during healing
• Biofilms and toxin release
• Detox pathways and healing reactions
• Microbiome changes during recovery
• Nutrient depletion and replenishment
• Nervous system regulation and healing

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Antibiotics have transformed modern medicine and remain essential for treating serious bacterial infections—but are they being overused? In this episode, Josh explores the growing concern around unnecessary antibiotic use and what it means for your gut health, microbiome, immune system, and long-term recovery from chronic digestive conditions.

Drawing on CDC statistics, Josh explains why many antibiotic prescriptions may be avoidable and how repeated exposure can contribute to microbiome disruption, dysbiosis, inflammation, antibiotic-associated diarrhea, and increased susceptibility to opportunistic infections. He also explains the science behind how antibiotics work, including their effects on bacterial cell walls, protein synthesis, DNA replication, and metabolic pathways.

Josh emphasizes a root cause approach to gut health, encouraging listeners to become informed advocates for their own care by asking better questions before starting antibiotics while recognizing that life-threatening infections still require conventional medical treatment.

If you're looking to better understand the relationship between antibiotics, the microbiome, inflammation, immune function, and chronic digestive disease, this episode provides a practical framework for making more informed decisions about your health.

TOPICS DISCUSSED:

• Antibiotic overuse and CDC statistics
• How antibiotics affect the gut microbiome and immune system
• How antibiotics work biologically
• Natural antimicrobials and their mechanisms
• Oregano, garlic, berberine and other natural options
• Biofilms, quorum sensing and bacterial resistance
• When antibiotics are absolutely necessary

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Is taking probiotics really the best way to restore your gut microbiome—or could it actually be keeping you stuck?

Josh explains how the gut microbiome develops, why modern lifestyles contribute to chronic inflammation, immune dysfunction, and microbial imbalance, and how factors like ultra-processed foods, chronic stress, environmental toxins, poor sleep, mold exposure, and repeated antibiotic use influence long-term gut health.

He also discusses why many probiotics are transient rather than permanent colonizers, why aggressive "kill-the-bad-bacteria" protocols can sometimes worsen symptoms, and how drainage pathways, detoxification, nutrient status, and gut lining repair all influence whether beneficial bacteria can successfully thrive.

Whether you're living with Crohn's disease, ulcerative colitis, IBS, chronic digestive symptoms, or persistent inflammation, this episode offers a functional medicine perspective on why lasting healing requires more than simply adding another supplement. You'll learn why the order of healing matters and how creating the right internal environment may be the missing piece in rebuilding a resilient microbiome naturally.

TOPICS DISCUSSED:

• Root causes of gut dysbiosis and microbiome imbalance
• Why probiotics often fail to create lasting change
• The 5R gut healing framework
• Environmental factors affecting gut health (toxins, mold, processed food, stress)
• How the microbiome develops from infancy through adulthood
• Drainage pathways, detoxification, and congestion
• Why antimicrobial protocols can backfire

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