Evidence-based answers to your gut health questions
Gut health is foundational to overall wellness. Over 70% of the immune system resides in the gut, making it central to your body's defense mechanisms. The gut microbiome influences neurotransmitter production (over 90% of serotonin is produced in the gut), affects mood and cognition through the gut-brain axis, and is responsible for nutrient absorption and energy metabolism. A compromised gut can trigger systemic inflammation, autoimmune reactions, hormone imbalances, and mental health issues.
The three core principles are:
Healing time varies significantly based on the severity of the condition, individual factors, and adherence to protocols. Mild cases may see improvement in 3-6 months, while more severe or chronic conditions can take 12-24 months or longer. The key is consistency, proper root cause identification, and following a phased approach. Gut healing is not linear - you may experience ups and downs during the process.
Leaky gut (intestinal permeability) is a condition where the intestinal lining develops increased permeability, allowing partially digested food, toxins, and bacteria to penetrate the tissues beneath.
Common symptoms include:
Dysbiosis is an imbalance in the gut microbiome where diversity and balance of bacterial species are disrupted. Common causes include:
SIBO (Small Intestinal Bacterial Overgrowth) occurs when bacteria that normally live in the large intestine proliferate in the small intestine, causing gas, bloating, diarrhea, and malabsorption. Unlike general dysbiosis (which refers to microbial imbalance throughout the gut), SIBO is specifically bacterial overgrowth in the wrong location - the small intestine.
SIBO requires specific testing (breath test) to identify whether it's hydrogen or methane dominant, and treatment protocols differ from general dysbiosis. Common triggers include motility disorders, structural problems, and medications like proton pump inhibitors.
Histamine intolerance occurs when there's an imbalance between histamine accumulation and the body's ability to break it down, primarily due to DAO (diamine oxidase) enzyme deficiency. Symptoms include headaches/migraines, digestive issues, skin problems, nasal congestion, anxiety, sleep disturbances, and heart palpitations.
Gut health plays a crucial role because SIBO, leaky gut, and dysbiosis can all contribute to histamine intolerance. Certain gut bacteria produce histamine, and a compromised gut lining can lead to DAO deficiency. Addressing underlying gut issues is often essential for resolving histamine intolerance.
Essential tests include:
No single test is perfect - combining multiple tests provides the clearest picture of your gut health status.
While zonulin is a protein associated with intestinal permeability and plays a key role in regulating tight junctions, commercial zonulin tests have significant limitations. Research shows that current assays don't actually measure true zonulin and correlate poorly with validated measures of intestinal permeability. The lactulose-mannitol test is considered more reliable for assessing small intestinal permeability.
Yes, testing is highly recommended before starting protocols. One of the most common mistakes is treating symptoms without proper diagnosis. Over 70% of people with gut issues have been previously misdiagnosed, and many conditions (IBS, SIBO, celiac, colitis) present with similar symptoms. Without identifying the root cause through testing, you may follow protocols that don't address your specific issue, waste time and money, or even worsen your condition.
The carnivore diet can be useful as a short-term healing tool for severe cases, particularly when plant foods are highly irritating. However, it's not necessarily a permanent solution. Long-term restriction of carbohydrates may negatively affect thyroid function and gut motility in some individuals. The key is personalization - what works depends on your specific condition, tolerance, and individual response. Most people benefit from gradually reintroducing well-tolerated plant foods once initial healing occurs.
Fermented foods can be beneficial for most people as they provide beneficial bacteria and support microbiome diversity. However, they are problematic for those with histamine intolerance or SIBO. If fermented foods cause symptoms like headaches, digestive distress, anxiety, or worsening of existing issues, it's a sign they should be avoided temporarily. Once the underlying gut issues (especially histamine intolerance or SIBO) are resolved, many people can successfully reintroduce fermented foods.
During the initial healing phase, eliminate:
Focus on whole, unprocessed foods: quality proteins, healthy fats, and well-tolerated vegetables.
Fiber requirements are highly individual and context-dependent. While fiber can support beneficial bacteria and gut health, it can also be highly irritating during active inflammation or with certain conditions like SIBO or severe dysbiosis. Some people do better with lower fiber initially, then gradually increase as healing progresses. Others tolerate certain types of fiber (soluble vs insoluble) better than others. Pay attention to your individual response rather than following blanket recommendations.
Key supplements for gut lining repair include:
Dosages and combinations should be tailored to individual needs and underlying conditions.
Probiotics can be beneficial, but timing and strain selection matter. Taking random probiotics without understanding your specific microbiome imbalances is one of the common mistakes in gut healing. Some people react poorly to certain strains, especially with SIBO or histamine issues. It's often better to first address overgrowths and repair the gut lining, then introduce targeted probiotics. Multi-strain probiotics, soil-based organisms, spore-based probiotics, and Saccharomyces boulardii (for candida) each have different applications.
This is a common misconception. While mastic gum shows some antimicrobial activity against H. pylori, multiple studies confirm that mastic gum alone is insufficient for H. pylori eradication. It has limited efficacy as a standalone treatment. Comprehensive protocols involving multiple antimicrobials and gut lining repair are necessary for successful H. pylori treatment. Mastic gum can be part of a broader protocol but should not be relied upon as the sole intervention.
The 4R/5R protocol is a systematic framework used in functional medicine:
Each phase builds on the previous one, creating a structured path to gut healing.
First, identify the root cause: motility issues, thyroid dysfunction, magnesium deficiency, dysbiosis, low stomach acid, or stress. Then address it specifically:
SIBO requires specific testing (breath test) to identify hydrogen vs methane dominant types. Protocol includes:
Important: Address underlying motility issues and don't stay on restrictive diet long-term. Retest to confirm resolution.
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