Med Matrix functional medicine and wellness clinic

IBS, SIBO, and Leaky Gut: What Your Gastroenterologist Is Not Testing For

Cole Siefer, Dr. Sasha Rose28:11Gut HealthJanuary 14, 2026

Episode Summary

Cole and Dr. Rose cover gut health from first principles: what causes bloating, why IBS is a diagnosis of exclusion in conventional medicine, and how functional medicine digs deeper with comprehensive stool analysis. Dr. Rose, who has written a book on the mind-gut connection, explains the enteric nervous system (the "second brain"), the role of SIBO and SIFO as common IBS mimics, and the peptides she uses to heal gut inflammation and leaky gut. She expresses 90% confidence in being able to improve bowel habits for motivated patients, and lays out a clear decision framework for when to see a gastroenterologist versus a functional medicine provider.

Key Topics

  1. 1

    Top dietary habits that destroy gut health (processed sugars, alcohol, excessive gluten and dairy)

  2. 2

    The enteric nervous system and the two-way gut-brain connection

  3. 3

    How to recognize gut health symptoms from reflux all the way to hemorrhoids

  4. 4

    What actually causes bloating: anaerobic organisms producing hydrogen, methane, and hydrogen sulfate gas

  5. 5

    The low FODMAP diet as a self-directed bloating experiment

  6. 6

    IBS subtypes: diarrhea-dominant (IBS-D), constipation-dominant (IBS-C), and mixed

  7. 7

    Why IBS is a diagnosis of exclusion in conventional medicine

  8. 8

    SIBO (small intestine bacterial overgrowth) and SIFO (small intestine fungal overgrowth) as IBS mimics

  9. 9

    Comprehensive stool analysis versus colonoscopy: what each reveals

  10. 10

    When to refer to gastroenterology versus treat functionally

Quotable Moments

IBS is considered a diagnosis of exclusion. There's nothing else evident and so you're given an IBS diagnosis. You might be given a recommendation for Miralax and told to deal with your stress.

You come to a functional medicine provider with a previous diagnosis of IBS and we are going to dig deeper. We're going to make sure that it is IBS. It's not something else.

I am 90% confident that I can improve their bowel habits. Now they might not end up having a stellar bowel movement every day for the rest of their life, but 90% of the time I can improve the quality and frequency.

We think of the brain as being in the skull, but there's this whole second brain that's in the gut. It's this real intimate relationship between the nervous system and the gut. Yes, anxiety can affect your digestion, but also your digestive health can affect your mood.

With a leaky gut, the cells that line the gut normally line up together and are permeable enough to let nutrients in but close enough to keep things in the stool. With inflammation, things get through that shouldn't. Larazotide is a peptide that can come in and heal that tight junction.

Treatments Mentioned

Comprehensive stool analysis (GI map): microbiome profiling, inflammation markers, occult blood, infection screeningLow FODMAP diet: self-directed dietary experiment for bloatingInsoluble fiber supplementation: for constipation and stool bulkingMagnesium supplementation: for slow gut motilitySIBO treatment: antibiotics or natural antimicrobials targeting methane or hydrogen producersSIFO treatment: antifungal treatment for small intestine fungal overgrowthBPC-157 peptide: gut inflammation healing (also known for connective tissue applications)Larazotide (oral peptide): tight junction repair for leaky gut syndromeColonoscopy referral: for red-flag symptoms (blood, mucus, suspected inflammatory bowel disease)Food sensitivity testing: part of the functional workup for IBS

Gut Health FAQ

IBS is a diagnosis of exclusion given when nothing else is found. SIBO (small intestine bacterial overgrowth) can present identically with bloating, constipation, diarrhea, and cramping, but it is an actual infection requiring treatment. Many IBS patients actually have untreated SIBO.

Bloating is primarily caused by anaerobic organisms producing excess hydrogen, methane, or hydrogen sulfate gas. Methane-producing organisms slow gut motility, leading to both bloating and constipation. This is a treatable condition, not something to accept as normal.

Leaky gut (intestinal permeability) occurs when inflammation causes the cells lining the gut to separate, allowing molecules to pass into the bloodstream. Larazotide is an oral peptide that heals tight junctions. BPC-157 also helps reduce gut inflammation and restore the intestinal barrier.

See a gastroenterologist if you have blood in your stool, mucus, or symptoms suggesting inflammatory bowel disease. Colonoscopy is the only way to diagnose these. Chronic bloating, constipation, and IBS symptoms without red-flag signs can go directly to a functional medicine provider.

A comprehensive stool analysis reveals microbiome detail, gut inflammation markers, occult blood, and screens for bacterial, viral, parasitic, and candida infections. A colonoscopy primarily rules out structural disease. The two tests complement each other but assess fundamentally different things.

FODMAP stands for fermentable oligosaccharides, disaccharides, monosaccharides, and polyols. A low FODMAP diet temporarily restricts hard-to-digest starches. It can be an effective self-directed experiment to identify food triggers, though it is not intended as a permanent way of eating.

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