If you’ve tried diets, supplements, or multiple SIBO protocols and still don’t feel better, this article explains why. You’ll learn how SIBO, IMO, and SIFO actually develop, why treatment often fails without proper sequencing and nervous system support, and what a more sustainable, root-cause approach looks like. This is for people ready to stop chasing protocols and start rebuilding resilience. I want everyone to have the energy and peace to live out their purpose. 

1) Understanding SIBO, IMO, and SIFO and Why They Matter

Small Intestinal Bacterial Overgrowth (SIBO) is a form of dysbiosis where bacteria that should primarily live in the large intestine overgrow into the small intestine — a region designed for digestion and absorption, not fermentation. When this happens, food begins fermenting too early in the digestive process, producing hydrogen and/or methane gas and driving symptoms far beyond simple bloating.

We now recognize related patterns:

• SIBO (hydrogen-dominant) — commonly associated with diarrhea, bloating, urgency, and anxiety.

• IMO (Intestinal Methanogen Overgrowth) — driven by methanogenic archaea, often linked to constipation, slowed motility, weight gain, and fatigue. And in my case (Uncorrected hypothyroid and elevated TPO antibodies indicative of Hashimoto's Thyroiditis) Did you know that archaea (hardy single-celled organisms) are so resilient they can survive in Yellowstone’s boiling hot springs! 

  

Photo: Me inYellowstone National Park, October 2025

• SIFO (Small Intestinal Fungal Overgrowth) — frequently overlaps with SIBO and may show up as persistent bloating, sugar cravings, rashes, brain fog, or symptom flares after antibacterial treatment. I didn't have any of the typical hallmarks, but boy did I flare (see my Case Study photos)

SIBO is far more prevalent than once believed. Studies suggest it occurs in:

• 50–75% of people with IBS

• Up to 100% of those with fibromyalgia

• Many individuals with:

  • Rosacea: Treatment of SIBO is highly correlated with remission
  • Vitamin B12 and/or folate deficiencies, macrocytic anemia (high MCV value).
  • Joint pain
  • Fatty liver (non-alcoholic steatohepatitis)
  • Celiac disease, Crohn’s disease, ulcerative colitis

Common contributors include low stomach acid, prior antibiotic use, reduced motility (from hypothyroidism, diabetes, opioids, or chronic stress/burnout/overwhelm/trauma, alcohol use, and long-term grain and sugar consumption. Importantly, SIBO often explains why people feel partially better after cleaning up their diet but never fully well.

Left unaddressed, SIBO can perpetuate inflammation, impair nutrient absorption, worsen gut-brain-autoimmune symptoms, and increase long-term risk for metabolic and autoimmune disease. Identifying and addressing it is often a missing step in true gut recovery.

2) Diagnosing SIBO, IMO, and SIFO — Breath Testing Done Right

The most practical and non-invasive way to assess SIBO and IMO is hydrogen and methane breath testing. These tests measure gases produced by microbes, not human cells, after consuming a fermentable sugar. This is an important note, as many of Lifetime's Water & Wellness clients own in-home water ionizers that produce H2 gas. This is a therapeutic gas that reduces reactive oxygen species (ROS) and reduces cellular oxidation (cell aging). When we test for gas levels, we are measuring the levels your microbes produce using lactose (a sugar).

At-Home Breath Testing with FoodMarble (AIRE)

The FoodMarble AIRE device allows for repeated, real-time breath testing without purchasing single-use lab kits each time. When used correctly, it can be a powerful clinical and self-monitoring tool.

Step 1: Obtain the test substrate

• Request lactulose from your provider using CPT code 91065, specifying at-home breath testing.

• If unavailable, a traditional breath test kit can be ordered and used instead.

Step 2: Device setup

• Purchase a FoodMarble AIRE device (HSA/FSA approved)

• Update the app to the latest version (if you have an older version)

• Switch to Expert Mode (Profile → Preferences → Expert Mode) to view results in parts per million (PPM)

Diet Prep (24 hours before testing)

• Eliminate probiotics, long fermented yogurt, and fermented foods for at least 10 days

• Eat a low-fermentable diet (protein, fats, white rice, simple starches). I have pasture-raised ground beef seasoned with salt, cooked in ghee with rice for two meals. 

• Optional: elemental nutrition for the day prior (meal replacement packets)

• Fast 10–12 hours overnight

Test Day Protocol

• Wake up one hour before testing

• Avoid exercise, smoking, or mouthwash

• Record a baseline breath test

• Mix 15 mL (1 Tbsp) lactulose in 8 oz water and drink

• Breath test every 30 minutes for up to 3 hours

Interpreting Results

• Early rises (within 90 minutes) suggest SIBO/IMO

• A rise of ≥20 PPM hydrogen supports diagnosis for SIBO (hydrogen-dominant)

• A level of 10 PPM at any time suggests IMO or (methane-dominant)

• Testing can be repeated mid-protocol to assess response

While breath testing provides helpful data, frankly, it's a pain in the ass. I've done a challenged breath test seven times. Thankfully, in clinical practice, most SIBO doctors (Dr. Siebecker & Dr. Ruscio) recommend a single baseline test and monitoring symptoms. Symptoms still matter. In clinical practice, 90% improvement in hallmark symptoms (bloating, constipation, diarrhea, brain fog) is often more meaningful than chasing a perfectly “negative” test.

3) Treating SIBO, IMO, and SIFO — Sequencing Matters

Treatment is not just about eradication. Timing, tolerance, and nervous system capacity determine success.

Core Approaches:

1.  Low FODMAP Diet

• If you are an abstainer or have a SLOW or FAST COMT and prefer clear dietary guidelines, use this low FODMAP diet plan to ease symptoms.
• I DO NOT RECOMMEND A LOW FODMAP DIET TO CLIENTS. YOU CANNOT EAT YOUR WAY OUT OF THIS.

2.  Herbal or Prescription Antimicrobials

• Herbal options (Candibactin-AR/BR or FC-Cidal + Dysbiocide) have comparable or superior outcomes to rifaximin in some studies

• Courses typically last 14 days and often require repetition

• Pharmaceutical antibiotics may be appropriate in select cases, but carry cost and risk considerations

• CASE BY CASE BASIS. ANTI-MICROBIALS ARE ADDED SEQUENTIALLY IN MY SIGNATURE PROGRAM.

3. Targeted Probiotics
Certain keystone strains show unique benefits according to the work of Dr. William Davis, MD,  and author of the SUPER GUT book. I highly recommend joining his Infinite Health Membership. 

• Lactobacillus reuteri (DSM 17938 & ATCC PTA 6475)
  Shown to reduce methane, suppress Candida, improve constipation, and colonize the upper GI tract

• Lactobacillus gasseri BNR17
  Supports motility, reduces IBS symptoms, and helps rebalance Proteobacteria. It produces bacteriocins that fight gram-negative bacteria linked to SIBO, supports visceral fat reduction, and may persist long-term in the gut

• Bacillus subtilis (NEW!) (HU58/DE111) B. subtilis has replaced B. coagulans in the new SIBO yogurt recipe as it has proven to produce more consistent bacterial counts during fermentation. A reliable fermenter and powerhouse bacteriocin producer, it helps dismantle pathogen biofilms, reduces endotoxemia by activating intestinal alkaline phosphatase, and produces key B vitamins. This makes it a strong ally against harmful microbes and systemic inflammation.

  Together, these strains create a potent anti-SIBO blend that goes far beyond the “yogurt” you’d find at the grocery store. I recommend creating this yogurt over using antibiotics (prescription or herbal) to eradicate SIBO/IMO, due to these strains' ability to produce bacteriocins (natural antibiotics). B. subtilis produces 7 bacteriocins, and L. reuteri and L. Gasseri produce 2 each, for a total of 11! This is why it's called SUPER SIBO yogurt:)

4. Preventing Recurrence
True resolution requires root cause resolution:

• Address nervous system regulation and chronic stress
• Restore motility (drainage) and stomach acid
• Eliminate chronic infections
• Eliminate environmental toxins
• Support bile flow and nutrient absorption/methylation
• Seal leaky gut
• Reintroduce fermentable fibers gradually

SIBO is rarely a one-and-done condition. Like tending a garden, it requires observation, correction, and ongoing support, not repeated "killing" protocols.

Final Thought (TL;DR)

SIBO, IMO, and SIFO aren’t just gut conditions; they’re whole-system signals. When approached with proper sequencing, personalized pacing, and the right support, they become opportunities to rebuild health resilience rather than cycles of relapse. Get the right guide, with the right tools, and participate in the right community. I offer one signature program. Join Now and get the expert help you need.

Clinicians Influencing This Work

The approach outlined here is informed by clinical research and the real-world work of practitioners who have shaped how we understand and treat SIBO, IMO, and related gut-brain patterns. Thank you to Shivan Sharna and her book, Healing SIBO.

Dr. Mark Pimentel, MD
Director of the Medically Associated Science and Technology (MAST) Program at Cedars-Sinai, Dr. Pimentel’s research fundamentally changed how we understand IBS as a microbiome-driven condition. His work on hydrogen- and methane-dominant overgrowth, intestinal motility, and breath testing standards informs how SIBO and IMO are identified and monitored today (Pimentel et al., 2006; Pimentel & Rezaie, 2018). Methane production has been shown to slow intestinal transit, contributing to constipation-dominant symptoms (Pimentel et al., 2006).

Dr. Allison Siebecker, ND
A leading educator in the functional and naturopathic treatment of SIBO, Dr. Siebecker helped bridge conventional research with herbal and nutrition-based protocols. Her emphasis on root causes, treatment sequencing, and individualized care continues to guide practitioner-level SIBO management (Siebecker, 2014). Herbal antimicrobials have demonstrated comparable efficacy to rifaximin in some cases of SIBO (Chedid et al., 2014)

Dr. William Davis, MD
Author of Super Gut, Dr. Davis has expanded the conversation beyond eradication toward microbiome rebuilding. His work emphasizes targeted probiotic strategies, particularly upper-GI-colonizing strains such as Lactobacillus reuteri, and long-term microbial resilience. Additional clinical insights referenced here are drawn from his Inner Circle practitioner membership and educational materials (Davis, 2022). Targeted probiotic strategies may support both microbial balance and symptom improvement when used with proper sequencing (Davis, 2022)

Dr. Michael Ruscio, DC
Dr. Ruscio’s work highlights the importance of testing flexibility, symptom-based outcomes, and avoiding over-treatment. His pragmatic approach reinforces that gut healing is a process of rebuilding capacity rather than chasing perfect lab results (Ruscio, 2018). Clinical improvement often matters more than chasing a fully ‘negative’ breath test (Ruscio, 2018)