Exploring the Complex Physiology Behind SIBO and IBS

August 23, 2024

Defining SIBO and its Prevalence

Small intestinal bacterial overgrowth (SIBO) is a condition characterized by an abnormal increase in the number and/or type of bacteria, fungi, viruses and protozoa in the small intestine. Though the standard definition states that counts of ≥105 colony forming units (CFU)/mL of proximal jejunal aspirate is diagnostic of SIBO, experts like Dr. Mark Pimentel argue that as little as 103 CFU/mL can be considered pathological if certain gas-producing microbes are present.

SIBO is increasingly prevalent, affecting an estimated 15% of the general population. Up to 84% of irritable bowel syndrome (IBS) patients test positive for SIBO. IBS and SIBO share underlying pathophysiologic mechanisms, though they are not synonymous conditions.

Differentiating SIBO and SIFO

SIBO refers specifically to small intestinal bacterial overgrowth, while small intestinal fungal overgrowth (SIFO) refers to excessive fungi in the proximal small bowel, most commonly Candida species like C. albicans. These two types of small intestinal infections require different treatment approaches – SIFO is typically treated with anti-fungal medications, while SIBO requires antibiotics or antimicrobial botanicals.

Hydrogen vs Methane SIBO

There are different gas profiles associated with SIBO that correspond to the type of microbial flora present. Hydrogen-predominant SIBO occurs when fermentative bacteria like E.coli, Klebsiella or Streptococcus species overgrow and produce excess hydrogen gas. Methane-predominant SIBO involves archaea species like Methanobrevibacter smithii that generate methane by consuming hydrogen.

Methane slows intestinal transit, so methane-predominant SIBO is associated with chronic constipation. Hydrogen SIBO typically manifests with diarrhea or loose stools from the osmotic effects of unabsorbed short chain fatty acids and gases that pull fluid into the intestinal lumen.

Testing for SIBO

Small intestinal aspiration and culture is considered the gold standard for confirming SIBO, but this invasive method is rarely used clinically. Indirect testing is preferred, typically lactulose breath testing measuring hydrogen and methane gas production after lactulose administration. Glucose breath tests are also sometimes used.

More novel testing approaches have looked at serum anti-vinculin and anti-CdtB autoantibody levels. These markers suggest the possible autoimmune nature of SIBO for a subset of patients, particularly those with IBS overlap.

Causes and Risk Factors for SIBO

There are several theorized mechanisms that contribute to developing SIBO:

Food poisoning leading to post-infectious IBS
Medications slowing gastrointestinal motility like opioids or anticholinergics
Anatomic disruptions or strictures impairing small intestinal flow and transit
Gastroparesis or impaired stomach emptying
Hypochlorhydria and diminished upper GI tract acidity
Dysfunctional intestinal barrier (“leaky gut”)
Vagal and enteric nervous system impairments
Proton pump inhibitor (PPI) use
Aging and altered gastrointestinal physiology
Autoimmune factors

Pimentel’s Theory of Post-Infectious IBS/SIBO Autoimmunity

Dr. Mark Pimentel, a leading SIBO researcher, has proposed an autoimmune mechanism underlying methane-predominant SIBO and post-infectious IBS. The theory suggests that an acute bout of food poisoning from a pathogen like Campylobacter or Shigella triggers antibody development against exposed bacterial toxins like cytolethal distending toxin B (CdtB).

CdtB shares structural homology with vinculin, a protein important for communication between intestinal epithelial cells and the enteric nervous system. The immune system attacks vinculin, impairing vagal nerve signaling to the gut and disabling the migrating motor complex – the clearing waves that prevent bacterial overgrowth.

This leaves patients vulnerable to SIBO relapses without treating the underlying autoimmunity against vinculin perpetuating impaired motility and dysbiosis.

A Role for Lipopolysaccharides

Another pathogenesis theory involves lipopolysaccharides (LPS), inflammatory cell wall components released from gram negative bacteria that exacerbate leaky gut inflammatory responses. LPS crosses the intestinal barrier into circulation, promoting release of inflammatory cytokines like TNF-a and IL-6.

LPS travels to the brainstem and vagal nuclei, contributing to impaired function of the vagus nerve and migrating motor complex. This similarly leads to bacterial stasis and overgrowth in the small intestine.

Risks from Oral Dysbiosis

Interestingly, the oral microbiome may also seed SIBO, particularly in the case of Methanobrevibacter archaea and Candida albicans overgrowth. Those with poor oral hygiene or oral thrush can perpetually reintroduce pathogens into the GI tract through swallowing.

Treatment regimens should include oral rinses and antimicrobial botanical toothpastes targeting the oral microbial burden in addition to addressing the gut, particularly for stubborn, recurrent cases of SIBO.

Botanical Antimicrobials for Treating SIBO

While antibiotics like rifaximin are commonly used for SIBO, antibiotic resistance and adverse effects make them less than ideal for long-term use. Herbal antimicrobials like berberine, garlic, oregano, neem and anise can avoid many of these issues and have broad spectrum activity against things like biofilms.

Products like Biocidin combine multiple botanical extracts chosen specifically for antipathogenic effects against common SIBO organisms, including species of Pseudomonas, E.coli, Klebsiella, Campylobacter, Staphylococcus and Streptococcus, among others.

Biocidin liquid has the advantage of addressing oral microbial burden as well when used as an oral rinse before swallowing.

Avoiding SIFO During Treatment

One drawback of antibiotic therapies for SIBO is that they often predispose towards secondary Candida overgrowth, or SIFO. The antimicrobials wipe out commensal bacteria that normally keep Candida levels in check.

Botanical combinations like Biocidin avoid this by taking a selective approach, targeting pathogens while exerting minimal disruption on beneficial flora. This helps prevent fungal overgrowth as bacterial levels are brought under control.

Protocol for Treating SIBO

An integrative SIBO treatment protocol involves 5 key components:

Diet – An anti-inflammatory, low FODMAP, low sugar diet is advised to help manage symptoms without feeding pathogens long-term.
Antimicrobials – Herbal antimicrobials like Biocidin (and anti-fungal Olivirex when methane levels are high) help lower pathogen burden and biofilms in the small intestine without resistance issues.
Motility agents – Serotonin agonists or prokinetics can help stimulate migrating motor complex function, though these are not always necessary.
G.I. detox & binders – Activated charcoal and clay help bind endotoxins released during pathogen die-off, minimizing unpleasant Herxheimer reactions
Probiotics – Spore-forming probiotic species help restore commensal flora during and after antimicrobial treatment without disruption from the antimicrobials themselves.

The typical SIBO dosage for herbal antimicrobials like Biocidin is 15 drops twice daily, swished in the mouth then swallowed. Combining Biocidin with olivirex capsules improves efficacy against stubborn methane SIBO cases by adding oregano oil’s anti-fungal and prokinetic benefits.

Proflora probiotic is also advised to help accelerate restoration of healthy flora. Supporting gut detox pathways with binders like BioBotanical’s GI Detox prevents or limits symptoms during pathogen die-off and release of endotoxins.

Individualizing Support for Sustained SIBO Improvements

Generally a course of botanical antimicrobial treatment is recommended for at least 1-2 months, but this varies based on symptom severity and how advanced the dysbiosis is. For those with higher bacterial counts, more stubborn biofilm colonization, or presumed autoimmune components, a longer course of 6-12 months may be needed to eradicate SIBO long-term.

Some patients relapse after initial improvements if not treated aggressively or long enough to heal intestinal permeability, reverse microbial imbalance and calm systemic inflammation and autoimmunity enough for proper migrating motor complex function to recover on its own.

Benefits of an Empirical Approach

Though breath testing can confirm SIBO, it doesn’t change the treatment plan significantly. An experienced functional medicine practitioner can make a clinical SIBO diagnosis based on symptoms, risk factors and medical history. They then empirically treat with antimicrobial botanicals, using patient reported symptom improvements as feedback on efficacy.

This empirical approach based on clinical experience allows the practitioner to save patients money on diagnostic testing fees and provide rapid relief without waiting weeks for tests. The antimicrobials simultaneously act as “theranostics”, both diagnosing and treating dysbiosis in one step.

This simpler methodology was used successfully in a small unpublished case study where 100% of evaluated subjects saw either symptom improvements or complete resolution after using Biocidin and GI detox for one month without any dietary changes or adjunctive interventions.

A Complex, Multi-Factorial Condition

This exploration covers only some of the intricate factors contributing to SIBO pathophysiology – from migrating motor complex impairments and post-infectious autoimmunity to oral microbial translocation and LPS-driven inflammation. Ongoing revelations regarding these disease drivers highlight the importance of an integrated, individualized approach.

While conventional antibiotic treatments may seem effective initially, they rarely address underlying causes, leaving patients vulnerable to relapse. Botanical antimicrobials combined with dietary, nutraceutical and probiotic support provide a more holistic solution that calms systemic inflammation and nurtures inner ecosystem health.

Achieving and maintaining balance in the gut ultimately requires getting to the root of multiple potential disruptors across intestinal anatomy, nervous system signaling, immune function, microbial populations and metabolic processes. Though complex, digestive wellness is within reach with personalized, thoughtful interventions tailored to each unique clinical presentation.