Making Sense of SIBO: A Functional Nutrition Treatment Approach

October 29th, 2023

The gut microbiome is front and center in integrative and functional medicine. We now understand that maintaining balance in the gut microbial population is important for everything from immune system function and energy production to metabolism and nutritional status (1).  

While our resident microbes normally exist in a symbiotic state, there are many factors like diet, lifestyle, medication use, toxin exposure, and infections that can shift the balance toward dysbiosis (an imbalance in the microbiome)(1). Small intestinal bacterial overgrowth (SIBO) is one form of dysbiosis that’s become more commonly recognized. In this article, we’ll explain what SIBO is, how it develops, and how functional nutritionists go about treating it.

SIBO 101

The gastrointestinal (GI) tract contains a rich environment of bacteria, viruses, fungi, and more. When in balance, these resident inhabitants provide benefits like strengthening the intestinal barrier, producing antimicrobial compounds, preventing pathogen overgrowth, supporting healthy immune system function, and promoting the metabolism of nutrients, toxins, and medications (2).

The oral cavity, stomach, and duodenum contain microbes in relatively small amounts but as you move through the GI tract, bacterial numbers increase significantly with the largest concentration being found in the colon (1). In SIBO, the bacteria that normally reside in the colon migrate into the small intestine, which can cause uncomfortable symptoms like bloating, distention, abdominal pain, gas, flatulence, diarrhea, and constipation. Common underlying causes of SIBO include motility issues, digestive enzyme insufficiencies and deficiencies, structural abnormalities, and immunodeficiency.

  • Dysmotility. The migrating motor complex (MMC) is a process the body uses in the fasted state to act as the housekeeper of the intestine. MMC action starts in the stomach and continues throughout the small intestine to sweep away debris (including bacteria) that may be hanging out there (3). MMC may be impaired after a bout of food poisoning when vinculin and cytolethal distending toxin B (CdtB) antibodies are produced (4). These antibodies damage the MMC, which allows bacteria to accumulate in the small intestine but also allows colonic bacteria to move up into the small intestine. Anti-vinculin and anti-CdtB antibodies are considered a trigger for the development of irritable bowel syndrome (IBS)(4).

Other conditions and factors associated with dysmotility include gastroparesis, inflammatory bowel disease (IBD), celiac disease, Ehlers-Danlos syndrome, traumatic brain injury, hypothyroidism, the use of medications like opioids, chronic stress, gastrointestinal surgery, fistulas, and stenosis (1,5-8).

  • Digestive Enzyme and Hydrochloric Acid Deficiency. The digestive process is complex and requires adequate production of hydrochloric acid, bile, and digestive enzymes(9). When there’s not enough of these facilitators of digestion, large food particles enter the small intestine, contributing to bacterial fermentation and unpleasant digestive symptoms. Adequate stomach acid, bile, and digestive enzymes are also an important first line of defense against microbes taking hold in the body. Gastric acid and bile help to prevent bacteria that’s ingested with food from passing through the intestines, and pancreatic enzymes digest and neutralize bacteria within the intestine (9).
  • Structural Issues. The ileocecal valve (a sphincter separating the small intestine from the colon) and appropriate motility in the ileum are important to prevent colonic bacteria from entering the small intestine (9). If this valve isn’t working properly, fecal contents and gas from the colon can regurgitate into the small intestine causing SIBO (10).

Other structural issues in the bowel like abdominal and intestinal adhesions, diverticulosis, strictures, fistulas, and certain types of gastric bypass that impact motility can increase the likelihood of SIBO (9).

  • Immunodeficiency. People with immunodeficiency disorders (AIDS, combined variable immunodeficiency, and IgA deficiency) have an increased risk of SIBO due to inadequate secretory IgA production. SIgA helps to prevent bacterial overgrowth and serves to maintain a healthy immune response in the gut (9).

SIBO Subtypes

Researchers have identified three subtypes of SIBO:

  1. Hydrogen (H2)-Dominant: is associated with diarrhea-predominant irritable bowel syndrome (IBS-D) and IBS with mixed bowel habits (IBS-M)(11).  May be characterized by the overgrowth of Escherichia coli, Klebsiella, and Enterococcus (11).  
  2. Intestinal Methanogen Overgrowth (IMO): is associated with constipation-dominant IBS (IBS-C). Methanobrevibacter smithii (an archaeon previously classified as a type of bacteria) is thought to be the culprit and is not confined to the small intestine.
  3. Hydrogen Sulfide (H2S)-Dominant: is associated with IBS-D, and H2S producing bacteria like Fusobacterium and Desulfovibrio may be culprits (12).

How is SIBO Diagnosed?

Small bowel aspirate with microbial levels of ≥103 CFU/mL in the small intestine was previously considered the gold standard for diagnosing SIBO (12). But new research suggests comprehensive breath testing may be more accurate (12).

The theory behind breath testing is that H2, H2S, and methane (CH4) gasses are the result of microbial metabolism, and since these gasses are exhaled in the breath, it’s possible to measure their levels to give an indication of microbial overgrowths (12).  Carbohydrate breath testing for SIBO most often uses glucose (a monosaccharide that’s easily absorbed in the small intestine) and lactulose (a disaccharide that has limited absorption) (11). Research suggests that:

  • A rise in H2 of ≥ 20 parts per million (ppm) from baseline within 90 minutes of ingesting the test substrate indicates H2 SIBO(11).
  • A CH4 level of ≥ 10 ppm at any point during testing indicates CH4 SIBO(11). 
  • A H2S level of 3 ppm at any time during testing indicates H2S SIBO (13).

A Functional Nutrition Approach to Treating SIBO

SIBO can cause malabsorption and leaky gut, so serious complications like malnutrition and chronic inflammation can result when it’s left untreated (1,9). Effectively eradicating SIBO and preventing recurrence requires practitioners to zoom out and understand the root cause(s) of SIBO in a particular patient.  The IFN Academy STAIN model is a framework clinicians can use to assess the underlying dysfunction, which is crucial for determining the best course of action.

STAIN refers to stress, toxins, adverse food reactions, infections, and nutritional factors, all of which can be driving gut dysfunction leading to SIBO. Addressing root causes with nutrition, probiotics, antimicrobials, digestive support, and lifestyle can be very effective.

Diet Therapy for SIBO

The research is still emerging, so there isn’t one specific diet that’s recommended across the board for SIBO (14). However, a therapeutic elimination diet that reduces inflammation, immune system activation, and microbial fuel can provide symptom relief while working to rebalance the gut microbiome.

Diet-related options to consider for SIBO include:

Practitioners should tailor the diet therapy to the patient and be mindful that extreme dietary restriction is likely unnecessary. 

In addition to an elimination-type diet, patients should be educated to eat routine meals that are spaced about 4-5 hours apart, chew thoroughly, consider intermittent fasting, and practice pre-meal deep breathing to encourage proper MMC function (3).

Probiotics for SIBO

While it’s often recommended that probiotics be avoided during SIBO treatment, research clearly shows that probiotics are beneficial. Here’s a chart detailing the research findings:

Type of Trial Clinical Finding
2010 Randomized Controlled Trial A probiotic formula containing Lactobacillus casei, Lactobacillus plantarum, Streptococcus faecalis, and Bifidobacterium brevis was more effective for SIBO than metronidazol (a commonly used antibiotic for SIBO)(17).
2017 Meta-analysis of 18 clinical trials Probiotic supplementation effectively decontaminated SIBO, decreased H2 concentration, and relieved abdominal pain (15).
2018 Randomized Controlled Trial A probiotic formula containing Saccharomyces boulardii, Bifidobacterium lactis, Lactobacillus acidophilus, and Lactobacillus plantarum given to patients with IBS plus SIBO led to significant improvement in IBS symptom scores and pain (16).
2022 Narrative Review Three weeks of treatment with Saccharomyces boulardii, a probiotic yeast, led to improvements in symptoms like flatulence, diarrhea, gas, and pain in those with SIBO.

Three weeks of treatment with various lactobacillus strains led to improvements in stool consistency and abdominal pain in those with SIBO (18).

As you can see, a variety of probiotic strains have been effective, so you may not need to look for a specific strain. Overall, probiotics may impart their benefits by reinforcing the wall of the intestine, preventing pathogens from attaching to the gut wall, creating substances that eradicate or impede pathogens, and preparing the immune system to target pathogens (19). Probiotics may also help to repair MMC activity (20).

Antimicrobials for SIBO

While antibiotics (like rifaximin) are often the go-to for SIBO treatment, herbal antimicrobial preparations have been found to be just as effective at reducing unwanted bacteria throughout the GI tract (21, 22).  Oregano, berberine, and neem are all effective, however products that contain more than one herbal antimicrobial may be more effective for SIBO eradication(21).  

Digestive Support and Prokinetics for SIBO

Since maldigestion is a root cause of SIBO, ensuring adequate stomach acid and digestive enzyme production is critical. If inadequate stomach acid and/or pancreatic enzymes are a contributing factor, consider supplementing (9).

Likewise, natural prokinetic agents like ginger, melatonin, curcumin, and peppermint oil, can be used to help improve motility in the stomach and small intestine to discourage bacterial overgrowth and prevent SIBO recurrence (23,24,25).

Lifestyle Strategies for SIBO

In addition to diet and supplements, lifestyle strategies that support gut health and nervous system balance are equally important.  Chronic stress is a root cause of SIBO and vagus nerve dysregulation has been found in those with bacterial overgrowth (6, 26). Patients should be encouraged to practice daily techniques to optimize parasympathetic tone and allow optimal production and delivery of digestive secretions via a healthy vagus nerve. Research-supported techniques include aerobic exercise, walking, meditation, massage, yoga, singing and humming, breathwork, and emotional freedom technique (27, 28, 29, 30, 31,32, 33).

SIBO Treatment: Putting It All Together

SIBO is a form of dysbiosis that can cause uncomfortable digestive symptoms like bloating, gas, diarrhea, constipation, and abdominal pain. If left untreated, SIBO can lead to serious complications like malabsorption and increased intestinal permeability. Effective SIBO treatment requires an investigation of root causes and a treatment plan that’s personalized to the individual. Functional nutritionists can use diet therapy, probiotics, antimicrobials, digestive support, and lifestyle modification to help patients successfully overcome SIBO. Sign up for your IFN Academy training to learn more about treating SIBO and other gut-related disorders.

By: Kellie Blake, RDN, LD, IFNCP


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