Can SIBO Cause Acid Reflux?

Can SIBO Cause Acid Reflux? The Scientific Connection Explained

If you’ve been struggling with persistent acid reflux that doesn’t respond well to medication, you might be dealing with more than just gastroesophageal reflux disease (GERD). Recent research has uncovered a surprising connection between small intestinal bacterial overgrowth (SIBO) and acid reflux symptoms. Understanding this relationship could be the key to finding lasting relief.

What Is SIBO?

Small intestinal bacterial overgrowth (SIBO) occurs when there’s an abnormal increase in the number or types of bacteria in the small intestine. Normally, the small intestine maintains a relatively sterile environment due to gastric acid and bile, which naturally inhibit bacterial growth. When this balance is disrupted, bacteria multiply excessively, leading to various digestive symptoms.

SIBO is typically diagnosed using hydrogen-methane breath tests, which detect gases produced by bacterial fermentation in the small intestine.

The SIBO-Acid Reflux Connection: What Research Shows

Strong Statistical Link

A comprehensive 2025 study published in the Journal of Inflammation Research examined 394 patients and found compelling evidence linking SIBO to GERD. The research revealed that 72.8% of patients in the study had SIBO, and the incidence of GERD was significantly higher in SIBO-positive patients (24.4%) compared to SIBO-negative patients (13.2%). Most importantly, logistic regression analysis identified GERD as an independent risk factor for developing SIBO.

Methane vs. Hydrogen: Different Types Matter

Not all SIBO is the same. The research identified that GERD has a particularly strong association with methane-producing SIBO (SIBO-CH4), which was more prevalent than hydrogen-producing SIBO (SIBO-H2) in reflux patients. This finding suggests that specific bacterial populations that produce methane may play a unique role in reflux symptoms.

High Prevalence in Reflux Patients

Another study in Surgical Endoscopy found that among 104 patients being evaluated for anti-reflux surgery, a striking 60.6% had intestinal dysbiosis—39.4% had SIBO and 35.6% had intestinal methanogen overgrowth (IMO). Patients with dysbiosis were significantly more likely to report troublesome bloating and belching.

How Does SIBO Cause Acid Reflux? The Mechanisms

1. Increased Intra-Abdominal Pressure

When bacteria in the small intestine ferment undigested food, they produce gases like hydrogen and methane. This gas accumulation increases pressure in the abdomen, which can push stomach contents upward into the oesophagus. Research has shown that hydrogen gas production was significantly greater in patients with reflux-associated regurgitation.

2. Transient Lower Esophageal Sphincter Relaxations (TLOSRs)

The lower oesophageal sphincter (LES) normally acts as a valve preventing stomach contents from flowing back into the oesophagus. However, increased gas and pressure from SIBO trigger more frequent spontaneous relaxations of this valve—called TLOSRs—allowing acid and gas to reflux upward. Studies have found that patients with SIBO and dysbiosis had a positive reflux-symptom association in 76.2% of cases, compared to only 31.7% in those without dysbiosis.

3. Impaired Gut Motility

SIBO is often associated with slowed intestinal movement, which delays gastric emptying. When food stays in the stomach longer, there’s more opportunity for reflux to occur. This motility dysfunction creates a vicious cycle where SIBO worsens reflux, and reflux conditions may promote SIBO.

4. Belching and Gas Aerosol

The excessive gas produced by SIBO leads to belching, which creates an aerosol effect—spraying stomach contents, including acid and the enzyme pepsin, up the oesophagus and into the throat. This mechanism explains why many SIBO patients experience both typical reflux symptoms and laryngopharyngeal reflux (LPR) symptoms like throat clearing, hoarseness, and chronic cough.

The Role of Acid-Suppressing Medications

One of the most important findings in recent research concerns proton pump inhibitors (PPIs)—the most commonly prescribed medications for acid reflux.

The PPI Paradox

While PPIs effectively reduce stomach acid, they can create conditions favorable for SIBO development. By reducing gastric acid, PPIs compromise the stomach’s natural antibacterial barrier, potentially allowing bacteria to migrate from the stomach into the small intestine. Research shows that patients with GERD taking long-term PPIs are at increased risk of developing SIBO.

However, the 2025 study found that short-term, low-dose acid-suppressive therapy (averaging 9-10 days) did not significantly affect SIBO development. This suggests that the duration and dose of PPI therapy matter more than short-term use.

Breaking the Cycle

This creates a challenging situation: you take PPIs for reflux, which may contribute to SIBO, which then worsens reflux symptoms—creating a cycle that makes symptoms increasingly difficult to manage with medication alone.

Gut Microbiome Changes in SIBO and Reflux

The 2025 microbiome analysis using 16S rRNA sequencing revealed significant differences in gut bacteria between healthy individuals and those with both SIBO and GERD:

• Dominant bacteria: Patients with SIBO and GERD showed elevated levels of Bacteroides uniformis and Bacteroides stercoris
• Metabolic changes: These patients had differential metabolites primarily associated with ATP-Binding Cassette (ABC) transporters, which play crucial roles in nutrient transport and gut health
• Protective bacteria: Interestingly, Bacteroides uniformis is typically considered beneficial, suggesting complex interactions between gut bacteria and disease states

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Recognising SIBO-Related Reflux Symptoms

If you have acid reflux plus several of these symptoms, SIBO might be contributing:

• Bloating, especially after eating carbohydrates
• Excessive belching or gas
• Upper abdominal discomfort
• Regurgitation (food coming back up)
• Non-acidic reflux that doesn’t respond well to PPIs
• Laryngopharyngeal symptoms: chronic throat clearing, hoarseness, sensation of lump in throat
• Alternating diarrhoea and constipation
• Unintentional weight loss
• Nutritional deficiencies (B12, iron)

Research indicates that patients with SIBO are more likely to have a positive symptom-reflux association, meaning their symptoms directly correlate with reflux episodes detected on testing.

Getting Tested for SIBO

If you suspect SIBO may be contributing to your reflux symptoms, consider:

Hydrogen-Methane Breath Test

This non-invasive test is the clinical gold standard for SIBO diagnosis. After drinking a lactulose or glucose solution, breath samples are collected over 2-3 hours to measure hydrogen and methane production.

Order your SIBO test here.

Positive results indicate:

• Hydrogen increase >20 ppm from baseline within 90 minutes
• Methane concentration >10 ppm at any time point

Additional Testing

Your healthcare provider may also recommend:

• Upper endoscopy to rule out other causes
• 24-hour pH monitoring to assess acid exposure
• Gastric emptying studies
• The Ultimate Gut Health Test

Treatment Approaches: Addressing Both Conditions

Treating SIBO

Research on treating SIBO and its associated reflux symptoms has shown promising results:

• Antibiotics: Rifaximin is commonly prescribed for SIBO treatment
• Herbal antimicrobials: Natural alternatives have shown efficacy in some studies
• Prokinetics: Medications that improve gut motility may reduce SIBO risk, especially when combined with PPIs
• Dietary modifications: Low FODMAP diet can reduce fermentation and gas production

A 2025 study found that treating SIBO in reflux patients led to significant improvements, with 95% of patients able to reduce or stop PPI use entirely after SIBO treatment.

Learn how to treat SIBO naturally (without antibiotics) here.

Addressing Reflux

• Targeted PPI use: Short-term, appropriate-dose PPI therapy when needed
• Alternative acid suppressors: H2 blockers or potassium-competitive acid blockers may have different effects on gut microbiome
• Lifestyle modifications: Elevating head of bed, avoiding trigger foods, eating smaller meals
• Weight management: If applicable, as obesity is a GERD risk factor

Restoring Gut Health

• Probiotics: Specific strains such as Bifido Lactis HN019 or Lactobacillus Rhamnosus GG may help alleviate reflux.
• Prebiotics: Feed beneficial bacteria
• Dietary changes: Emphasise whole foods, reduce processed carbohydrates
• Stress management: The gut-brain connection significantly impacts digestive health

When to See a Healthcare Provider

Seek medical attention if you experience:

• Persistent heartburn despite medication
• Difficulty swallowing
• Unintended weight loss
• Severe abdominal pain
• Blood in stool or vomit
• Symptoms affecting quality of life
• Need for PPI therapy lasting more than 2 weeks

The Bottom Line

Current research strongly supports a bidirectional relationship between SIBO and acid reflux. SIBO can worsen reflux symptoms through multiple mechanisms including increased abdominal pressure, impaired motility, and excessive gas production. Conversely, treating acid reflux with PPIs may create conditions that promote SIBO development, particularly with long-term use.

If you’ve been struggling with refractory reflux symptoms—especially if accompanied by bloating, belching, and poor response to acid-suppressing medications—it’s worth discussing SIBO testing with your healthcare provider. Addressing both conditions together may provide the relief that treating acid reflux alone hasn’t achieved.

The emerging understanding of the SIBO-reflux connection represents an important shift in how we approach digestive health, emphasizing the need to look beyond acid suppression to address root causes of symptoms.

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References

1. Wang ZT, Tan WT, Huang JL, et al. Correlation Between Gastroesophageal Reflux Disease and Small Intestinal Bacterial Overgrowth: Analysis of Intestinal Microbiome and Metabolic Characteristics. J Inflamm Res. 2025;18:33-51. https://pubmed.ncbi.nlm.nih.gov/39780983/
2. Boyle N, Hobson A, Vales A, Haworth J. The prevalence of intestinal dysbiosis in patients referred for antireflux surgery. Surg Endosc. 2021;35(9):4857-4864. https://pubmed.ncbi.nlm.nih.gov/33475845/
3. Gu X, Wang Y, Chen S, et al. Association of gastroesophageal reflux disease with small intestinal bacterial overgrowth: a case-control study. BMC Gastroenterol. 2024;24(1):403. https://pmc.ncbi.nlm.nih.gov/articles/PMC12551192/
4. Sood K, Chaudhary A, Singh S, Sharma S, Daoud M, Sharma S. Treatment of oesophageal and laryngo-pharyngeal symptoms of reflux in patients diagnosed with SIBO and IMO with antibiotics. Dig Endosc. 2025 Jan 7. https://pubmed.ncbi.nlm.nih.gov/40173331/
5. Xu J, Qu Q, Yang Y, et al. The Lactulose Breath Test Can Predict Refractory Gastroesophageal Reflux Disease by Measuring Bacterial Overgrowth in the Small Intestine. J Clin Gastroenterol. 2024. https://pubmed.ncbi.nlm.nih.gov/38896424/
6. Revaiah PC, Kochhar R, Rana SV, et al. Risk of small intestinal bacterial overgrowth in patients receiving proton pump inhibitors versus proton pump inhibitors plus prokinetics. JGH Open. 2018;2(2):47-53. https://pmc.ncbi.nlm.nih.gov/articles/PMC6206996/
7. Pimentel M, Saad RJ, Long MD, Rao S. ACG Clinical Guideline: Small Intestinal Bacterial Overgrowth. Am J Gastroenterol. 2020;115(2):165-178.
8. Hunt R, Armstrong D, Katelaris P, et al. World Gastroenterology Organisation Global Guidelines: GERD Global Perspective on Gastroesophageal Reflux Disease. J Clin Gastroenterol. 2017;51(6):467-478.

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This article is for informational purposes only and does not constitute medical advice. Always consult with a qualified healthcare provider for diagnosis and treatment of digestive conditions.