H. Pylori and SIBO: Low Stomach Acid, Gastritis & Hypochlorhydria

In short: Helicobacter pylori is a common stomach infection. In some people it lowers stomach acid, one of the body’s main defenses against bacteria reaching the small intestine. A 2023 meta-analysis found that people with H. pylori had 1.8 times the odds of SIBO¹, and in a 2024 study, treating H. pylori also cleared SIBO in two-thirds of those who had both⁴. The two conditions are tested differently, and there is no guideline yet on how to treat them together³.

This guide explains how H. pylori affects stomach acid, what studies show about its link with SIBO, and how the two are diagnosed and treated. For other causes of SIBO, see our causes guide.

What is H. pylori?

H. pylori is a bacterium that lives in the lining of the stomach. It infects more than half of adults worldwide; in the United States, between 20% and 40% of people are infected³. It can cause gastritis (inflammation of the stomach lining), indigestion, peptic ulcers and stomach cancer⁸.

How H. pylori affects stomach acid

Stomach acid kills most of the bacteria we swallow. When acid is low (hypochlorhydriaHypochlorhydria Low stomach acid. It weakens the stomach's first barrier against bacteria. Common causes include long-term acid-reducing medication, H. pylori infection and aging.), more bacteria survive the trip into the small intestine. This is why acid-suppressing medicines (proton pump inhibitorsProton pump inhibitor (PPI) A class of acid-reducing medication used for reflux, such as omeprazole. Long-term use lowers stomach acid and is associated with a higher risk of SIBO., PPIs) are linked to SIBO: a 2013 meta-analysis of 11 studies found PPI users about twice as likely to have it⁹.

H. pylori can lower acid in two ways:

• Urease. The bacterium makes an enzyme, urease, that breaks down urea into ammonia. The ammonia neutralizes acid around the bacterium and raises the pH of the stomach³.
• Gastritis and atrophy. Long-term inflammation can damage the acid-producing lining of the upper stomach (the corpus). Gastritis that mainly affects the corpus, and the thinning of the lining that can follow (atrophy), lead to low acid².

The effect is not the same in everyone. Acid output falls briefly in the early phase of infection. Later, when inflammation mainly affects the lower stomach (the antrum), acid output can actually rise, which is the pattern behind duodenal ulcers². So H. pylori does not always mean low stomach acid.

What the studies show

The meta-analysis found the link held regardless of country, PPI use or testing method¹. All of these studies are observational, so they show an association, not that H. pylori causes SIBO. The methane findings suggest that H. pylori may also be linked to methane overgrowth⁴⁵.

Does treating H. pylori clear SIBO?

Two small studies suggest it can help:

• In the 2024 study, 50 people successfully cleared H. pylori with bismuth quadruple therapy. Six weeks later, SIBO had resolved in 67% of those who had it, methane overgrowth in 77%, and gut symptom scores had fallen⁴. The treatment contains two antibiotics, metronidazole and amoxicillin, which are also used for SIBO, so this does not prove that removing H. pylori itself was the reason.
• In a 2018 study of 62 people with both conditions, 10 days of pantoprazole and amoxicillin with either metronidazole or rifaximinRifaximin An antibiotic that is barely absorbed into the bloodstream, so it acts mainly inside the gut. It is a common prescription treatment for SIBO. lowered breath hydrogen in both groups. H. pylori was cleared in 63% and 59%⁷.

The opposite effect is also possible, because H. pylori treatment includes a PPI. In the 2017 study, 35% of the 54 people who had already completed one to four courses of H. pylori treatment had SIBO⁶.

Testing for H. pylori and SIBO

Both conditions can be tested with a breath test, but they are different tests:

• H. pylori is tested with a urea breath test, a stool antigen test or a biopsy during endoscopy. PPIs can make these tests less accurate and should be stopped beforehand; the stool antigen test is the least affected³. A follow-up test at least a month after treatment is needed to confirm that the infection has gone³⁸.
• SIBO is tested with a hydrogen and methane breath test after drinking glucose or lactuloseLactulose A synthetic sugar the body cannot digest or absorb. As a breath-test substrate it travels the whole small intestine, which also makes false positives more likely., or by culturing fluid from the small intestine³. See our breath test guide and diagnosis guide.

Testing for H. pylori is recommended for people with indigestion, unexplained iron deficiency anemia, a current or past peptic ulcer, or long-term use of anti-inflammatory painkillers³. Because the symptoms of the two conditions overlap, a 2023 meta-analysis supports also checking for SIBO in people with gut symptoms and H. pylori¹.

Treatment

H. pylori is treated with a combination of antibiotics and acid suppression. The 2024 US guideline recommends 14 days of bismuth quadruple therapy (a PPI, bismuth, tetracycline and metronidazole) as the first choice when antibiotic resistance is unknown. Alternatives include rifabutin-based triple therapy and dual therapy with a newer acid blocker (vonoprazan) and amoxicillin. The guideline recommends testing everyone after treatment to confirm cure⁸.

There is no guideline on whether to treat H. pylori and SIBO together or one after the other³. Because H. pylori treatment cleared SIBO in many people in the 2024 study⁴, one approach is to treat H. pylori first and repeat the SIBO breath test afterwards if symptoms persist. See our guide to SIBO antibiotics.

Common questions

Can H. pylori cause SIBO?

It is linked to SIBO, most likely by lowering stomach acid in some people, but studies so far show an association rather than proof of cause¹².

Should I get tested for H. pylori if I have SIBO?

Ask your doctor, especially if you have indigestion, upper abdominal pain, iron deficiency or a history of ulcers³. H. pylori is worth finding in its own right, because it can cause ulcers and stomach cancer⁸.

Will a SIBO breath test detect H. pylori?

No. The hydrogen and methane breath test for SIBO and the urea breath test for H. pylori measure different things, and each needs its own test³.