Re-examining Small Intestinal Bacterial Overgrowth: Dr. Eamonn Quigley Urges Caution in Overreliance on Breath Tests

The diagnosis of small intestinal bacterial overgrowth (SIBO), once confined to patients with anatomical or physiological abnormalities leading to malabsorption, has undergone a major conceptual drift — and not necessarily for the better, according to a recent review by Houston Methodist Gastroenterologist Dr. Eamonn Quigley.

In his paper, Small Intestinal Bacterial Overgrowth: From Malabsorption to Misinterpretation, Dr. Quigley revisits the origins of SIBO and issues a warning about its modern overdiagnosis, particularly when based solely on breath hydrogen testing.

"We've reached a point where SIBO is being invoked to explain almost every gastrointestinal symptom," said Dr. Quigley, Houston Methodist's chief of Gastroenterology. "That's concerning, because many of these cases are being diagnosed using breath tests that were never designed — or validated — for that purpose."

Click here to view Dr. Quigley's SIBO presentation from Digestive Disease Week 2025.

From classical to "modern" SIBO

Historically, small intestinal bacterial overgrowth was a well-defined condition tied to maldigestion and malabsorption, where bacterial proliferation in the small intestine disrupted bile acid metabolism and nutrient absorption.

"We understood what caused it, what its physiological impacts were and what clinical consequences ensued," Dr. Quigley noted.

However, over the past two decades, the condition has been repurposed as an explanation for nonspecific symptoms such as bloating, diarrhea and constipation — particularly in patients with irritable bowel syndrome (IBS). This shift coincided with the rise of lactulose and glucose breath testing, which promised a convenient, noninvasive diagnostic alternative to jejunal aspirates.

The problem with breath testing

Breath tests, Dr. Quigley explained, rely on the detection of hydrogen, methane and hydrogen sulfide — gases produced when bacteria ferment carbohydrates. A premature rise in hydrogen after ingesting lactulose is often interpreted as evidence of bacterial overgrowth. Yet, as Dr. Quigley points out, such results are easily confounded by rapid intestinal transit rather than true microbial proliferation.

"We've learned that lactulose can reach the colon within 40 to 70 minutes in perfectly healthy individuals," he said. "That means a so-called 'early hydrogen peak' can simply reflect fast transit — not SIBO."

Even glucose breath tests, though more accurate, suffer from false positives, especially in patients with prior gastrointestinal surgery. "The simple truth," Dr. Quigley wrote, "is that intestinal gas dynamics are complex and not completely understood. The potential for misinterpretation is enormous."

The science behind the skepticism

Dr. Quigley's caution is grounded in decades of physiological and microbiological evidence showing that breath gases are influenced by multiple variables beyond bacterial overgrowth, including orocecal transit time, substrate dose and site of fermentation.

Lactulose, for instance, can reach the cecum in under an hour — leading to hydrogen peaks that mimic small intestinal bacterial overgrowth even in healthy subjects.

Additionally, research comparing breath testing with jejunal aspirates has revealed poor correlation between the two, suggesting that many "positive" breath tests reflect colonic fermentation rather than bacterial proliferation in the small intestine.

Methane detection adds further complexity: unlike hydrogen, methane levels often remain high throughout testing, indicating that methanogens likely reside in the colon, not the small bowel.

"We've known for decades that the physiology of gas production is far more nuanced than these tests allow for," Dr. Quigley said. "When breath test data don't align with direct culture or sequencing findings, we must question our assumptions rather than stretch them."

A call for modern microbiology

In the paper, published this spring in Minerva Gastroenterology, Dr. Quigley advocates for direct, molecular characterization of the small intestinal microbiome — an area that has lagged far behind research on the colon. Unlike outdated diagnostic proxies, new sequencing technologies, telemetric gas-sensing capsules and targeted luminal sampling devices now offer unprecedented opportunities to define what a "normal" small intestinal microbiome truly looks like.

"Until we can agree on what constitutes a normal small intestinal microbiome — and how it varies between individuals — the relationship between SIBO and IBS will remain speculative at best," he said. "We need to move beyond breath tests and into a molecular era of precision gastroenterology."

Rethinking treatment

Dr. Quigley also cautions against reflexively prescribing antibiotics such as rifaximin based on uncertain breath test results. While rifaximin has shown modest benefit for some IBS patients, he argues that its mechanism likely lies in reducing colonic, not small bowel, fermentation.

"We should not treat symptoms assigned to small intestinal bacterial overgrowth when the diagnosis rests on faulty methodology," he said. "Instead, let's use rigorous, microbiome-driven science to understand which patients truly benefit from therapy."

Dr. Quigley concludes that redefining SIBO through modern microbiological tools will not only clarify its true prevalence but also protect patients from unnecessary testing and treatment.

"This is not about discarding old ideas," he emphasized, "but about refining them with better tools and better evidence — that's how medicine advances."