Houston Methodist Researcher Calls for Scientific Rigor in Probiotics Claims

Houston Methodist gastroenterologist Dr. Eamonn Quigley is calling for a fundamental reset in how scientific and medical communities — and the public — think about probiotics, the increasingly trendy intervention for some gut problems.

In a recent article in the Annual Review of Medicine, Dr. Quigley and Irish gastroenterologist Dr. Fergus Shanahan wrote that while the probiotic concept remains "biologically plausible and mechanistically well established in some cases," its clinical application has been plagued by "inconsistent definitions, poor trial design and overextended claims."

"It's time we separate science from snake oil," said Dr. Quigley, chief of Gastroenterology and director of the Lynda K. and David M. Underwood Center for Digestive Disorders at Houston Methodist Hospital "The enthusiasm surrounding probiotic supplements has often outpaced the evidence. We need to return to precision, in terminology, in strain identification and in clinical testing."

The review offers one of the most comprehensive assessments to date of the evidence base supporting probiotic use — and where that evidence falls short.

Dr. Quigley and Dr. Shanahan are international leaders in gut microbiome research. They worked together extensively at University College Cork, still Dr. Shanahan's research home, before Dr. Quigley came to Houston Methodist in 2013.

The problem with "lazy language"

A major theme of the review is linguistic and conceptual imprecision. The term probiotic was formally defined two decades ago by the World Health Organization as "live microorganisms which, when administered in adequate amounts, confer a health benefit on the host." Yet, Dr. Quigley noted, the term is frequently misused to describe any beneficial microbe, dead bacteria, or even microbial fragments.

"Referring to all probiotics as if they were interchangeable is as meaningless as asking if pills or tablets work better," Dr. Quigley explained. "Each strain is unique — and unless an organism's viability, dosage and proven health benefit are demonstrated in rigorous trials, it does not meet the definition of a probiotic."

According to the paper, fewer than half of more than 1,000 clinical trials registered globally report proper dosing data, and even fewer adequately identify the microbial strain being tested. This lack of standardization has rendered many meta-analyses nearly meaningless, as they aggregate data across unrelated strains and study designs.

The regulatory line between probiotics and drugs

Dr. Quigley also highlighted new regulatory distinctions that may improve scientific clarity. In both the United States and Europe, probiotics are now categorized as dietary supplements or foods, while live biotherapeutic products (LBPs) — microbial preparations intended to prevent, treat or cure disease — are regulated as drugs. The distinction lies not in biology, but in intent.

"A microbe may be identical at the genomic level, but if it's used to treat disease, it should be held to the same clinical standards as any pharmaceutical," Dr. Quigley asserted. "That means demonstrating safety and efficacy in randomized, controlled clinical trials."

Still, Dr. Quigley cautioned, the marketplace remains crowded with unregulated products making unsubstantiated claims. Consumers and clinicians alike, he said, should demand transparency on strain identity, clinical evidence and manufacturing quality.

When they work — and when they don't

The review acknowledges specific areas where probiotic supplements show consistent benefits. Prophylactic use in preterm infants at risk for necrotizing enterocolitis (NEC) remains one of the few cases with robust evidence, supported by reductions in mortality and morbidity in large, randomized trials. Other conditions — such as antibiotic-associated diarrhea, including Clostridioides difficile infection — show moderate evidence, though study heterogeneity limits firm conclusions.

By contrast, the evidence for probiotic treatments in irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD) remains inconsistent. Despite promising preclinical data, human studies have been hampered by underpowered designs and poorly defined endpoints, Dr. Quigley said. Even in healthy populations, probiotic consumption rarely produces measurable or beneficial changes in the gut microbiota.

"There's an understandable appeal in the idea of correcting the microbiome," Dr. Quigley said. "But the human gut is extraordinarily complex, and our tools for modifying it are still crude. We must avoid the temptation to oversimplify."

A call for precision — and restraint

The review concludes with a straightforward message: scientific rigor must replace marketing enthusiasm. Probiotics — like any medical intervention — should be defined by evidence, not by aspiration, Dr. Quigley warns.

"The probiotic field hasn't suffered from too much regulation," he said. "It's suffered from too little. We need clear definitions, standardized methodologies, and the courage to admit when the data aren't there yet."

For clinicians, he offers practical advice summarized in the review's consumer guidance: probiotics are adjuncts, not alternatives, to medicine and diet; their benefits are strain-specific; and in most cases, any effect ceases once consumption stops.

"Patients deserve accuracy, not ambiguity," Dr. Quigley said. "If a product claims to improve health, it should meet the same evidentiary standards we apply to any therapeutic agent."