Analysis of 352 probiotic supplements finds mismatched microbes across marketed health benefits

Probiotic supplements found in drugstores nationwide contain an assortment of microbes sold for specific health purposes despite limited understanding of the microbes' connections to their marketed use, new University of Virginia School of Medicine research reveals. But the scientists have assembled sophisticated computer models that could lead to more effective products to shape our microbiomes to improve health.

UVA researchers led by Jason Papin, Ph.D., analyzed more than 350 over-the-counter probiotics sold at the three largest pharmacy chains in the United States—CVS, Walgreens and Walmart. Those 352 products were found to contain, collectively, only 36 unique species of bacteria. The most common species were forms of Lactobacillus, a type of bacteria commonly found in yogurt. The study is published in the journal Nature Microbiology .

More than half the products contained only one probiotic species. The products with the most unique species topped out at 17. Some brands maintained a consistent number of bacterial strains across products, while others did not.

Based on their analysis, the scientists concluded that there was no real consistency in the combination of species used to support gut health, vaginal health or other health claims.

"It is truly fascinating to discover that these probiotic bacteria hold a unique, specialized niche among the trillions of microbes in and on the human body," said Glynis Kolling, Ph.D., a research faculty member in UVA's Department of Biomedical Engineering who works closely with Papin. "By combining our advanced methods, we have the potential to vastly expand the pool of beneficial bacteria and pave the way for targeted solutions to support human health."

University of Virginia School of Medicine researchers led by Jason Papin, Ph.D., analyzed more than 350 over-the-counter probiotics sold at the three largest pharmacy chains in the United States. Those 352 products were found to contain, collectively, only 36 unique species of bacteria. The most common species were forms of Lactobacillus , a type of bacteria commonly found in yogurt. Credit: UVA Health

Targeting the microbiome

We have at least as many microorganisms living on and inside us as we have cells in our bodies. Scientists have increasingly come to appreciate the role these microorganisms—collectively known as the microbiome—play in maintaining our health. We can get beneficial bacteria from our diets, such as from yogurt and fermented foods, but there has also been an explosion in "probiotic" products over the last two decades.

So far, the federal Food and Drug Administration has approved only two microbial products for therapeutic purposes, and both are used to treat recurrent C. difficile infections in the colon. Supplements, however, are not regulated as strictly as drugs in the United States, and there is limited understanding of connections between bacteria and marketed use for many probiotic products, the UVA researchers found.

To improve the effectiveness of probiotic products, Papin and his team have developed HaPaPro, a collection of more than 1,000 computer models of bacterial metabolism. They used these models to see if they could identify probiotics with the potential to improve women's vaginal health.

The vaginal microbiome is a natural ecosystem of bacteria, fungi and other microbes that help support health. Bacterial vaginosis occurs when this natural ecosystem is disrupted, leading to pregnancy complications, pelvic inflammatory disease, a higher risk of sexually transmitted diseases and general discomfort. The researchers were able to use their models to identify microbes that have the potential to help prevent bacterial vaginosis.

The successful results, Papin says, demonstrate HaPaPro's potential for identifying ways to manipulate the microbiome that will have concrete benefits. Such insights, he hopes, will lead to better probiotic products that deliver on their promises.

"It is remarkable how much microbes play a role in human health and well-being," Papin said. "I love seeing how computational models of these complex biological systems are leading to new ideas for therapies and helping us understand such fundamental biological processes."

The research team consisted of Emma M. Glass, Kolling and Papin. The scientists have no financial interest in the probiotic industry, but Papin disclosed that he has a stake in Cerillo, the manufacturer of instrumentation used in some of the analyses.

Publication details

Emma M. Glass et al, Genome-scale metabolic modelling identifies vaginal microbiome members as potential probiotics, Nature Microbiology (2026). DOI: 10.1038/s41564-026-02380-w

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