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Probiotic bacteria evolve inside mice’s GI tracts

Findings suggest effectiveness, safety of probiotic therapies could change over time

by Tamara BhandariMarch 26, 2019

Mark Hallett, Huy Mach, Gaia Remerowski

Probiotics – which are living bacteria taken to promote digestive health – can evolve once inside the body and have the potential to become less effective and sometimes even harmful, according to a new study from Washington University School of Medicine in St. Louis.

Researchers studying a strain of Escherichia coli (E. coli) bacteria sold in Europe as an anti-diarrheal probiotic found that the bacteria’s DNA changed and they developed new capabilities after living in mice’s intestines for a few weeks. Under some conditions, the probiotics even turned on their hosts and acquired the ability to eat the protective coating on the intestine. Destruction of this layer has been linked to irritable bowel syndrome. The mice’s diets and the make-up of their gut bacterial community influenced how much the probiotic evolved and in what ways.

The findings, published March 26 in Cell Host and Microbe, suggest that probiotics aren’t a one-size-fits-all therapy. A probiotic that provides relief to one person could evolve to become ineffective or even harmful in another. Probiotics have been linked to serious infections in some people.

“If we’re going to use living things as medicines, we need to recognize that they’re going to adapt, and that means that what you put in your body is not necessarily what’s going to be there even a couple hours later,” said senior author Gautam Dantas, PhD, a professor of pathology and immunology, of molecular microbiology, and of biomedical engineering. “There is no microbe out there that is immune to evolution. This isn’t a reason not to develop probiotic-based therapies, but it is a reason to make sure we understand how they change and under what conditions.”

Everyone hosts a vast community of bacteria, viruses and fungi known as the gut microbiome in their digestive tracts. A well-balanced microbiome supplies us with vitamins, helps digest food, regulates inflammation and keeps disease-causing microbes in check. Probiotics in foods and dietary supplements are marketed as ways to keep healthy bacteria plentiful and digestion running smoothly.

They also are being developed as treatments for serious medical conditions such as inflammatory bowel disease; phenylketonuria (PKU), a metabolic disorder that causes neurological damage; and necrotizing enterocolitis, a life-threatening intestinal infection that affects premature babies. Like any other medication, a probiotic-based treatment must be proven safe and effective before the FDA will approve it for use in people. But when the therapy is a living thing that can change after it is administered, proving safety and efficacy poses special problems.

Understanding the principles that govern evolution in the digestive tract is a key step toward creating safe and effective probiotic therapeutics, the researchers said. Dantas and colleagues, including first authors Aura Ferreiro, a graduate student, and Nathan Crook, PhD, a former postdoctoral researcher in Dantas’ lab, turned to a probiotic known as E. coli Nissle 1917. The strain was isolated more than a century ago from a World War I soldier who emerged unscathed from an epidemic of severe diarrheal disease that sickened his comrades.

To study how the probiotic responds to different microbial communities, the researchers used mice that harbored four kinds of gut microbiomes: one with no pre-existing bacteria; another with a limited set of bacteria, characteristic of an unhealthy gut; a normal microbiome; and a normal microbiome after antibiotic treatment. The researchers gave the mice the probiotic, and then varied the food the mice ate, giving them either mouse chow, high-fiber pellets that mimic the natural mouse diet; high-fat, high-sugar, low-fiber pellets meant to model typical Western eating habits; and Western pellets plus fiber. After five weeks, the researchers obtained the bacteria from the mice’s guts and analyzed the microbes’ DNA.

“In a healthy, high-diversity background we didn’t capture a lot of adaptation, maybe because this is the background that Nissle is used to,” Ferreiro said. “But you have to remember that quite often we wouldn’t be using probiotics in people with a healthy microbiome. We’d be using them in sick people who have a low-diversity, unhealthy microbiome. And that seems to be the condition when the probiotic is most likely to evolve.”

Dantas and his colleagues applied these findings to designing a potential probiotic therapy for PKU. People with PKU are unable to break down phenylalanine, a protein building block found in many foods. High phenylalanine levels cause brain damage, so people with PKU must strictly adhere to a low-protein diet.

The researchers inserted a gene into Nissle that gave the bacteria the ability to degrade phenylalanine into a compound that is safely excreted in the urine. Then, they gave the bio-engineered bacteria to mice that lacked the capacity to metabolize phenylalanine. The next day, phenylalanine levels in some of the mice had dropped by half.

Moreover, the researchers did not find significant changes to the DNA of the engineered strain after one week of treatment, suggesting Nissle might be safe to use as a chassis for probiotic therapies over short time scales.

The finding that probiotics evolve and behave differently in individuals with disparate microbiomes and diets opens up avenues for personalizing probiotic-based medicine.

“Evolution is a given. Everything is going to evolve,” Dantas said. “We don’t need to be scared of it. We can use the principles of evolution to design a better therapeutic that is carefully tailored to the people who need it. This is an opportunity, not a problem.”

Crook N, Ferreiro A, Gasparrini AJ, Pesesky MW, Gibson MK, Wang B, Sun X, Condiotte Z, Dobrowolski S, Peterson D, Dantas G. Adaptive strategies of the candidate probiotic E. coli Nissle in the mammalian gut. Cell Host and Microbe. March 26, 2019. DOI: 10.1016/j.chom.2019.02.005

This work was supported by the National Institutes of Health (NIH), grant numbers DP2DK098089, R01GM099538, R01AI123394, R01HD092414, T32DK077653, and T32GM007067; the National Science Foundation, grant number DGE-1143954; the Kenneth Rainin Foundation, grant number 13H5; the Chancellor’s Graduate Research Fellowship Program at Washington University in St. Louis; and the Mr. and Mrs. Spencer T. Olin Fellowship at Washington University in St Louis.

Washington University School of Medicine’s 1,500 faculty physicians also are the medical staff of Barnes-Jewish and St. Louis Children’s hospitals. The School of Medicine is a leader in medical research, teaching and patient care, ranking among the top 10 medical schools in the nation by U.S. News & World Report. Through its affiliations with Barnes-Jewish and St. Louis Children’s hospitals, the School of Medicine is linked to BJC HealthCare.

Tamara covers infectious diseases, molecular microbiology, neurology, neuroscience, surgery, the Institute for Informatics, the Division of Physician-Scientists and the MSTP program. She holds a double bachelor's degree in molecular biophysics & biochemistry and in sociology from Yale University, a master's in public health from the University of California, Berkeley, and a PhD in biomedical science from the University of California, San Diego. She joined WashU Medicine Marketing & Communications in 2016. She has received three Robert G. Fenley writing awards from the American Association of Medical Colleges: a bronze in 2020 for "Mind’s quality control center found in long-ignored brain area," a silver in 2022 for "Mice with hallucination-like behaviors reveal insight into psychotic illness," and a bronze in 2023 for "Race of people given Alzheimer’s blood tests may affect interpretation of results." Since January of 2024, Tamara has been writing under the name Tamara Schneider.

Huy uses visual storytelling in his coverage of medical education, patient care, and research. He was part of a team of photographers at the St. Louis Post-Dispatch that won the Pulitzer Prize for breaking news photography in 2015. He has a bachelor's degree in photojournalism from Western Kentucky University.