Synthetic microbiome therapy offers new hope against C. difficile infections

Synthetic microbiome therapy offers new hope against C. difficile infections

A synthetic microbiome therapy tested in mice protects against severe symptoms of an intestinal infection that is difficult to treat and potentially life-threatening, according to a team of Penn State researchers. The team developed the treatment for Clostridioides difficile, or C. difficile, a bacteria that can cause severe diarrhea, abdominal pain and colon inflammation. C. difficile can overgrow when the balance of the gut microbiome – the trillions of organisms that keep your body healthy – is disrupted. The team said their findings could lead to the development of new probiotic strategies for humans to treat C. difficile infections as an alternative to antibiotics and conventional fecal microbiota transplants.

While it relies on the idea of ​​human fecal transplants, a medical procedure in which bacteria from a healthy donor's stool are transferred to a patient's gastrointestinal tract to restore balance to the microbiome will not require a fecal matter for the new approach. Instead, this microbiome therapy uses fewer but more precise strains of bacteria that have been linked to C. diffrigile suppression. It was as effective as human fecal transplants in mice against C. difficile infection and with fewer safety concerns.

The results were published today (March 3) in the journalCell host & microbe. The researchers also submitted a preliminary application to patent the technology described in the paper.

“We need to be much more targeted in our microbiome interventions,” said senior author Jordan Bisanz, assistant professor of biochemistry and molecular biology, and Dorothy Foehr Huck and J. Lloyd Huck Early Career Chair in Guest Microbiome Interactions.

He emphasized that applications that improve people's lives often start with basic discovery science.

“This project is a first step toward understanding how complex microbial communities affect the host and then pivoting to learn how to develop microbiome-derived therapies,” Bisanz said.

Typically, the organisms in the microbiome keep each other in check. While many people carry C. difficile in their intestines, it usually doesn't cause a problem. However, antibiotics can tip the scales and create an environment in which C. difficile can thrive by eliminating good bacteria along with harmful ones. C. difficile accounts for 15 to 25% of antibiotic-associated diarrhea. Infections can often set in after a visit to the hospital or other healthcare setting.

Treating these infections is challenging. Antibiotics are not effective against C. difficile because the bacteria are drug-resistant. Antibiotics also further disrupt the gut microbiome, creating a positive feedback loop that leads to recurrent infections. According to the Centers for Disease Control and Prevention, C. difficile causes 500,000 infections and is associated with $1.5 billion in healthcare costs annually in the United States.

One therapy that has been shown to be effective is fecal microbiota transplantation, which restores a healthy balance of bacteria in the gut. However, it is not without risks.

To some extent, a fecal transplant is almost like going to the pharmacist where they take a little bit of everything off the shelf and put it in a pill, assuming something is likely to help. But we don't know 100% what's in there. “

Jordan Bisanz, senior author

Sometimes, Bisanz says, fecal transplants can unknowingly contain disease-causing bacteria.

The researchers wondered, instead of a random mix of bacteria, could they identify the microorganisms that can best suppress C. difficile by colonizing the gut and causing infection? Could they then recreate this mixture in the laboratory and design a targeted version of a fecal transplant with this selective bacterial community?

“The idea was to take our understanding of basic microbiome science and turn it into precision-like therapies that take what we learned from fecal transplants, but do not require fecal transplants,” Bisanz said.

The research team set out to identify C. difficiles “friends” and “enemies”; In other words, those who are prone to either C. difficile or those who can reduce the growth of C. difficile. They collected information about the human microbiome from 12 previously published studies that included microbiome sequencing data and clinical diagnoses of C. difficile colonization. They then used machine learning to identify the key characteristics of home microorganisms that were positively and negatively associated with C. difficile.

Thirty-seven bacterial strains were found to be negatively correlated with C. difficile. In other words, when these microorganisms were present, there was no C. difficile infection. An additional 25 bacteria were positively correlated with C. difficile, meaning they were present alongside C. difficile infection. In the lab, the researchers then combined bacteria that appeared to suppress C. difficile and developed a synthetic version of a fecal transplant.

In mice tested in vitro and orally, synthetic microbiome therapy significantly reduced C. difficile growth, was effective in infection, and was as effective as traditional human fecal transplantation. It has also been shown in mice to protect against severe disease, delay relapse, and reduce the severity of recurrent infections caused by antibiotic use.

Through experiments, the researchers determined that only one strain of bacteria was critical for suppressing C. difficile. On its own, it was as effective as a human fecal transplant in preventing infection in a mouse model.

"If you have this Peptostreptococcus strain, you don't have C. diffrigile. It is a very effective suppressor and is actually better than all 37 strains combined," Bisanz said, explaining that the bacteria are particularly good at scavenging the amino acid proline, which is what C. difficile needs to grow. Previous studies identified another mechanism, secondary bile acid metabolism, as critical for resistance to C. difficile. Bisanz explained that these new results highlight that proline competition may instead play a larger role, opening new potential avenues for therapeutic treatment.

Bisanz said the team's approach to microbiome science could be used to understand complex host-microbial interactions among other diseases such as inflammatory bowel disease, with the potential to develop new therapies.

“The goal is to develop the microbes as targeted drugs and therapies,” he said.

Other Penn State authors on the paper include Shuchang Tian and Min Soo Kim, graduate students in biochemistry and molecular biology; Jingcheng Zhao, postdoctoral researcher; Kerim Heber, student; Fuhua Hao, postdoctoral researcher; David Koslicki, associate professor of computer science and engineering and biology; and Andrew Patterson, John T. and Paige S. Smith Professorship and Professor of Molecular Toxicology and Biochemistry and Molecular Biology.

Funding from the National Institute of Allergy and Infectious Diseases, National Institute of General Medical Sciences, National Institute of Diabetes and Digestion and Kidney Diseases, the Penn State Department of Biochemistry and Molecular Biology, and the Huck Life Sciences Institute supported this work.

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