Synthetic microbiome therapy suppresses bacterial infection without antibiotics

UNIVERSITY PARK, Pa. — A synthetic microbiome therapy, tested in mice, protects against severe symptoms of a gut infection that is notoriously difficult-to-treat and potentially life threatening in humans, according to a team of researchers at Penn State. The team developed the treatment for Clostridioides difficile, or C. difficile, a bacterium 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 draws on the idea of human fecal transplants, a medical procedure where bacteria from a healthy donor’s stool is transferred to a patient’s gastrointestinal tract to restore balance to the microbiome, the new approach doesn’t require any fecal matter. Instead, this microbiome therapy uses fewer but more precise bacteria strains that have been linked to C. difficile suppression. It was as effective as human fecal transplants in mice against C. difficile infection and with fewer safety concerns.

The findings were published today (March 3) in the journal Cell Host & Microbe. The researchers also filed a provisional 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 Host-Microbiome Interactions.

He emphasized that applications that improve people’s lives often begin with basic discovery science.

“This project is a first step in trying to understand how complex microbial communities function to affect the host, then turning that around to learn how to develop microbiome-targeted therapies,” Bisanz said.

Typically, the organisms in the microbiome keep each other in check. While many people carry C. difficile in their gut, it usually doesn’t cause a problem. However, antibiotics can tip the scales, creating an environment where C. difficile can flourish by knocking out good bacteria along with harmful ones. C. difficile accounts for 15% to 25% of antibiotic-associated diarrhea. Infection can often set in after a visit to the hospital or other health care setting.

Treating these infections is challenging. Antibiotics aren’t 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 dollars in health care costs in the United States annually.

One therapy that has proven effective, Bisanz said, is a fecal microbiota transplant, which is designed to restore a healthy balance of bacteria in the gut. However, it’s not without risks.

“To a certain 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 into one pill, assuming that something will probably help,” Bisanz said. “But we don’t know 100% what’s in there.”

Sometimes, Bisanz said, fecal transplants may unknowingly contain disease-causing bacteria.

The researchers wondered, instead of a random mix of bacteria, could they identify the microorganisms that are best able to suppress C. difficile from colonizing the gut and causing an infection? Could they then reconstruct that mixture in the lab and design a targeted version of a fecal transplant with this selective community of bacteria?

“The idea was to take our understanding of basic microbiome sciences and turn it into precision-like therapies that take what we’ve learned from fecal transplants but doesn’t actually require a fecal transplant,” Bisanz said.

The research team set out to identify C. difficile’s “friends” and “foes;” in other words, those that tend to either co-occur with C. difficile or those that may reduce the growth of C. difficile. They gathered information on the human microbiome from 12 previously published studies, which included microbiome sequencing data and clinical diagnoses of C. difficile colonization. They then used machine learning to home in on the key features of microorganisms that were positively and negatively associated with C. difficile.

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

When tested in vitro and given orally to mice, the synthetic microbiome therapy significantly reduced growth of C. difficile, resisted infection and was as effective as a traditional human fecal transplant. In mice, it was also shown to protect against severe disease, delay relapse and decrease severity of recurrent infections caused by antibiotic use.

Through experiments, the researchers determined that just one bacterial strain was critical for suppressing C. difficile. Alone, it was just 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. difficile. It’s a very potent 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 C. difficile needs to grow. Previous studies identified a different mechanism, secondary bile acid metabolism, as critical for resisting C. difficile. Bisanz explained that these new findings highlight that proline competition may play a bigger role instead, which opens up new potential avenues for therapeutic treatment.

Bisanz said that the team’s approach to microbiome science could be used to understand complex host-microbial interactions in other conditions like inflammatory bowel disease with the potential to develop novel 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, doctoral students in biochemistry and molecular biology; Jingcheng Zhao, postdoctoral researcher; Kerim Heber, undergraduate student; Fuhua Hao, postdoctoral scholar; David Koslicki, associate professor of computer science and engineering and of biology; and Andrew Patterson, John T. And Paige S. Smith Professorship and professor of molecular toxicology and of biochemistry and molecular biology.

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