Overcoming donor variability and risks associated with fecal microbiota transplants through bacteriophage-mediated treatments

Abstract

ABSTRACTFecal microbiota transplantation (FMT) and fecal virome transplantation (FVT, sterile filtrated donor feces) have proven effective in treating recurrentClostridioides difficileinfection (rCDI). However, variability in donor materials and costly screening, coupled with concerns (motivated by case reports) over pathogen transfer with FMT or FVT, hinders their wider clinical application in treating less acute diseases. Although FVT presents safety advantages over FMT by transferring no bacteria, the presence of eukaryotic viruses poses a risk of harmful infections. To overcome these challenges, we developed methods to broaden FVT’s clinical application while maintaining efficacy and increasing safety. Namely: 1) chemostat-fermentation to reproduce the bacteriophage FVT component and remove eukaryotic viruses (FVT-ChP); 2) solvent-detergent treatment to inactivate enveloped viruses (FVT-SDT); and 3) pyronin-Y treatment to block RNA-virus replication (FVT-PyT). We evaluated the efficacy of these processed FVTs using a CDI mouse model and compared them with untreated FVT (FVT-UnT), FMT, and saline control. FVT-UnT, FVT-SDT, and FVT-ChP significantly reducedC. difficilecolonization, limited CDI symptoms and reduced the incidence of mice reaching humane endpoints compared with the saline control. This proof-of-concept opens the possibility of developing safer and more effective phage-mediated therapies for a broad range of gut-related diseases and addresses the reproducibility issues associated with fecal donor material.SummaryFecal viromes depleted of enveloped viruses efficiently treatClostridioides difficile- associated diarrhea in a murine model.