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

Torben Sølbeck Rasmussen*, Xiaotian Mao, Sarah Forster, Sabina Birgitte Larsen, Alexandra Von Münchow, Kaare Dyekær Tranæs, Anders Brunse, Frej Larsen, Josue Leonardo Castro Mejia, Signe Adamberg, Axel Kornerup Hansen, Kaarel Adamberg, Camilla Hartmann Friis Hansen, Dennis Sandris Nielsen*

*Corresponding author af dette arbejde

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Abstract

Background: Fecal microbiota transplantation (FMT) and fecal virome transplantation (FVT, sterile filtrated donor feces) have been effective in treating recurrent Clostridioides difficile infections, possibly through bacteriophage-mediated modulation of the gut microbiome. However, challenges like donor variability, costly screening, coupled with concerns over pathogen transfer (incl. eukaryotic viruses) with FMT or FVT hinder their wider clinical application in treating less acute diseases. Methods: To overcome these challenges, we developed methods to broaden FVT’s clinical application while maintaining efficacy and increasing safety. Specifically, we employed the following approaches: (1) chemostat-fermentation to reproduce the bacteriophage FVT donor component and remove eukaryotic viruses (FVT-ChP), (2) solvent-detergent treatment to inactivate enveloped viruses (FVT-SDT), and (3) pyronin-Y treatment to inhibit RNA virus replication (FVT-PyT). We assessed the efficacy of these processed FVTs in a C. difficile infection mouse model and compared them with untreated FVT (FVT-UnT), FMT, and saline. Results: FVT-SDT, FVT-UnT, and FVT-ChP reduced the incidence of mice reaching the humane endpoint (0/8, 2/7, and 3/8, respectively) compared to FMT, FVT-PyT, and saline (5/8, 7/8, and 5/7, respectively) and significantly reduced the load of colonizing C. difficile cells and associated toxin A/B levels. There was a potential elimination of C. difficile colonization, with seven out of eight mice treated with FVT-SDT testing negative with qPCR. In contrast, all other treatments exhibited the continued presence of C. difficile. Moreover, the results were supported by changes in the gut microbiome profiles, cecal cytokine levels, and histopathological findings. Assessment of viral engraftment following FMT/FVT treatment and host-phage correlations analysis suggested that transfer of phages likely were an important contributing factor associated with treatment efficacy. Conclusions: This proof-of-concept study shows that specific modifications of FVT hold promise in addressing challenges related to donor variability and infection risks. Two strategies lead to treatments significantly limiting C. difficile colonization in mice, with solvent/detergent treatment and chemostat propagation of donor phages emerging as promising approaches. DixucG6bYNjUQ1q5irdn5dVideo Abstract

OriginalsprogEngelsk
Artikelnummer119
TidsskriftMicrobiome
Vol/bind12
Antal sider24
ISSN2049-2618
DOI
StatusUdgivet - 2024

Bibliografisk note

Funding Information:
Open access funding provided by Copenhagen University Funding was provided by The Lundbeck Foundation with grant ID: R324-2019-1880 under the acronym \u201CSafeVir\u201D and The Novo Nordisk Foundation with grant ID: NNF-20OC0063874 under the acronym \u201CPrePhage\u201D.

Funding Information:
We would like to express our gratitude to the staff of veterinarians and animal caretakers at the Department of Experimental Medicine (AEM, University of Copenhagen, Denmark) for their cooperation in housing, handling, and monitoring the mice. We would also like to extend our thanks to PhD Casper Normann Nurup for his assistance in the initial setup of the column chromatography and to Lab Trainee Mariam Al-Batool Samir S. Bagi for performing the ELISA assay. We would also like to acknowledge the Food & Health Open Innovation project (FOODHAY), granted by the Danish Ministry of Education and Research, for funding the qPCR equipment (Bio-Rad Laboratories CFX96) used in this study. Lastly, we are grateful for the funding bodies that financially have supported our work.

Publisher Copyright:
© The Author(s) 2024.

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