Gut bacteriophages in Clostridioides difficile patients and fecal microbiota transplantation donors

Clostridioides difficile infection (CDI) is a concern for health care providers around the world because CDI can be acquired nosocomially, and has high rates of treatment failure and recurrence (rCDI). Alternative therapeutic options have been explored, including fecal microbiota transplantation (FMT). FMT is a promising alternative to antibiotics that has been shown to achieve high cure rates for rCDI. Its mechanism of success and its risks are not fully understood and could potentially involve gut bacteriophages (phages), so we investigated the gut phage changes after FMT treatment of refractory or recurrent CDI. To achieve these objectives, we purified DNA phages from fecal samples from rCDI patients treated with FMT, and from FMT donor samples. Then, metagenomic shotgun sequencing of the DNA phages was performed.