Fujimoto K, Kimura Y, Allegretti JR, et al. - This study was undertaken to determine if functional restoration of the bacteriomes and viromes by fecal microbiota transplantation (FMT) could be an indicator of successful FMT. Nine patients with recurrent Clostridioides difficile infection (rCDI) who had undergone successful FMT and their donors were analyzed for human intestinal bacteriomes and viromes. They assessed the gene functions of intestinal microorganisms affected by FMT. FMT does change the features of intestinal bacteriomes and viromes in recipients following FMT relative to those before FMT, as seen with metagenomic sequencing of both the viromes and bacteriomes. In particular, several Proteobacteria were eliminated, the fecal abundance of which was high before FMT; the proportion of Microviridae was also higher in recipients. The intestinal flora of the recipients was restored by coordinated action by phages and their host bacteria.