Bacteriophages are influential within the human gut microbiota, yet they remain understudied relative to bacteria. This is a limitation of studies on fecal microbiota transplantation (FMT) where bacteriophages likely influence outcome. Here, using metagenomics, we profiled bacteriophage populations - the phageome - in of patients and donors recruited to two independent randomized clinical trials of FMT in ulcerative colitis using shotgun metagenomics using MetaPhage. Through assessment of patients and donors at different timepoints in the trials, we were able to study bacteriophage populations in clinically validated healthy individuals and contrast this with active disease, showing temporal stability in health, dysbiosis in active disease, modulation by antibiotic treatment and by FMT. We identified a donor bacteriophage consistently associated with disease remission, which on genomic analysis was found integrated in a bacterium classified to Oscillospiraceae, previously isolated from a centenarian and predicted to produce vitamin B complex except B12. Our study provides an in-depth assessment of bacteriophage populations during different states and suggests that bacteriophage tracking has utility in identifying determinants of disease activity and resolution.