Viruses in the human gut are dominated by bacteriophages – viruses that infect bacteria. The microbiome is affected by, and affects, many medications, but the interactions between therapeutics and viruses are less well characterized. Although viruses are about ten times more abundant than bacteria, they have significantly smaller genomes and do not share common markers that could be used for amplicon-based studies. We have perfected new experimental techniques for viromic DNA extraction, and new bioinformatics techniques to identify the viral DNA from the bacterial and human host DNA. Comparing the viromes of cancer patients before and after treatment has revealed the effect of chemotherapeutics on the human gut virome.