The gut microbiome hosts a wide range of microbes that affect our health. Understanding community dynamics is a key way to understand infectious diseases and how the gut microbiome can positively or negatively affect our overall health. However, an important part of this community is rather unknown. Bacteriophages are viruses in microbial communities that target bacteria. Understanding how bacteriophages shape community structure and function will allow us to understand the holistic picture regarding the microbiome.