Abstract
The recently discovered crAssphage is by far the most abundant and ubiquitous known human gut bacteriophage. It appears to be highly specific to the human gastrointestinal tract; however, the patterns of transmission and persistence of this bacteriophage are unknown. Here, we identify modes of transmission and describe long-term persistence of crAssphage in several human populations. We find that most humans harbor a single, dominant strain of crAssphage in their microbiome. This is in contrast to the bacterial microbiota, where individuals can harbor a variety of closely- or distantly-related strains of the same bacterial species. We show that crAssphage can be vertically transmitted from mother to infant, acquired through fecal microbiota transplantation, and transmitted in immunocompromised hosts in a hospital setting. We also observe that once a crAssphage strain is acquired, it persists stably within an individual over a timescale of months. These results enhance our understanding of the dynamics of crAssphage, which has emerged as one of the most successful human-associated microbes, and provide a foundation for future studies of the role of this phage in the biology of the human microbiome.
