A composite bacteriophage alters colonization by an intestinal commensal bacterium

The mammalian intestine is home to a dense community of bacteria and its associated bacteriophage (phage). Virtually nothing is known about how phages impact the establishment and maintenance of resident bacterial communities in the intestine. Here, we examine the phages harbored by Enterococcus faecalis, a commensal of the human intestine. We show that E. faecalis strain V583 produces a composite phage (ΦV1/7) derived from two distinct chromosomally encoded prophage elements. One prophage, prophage 1 (ΦV1), encodes the structural genes necessary for phage particle production. Another prophage, prophage 7 (ΦV7), is required for phage infection of susceptible host bacteria. Production of ΦV1/7 is controlled, in part, by nutrient availability, because ΦV1/7 particle numbers are elevated by free amino acids in culture and during growth in the mouse intestine. ΦV1/7 confers an advantage to E. faecalis V583 during competition with other E. faecalis strains in vitro and in vivo. Thus, we propose that E. faecalis V583 uses phage particles to establish and maintain dominance of its intestinal niche in the presence of closely related competing strains. Our findings indicate that bacteriophages can impact the dynamics of bacterial colonization in the mammalian intestinal ecosystem.