Figure 1.

Overview of phage-host dynamics in the gut. (A) Phage infection can lead to virulent or temperate replication cycles. Integrated temperate phage use internal and external signals from hosts to determine if or when to enter the lytic cycle. (B) Bacteria can possess a wide array of defense mechanisms which target different steps of the phage replication cycle. Similarly, phage encode a wide array of counter-defense mechanisms which target host defenses and allow the phage to remain infectious. (C) Physical separation of phage and host (e.g., in mucous or in lumen) means that dynamics change along the radial and longitudinal axes of the gut. (D) Strain-level variation can result from resistance by mutation or by phase variation.