Figure 2. Potential consequences of a temperate phage lifecycle in the human gut.

Viral metagenomic show that the phage population associated with the adult human gut microbiota is characterized by a relatively low number of virotypes compared to other ecosystems (e.g., soils, sediments, marine environments). These gut populations also exhibit high temporal stability of virotypes with respect to both viral community structure and nucleotide sequence conservation, and a high prevalence of temperate phages. These characteristics suggest that a temperate lifestyle is dominant in the distal human gut versus the lytic lifestyle observed in open oceans. (a–c) Illustration of the benefits of this temperate lifestyle on phage-host dynamics. (a) Integration as a prophage protects the host from superinfection, effectively ‘immunizing’ the bacterial host against infection from the same or closely related phages. Furthermore, the genes encoded by the viral genome may expand the niche of the bacterial host by enabling metabolism of new nutrient sources (e.g., carbohydrates), providing antibiotic resistance, conveying virulence factors, or altering host gene expression. This temperate lifecycle allows viral expansion in a 1:1 ratio with the bacterial host. If the integrated virus conveys increased fitness to its bacterial host, there will be increased prevalence of the host and phage in the microbiota. (b) Induction of a lytic cycle may follow a lysogenic state and can be triggered by environmental stress. As a consequence, bacterial turnover is accelerated and energy utilization optimized through ‘phage shunts’, where the debris remaining after lysis is used as a nutrient source by the surviving population. Furthermore, a subpopulation of bacteria that undergoes lytic induction sweeps away other sensitive species and increases the niche for survivors (i.e., bacteria that already have an integrated phage). Periodic induction of prophages can also lead to a constant diversity dynamic ¹¹⁵, which helps maintain community structure and functional efficiency. (c) Novel infections or infections of novel bacterial hosts by phages bring the benefit of horizontally transferred genes, and create selective pressure on the hosts for diversification of their phage receptors, which are often involved in carbohydrate utilization.