Code supporting "Lysogeny destabilizes computationally simulated microbiomes" (Gilman et al 2024)

We used Lotka-Volterra-like models to study the effects of temperate and virulent phages on diversity and stability in computationally simulated microbiomes. The presence of either phage type in a microbiome increased bacterial diversity. Bacterial populations were more likely to fluctuate over time when there were more temperate phages in the system. When microbiomes were disturbed from their steady states, both phage types affected return times, but in different ways. Bacterial species returned to their pre-disturbance densities more slowly when there were more temperate phage species, but cycles engendered by disturbances dampened more slowly when there were more virulent phage species.