Each bacterial phylum grows logistically toward a shared gut carrying capacity K, but the whole community is also hunted by the gut virome — bacteriophages that infect and lyse their bacterial hosts. Real gut phage populations show frequency-dependent (kill-the-winner) predation: a lytic phage's own replication rate scales with how often it meets a susceptible host, so whichever phylum is currently most abundant gets hunted hardest.
dB_i/dt = r_i · B_i · (1 − S/K) − φ · (B_i / S)^n · B_i
S = Σ B_i (total bacterial population)
r_i (intrinsic growth rate of phylum i)
φ = predation strength (overall lytic pressure)
n = selectivity exponent (0 = density-independent kill, higher = sharper "hunt the winner")
H = − Σ p_i · ln(p_i), p_i = B_i / S (Shannon diversity)
- Predation strength — scales how much lytic pressure the virome exerts overall. At 0, phages have no effect and the fastest grower eventually excludes the rest.
- Kill-the-winner selectivity (n) — how sharply phage attack concentrates on the currently dominant phylum. At n = 0 predation is spread evenly by abundance only; increasing n turns it into targeted suppression of whoever is winning, which is what keeps diversity high in a real gut.
- Diet skew — a Western, high-sugar/low-fibre diet gives Firmicutes an intrinsic growth advantage; raise it to see how strong the phage response needs to be to stop that advantage collapsing the community into one phylum.
- Antibiotic pulse — wipes out most of every phylum at once (both susceptible bacteria and their resident phages lose their hosts), then lets you watch the community re-equilibrate under the current predation settings.
The radial map on the right shows the gut lumen from above: five colony clusters sit at fixed stations around the ring, sized by live population, with phage particles (white diamonds) swarming whichever colony currently dominates. Drag the map to rotate the ring. Below it, a stacked-share chart tracks phylum composition over time and a second trace plots Shannon diversity — watch it collapse toward zero if predation can't keep up with diet skew, or hold high under strong kill-the-winner pressure.
This mechanism is why the gut virome is now studied alongside the bacterial microbiome: bacteriophages are not just bystanders, they are an active regulatory layer that suppresses competitive exclusion and preserves the phylum-level diversity that keeps the ecosystem — and its host — resilient.