Fig. 3: Phage adaptation and its effect on phage infectivity.
a, Experimental protocol for phage adaptation. Ancestral phage was propagated with target hosts for 24 h. Subsequently, the purified phage population was repropagated on a naive population of the same host, with this cycle repeated for 10 days. After 5 days, daily measurements of phage growth curves were conducted using the evolved population to find the optimum adaptation duration. The final evolved phages (that is, day 7) were isolated via two rounds of single-plaque purification to obtain an individual genotype of evolved phage mutants. Then, the growth characteristics of these single-genotype evolved phages were assessed. b–d, The relative EOPs of evolved phages (øEnA02 (b), øE2nC07 (c) and øEnC15 (d)) compared to their ancestral counterparts. The labels on top of the boxes represent the adaptation ECC host. Each point (n = 6) represents data from independent biological replicates. p values were calculated using a two-tailed t-test with Welch’s correction. Box bounds indicate 25th and 75th percentiles. e, Phage score of ancestor phages compared to their respective evolved phages, tested against a subset of 36 ECC isolates. Each dot represents a phage score (n = 36) and horizontal lines show means. p values were calculated using a two-tailed t-test with Welch’s correction. f–h, One-step growth curve of evolved phages (øEnA02 (f), øE2nC07 (g) and øEnC15 (h)) compared to their ancestral counterparts, propagated on their respective adaptation hosts. Data represent mean ± s.e.m of n = 3 biological replicates. Y axis represents phage titre, normalized to 100% at time 0. Data are displayed on a logarithmic scale (base 10) for visualization. The latency time (in minutes) and burst size (in p.f.u.s per infection) were calculated for each phage. Panel a created with BioRender.com.
