https://www.biorxiv.org/content/10.1101/774349v3.full

Diversity in host resistance often associates with reduced pathogen spread. This may result from ecological and evolutionary processes, likely with feedback between them. Theory and experiments on bacteria-phage interactions have shown that genetic diversity of the bacterial adaptive immune system can limit phage evolution to overcome resistance. Using the CRISPR-Cas bacterial immune system and lytic phage, we engineered a host-pathogen system where each bacterial host genotype could be infected by only one phage genotype. With this model system, we explored how CRISPR diversity impacts the spread of phage when they can overcome a resistance allele, how immune diversity affects the evolution of the phage to increase its host range, and if there was feedback between these processes. We show that increasing CRISPR diversity benefits susceptible bacteria via a dilution effect, which limits the spread of the phage. We suggest that this ecological effect impacts the evolution of novel phage genotypes, which then feeds back into phage population dynamics.

Hello! This repo contains all the raw data and associated code used in Common et al (2020).

Data includes the phage titre and selection rate data collected during the coinfection experiment, as well as data from stamp assays used to assess phage evolution. Included also is the sequence data for the bacteriophage-insensitive mutant (BIM) library and of phage that shifted host.

The code included is that used to generate raw data figures (Figures 2A, 3, 4A & B, 5A & B, and S1), analyse phage titre and selection rates using lme4, analyse phage evolution using MCMCglmm, and the generate the associated summary data and figures (Figures 2B, 3, 4C and 5C).

I hope that everything makes sense. You are very welcome to contact me on here or via the correspondence email in the paper if you have any queries.