This is the repository of scripts and data necessary to generate the figures in the main text and supplementary information of the article "Variability in plasmid fitness effects contributes to plasmid persistence in bacterial communities". Experimental data for each strain in our collection can be found at pOXA48/data/ODdata_strains/.
The following scripts can be found in pOXA48/code/m-files/:
Figure 5a-b: Modelling pOXA-48 fitness effects
- Plotting script: plotFigure5ab.m
Figure 5c: Fraction of plasmid-bearing as a function of conjugation rate
- Simulation script: runFigure5c.m
- Plotting script: plotFigure5c.m
Figure 5d: Fraction of plasmid-bearing cells as a function of the rate of HGT
- Simulation script: runFigure5d.m
- Plotting script: plotFigure5d.m
Figure 6: Modelling plasmid persistence in polymicrobial communities
- Simulation script: runFigure6.m
- Plotting script: plotFigure6.m
Figure 6e: Mean fraction of plasmid-bearing cells as a function of the number of strains in the community
- Simulation script: runFigure6e.m
- Plotting script: plotFigure6e.m
Supp Figure 7:In silico competition experiments
- Plotting script: plotSuppFigure7.m
Supplementary Figure 8. Comparison between in silico and experimental competition experiments
- Plotting script: plotSuppFigure8.m
Supp Figure 9. Plasmid stability as a function of the conjugation rate and plasmid cost
- Plotting script: plotSuppFigure9.m
Supp Figure 10: Effect of conjugation and community complexity in plasmid population dynamics
- Simulation script: runSuppFigure10.m
- Plotting script: plotSuppFigure10.m
Supp Figure 15: Sampling the distribution of plasmid fitness effects
- Simulation script: plotSuppFigure15.m
Parameters of the population dynamics model (specific affinity and cell efficiency) were jointly determined using a Markov chain Monte Carlo method with a Metropolis-Hastings sampler from growth curves measured as bacterial optical densities. It also implements a data cloning algorithm to assess the identifiability of the parameters.
R scripts to perform the parametrization for the strain collection presented in this manuscript can be run by executing the script runMe that can be found in pOXA48/code/MCMC/R/
MCMC chains are exported into .csv files that can be found in pOXA48/data/MCMC_chains/.
Diagnostic plots presented in Supplementary File 1 are produced with the following Matlab script:
Supp File 1. MCMC Diagnostic plots
- Plotting script: plotSuppFile1.m
- Gelman-Rubin statistics: runGelmanRubin.m