Phage Infection Fronts Trigger Early Sporulation and Collective Defense in Bacillus subtilis Populations

Description

This repository contains the computational models and data analysis related to our paper titled "Phage infection fronts trigger early sporulation and collective defense in Bacillus subtilis populations". In this study, we explore how phage infection fronts can trigger early sporulation and a collective defense mechanism in Bacillus subtilis thus affecting phage spread in spatially structured environments. Our findings suggest that sporulation can act as a collective defense mechanism against phage infections, highlighting alternative mechanisms by which infection-induced signaling can self-limit infections at population scales. The project encompasses computational models and experimental data analysis, aiming to provide insights into the dynamics of phage-bacteria interactions in spatially structured environments.

'Code for simulations' Contents

Code Files (Jupyter Notebooks)

• Model R: Model with Resource-only dependent dormancy.
• Model V: Model with Contact mediated dormancy (with and without time delay).
• Model M: Model with Messenger molecule mediated dormancy (with and without time delay).

Each Jupyter notebook runs independently and corresponds to a specific dormancy model explored in the study.

Data Files

Comparing theoretical predictions from our modeling with the actual experimental results.

• Splus_data: Plaque Size Data (Sporulating Bacteria): Experimental data on plaque sizes formed by phages lysing sporulating bacteria.
• Sminus_data: Plaque Size Data for Non-Sporulating Bacteria: Data for plaques formed on non-sporulating bacteria.

'Image analysis code' Contents

Subfolders for each figure

• Fig1_image_analysis: contains 'Fig1_README.rtf' describing how to reproduce Fig1.
• Fig2_timelapse_analysis: contains 'Fig2_README.rtf' describing how to reproduce Fig2.
• Fig3_GFP analysis: contains 'Fig3_README.rtf' describing how to reproduce Fig3.

Further Reading

For more detailed information on our models, experimental methods, and findings, please refer to our paper titled "Phage infection fronts trigger early sporulation and collective defense in Bacillus subtilis populations".