Environmental structure drives resistance to phages and antibiotics during phage therapy and to invading lysogens during colonisation.

Scientific Reports
Jorge A Moura de Sousa, Eduardo P C Rocha

Abstract

Microbial communities are shaped by bacteriophages through predation and lysogeny. A better understanding of the interactions between these processes across different types of environments is key to elucidate how phages mediate microbial competition and to design efficient phage therapies. We introduce an individual-based model (eVIVALDI) to investigate the role of environmental structure in the elimination of a population with a combined treatment of antibiotics and virulent phages, and in the invasion of a population of phage-sensitive bacteria by lysogens. We show that structured environments facilitate the emergence of double resistance, to antibiotics and phages, due to limited diffusion of phage particles and increased nutrient availability from dead cells. They also hinder phage amplification, thus decreasing the generation of phage genetic diversity and increasing the unpredictability of phage-bacteria arms-races. We used a machine learning approach to determine the variables most important for the invasion of sensitive populations by lysogens. They revealed that phage-associated traits and environmental structure are the key drivers of the process. Structured environments hinder invasions, and accounting for their exis...Continue Reading

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Citations

Jul 6, 2019·PLoS Pathogens·Alfred Fillol-SalomJakob Haaber
Feb 23, 2020·Scientific Reports·Rasmus Skytte EriksenKim Sneppen
Feb 6, 2020·MSystems·Rogelio A Rodriguez-GonzalezJoshua S Weitz
Dec 22, 2020·Research in Microbiology·Marco Túlio Pardini GontijoMarcelo Brocchi
Apr 6, 2021·Critical Reviews in Microbiology·Avijit GoswamiRachit Agarwal

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Software Mentioned

seaborn
eVIVALDI
pandas
Random Forest
randomForest
Random Forest Analysis RFA
R
Git
matplotlib

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