Mimicking prophage induction in the body: induction in the lab with pH gradients.

Taylor Miller-Ensminger,Andrea Garretto,Andrea Garretto,Catherine Putonti,Catherine Putonti,Nicole Stark,Nicole Stark

doi:10.7717/peerj.9718

Abstract

The majority of bacteria within the human body are lysogens, often harboring multiple bacteriophage sequences (prophages) within their genomes. While several different types of environmental stresses can trigger or induce prophages to enter into the lytic cycle, they have yet to be fully explored and understood in the human microbiota. In the laboratory, the most common induction method is the DNA damaging chemical Mitomycin C. Although pH has been listed in the literature as an induction method, it is not widely used. Here, we detail a protocol for prophage induction by culture under different pH conditions. We explored the effects of pH on prophage induction in bacterial isolates from the bladder, where the pH is well documented to vary significantly between individuals as well as between healthy individuals and individuals with urinary tract symptoms or disease. Using this protocol, we successfully induced phages from seven bladder E. coli strains. Testing conditions and stressors appropriate to the environment from which a lysogen is isolated may provide insight into community dynamics of the human microbiota.

Highlights

Exploration of the human microbiome has uncovered a vast diversity of viral species, bacteriophages
Growing isolates at various pH levels that may be experienced in vivo increases our understanding of phage induction
The pH protocol is efficient in the induction of prophages from E. coli isolates from the bladder

Summary

Introduction

Exploration of the human microbiome has uncovered a vast diversity of viral species, bacteriophages (see review García-López, Pérez-Brocal & Moya, 2019). Core phage communities have been identified within several niches of the human body, and the disruption of these communities has been associated with certain gastrointestinal (Wagner et al, 2013; Manrique et al, 2016) and oral (Ly et al, 2014). The majority of bacteria within the human body are lysogens harboring phage sequences (prophages) within their genomes, including the gut (Breitbart et al, 2003; Reyes et al, 2010; Minot et al, 2011), the oral cavity (Pride et al, 2012), the skin (Hannigan et al, 2015), and the urinary tract (Miller-Ensminger et al, 2018). Recent evidence suggests that the lysogenic life cycle may be the dominant life cycle for phages in many environments, not just niches of the body (Knowles et al, 2016)

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Discussion

Conclusion