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

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

doi:10.7717/peerj.9718

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

PeerJ. 2020 Aug 31:8:e9718. doi: 10.7717/peerj.9718. eCollection 2020.

Authors

Taylor Miller-Ensminger¹, Andrea Garretto^{1

2}, Nicole Stark^{3

4}, Catherine Putonti^{1

3

5}

Affiliations

¹ Bioinformatics Program, Loyola University of Chicago, Chicago, IL, United States of America.
² Department of Microbiology & Immunology, University of Michigan-Ann Arbor, Ann Arbor, MI, United States of America.
³ Department of Biology, Loyola University of Chicago, Chicago, IL, United States of America.
⁴ Department of Biology, Indiana University at Bloomington, Bloomington, IN, United States of America.
⁵ Department of Microbiology and Immunology, Loyola University of Chicago, Maywood, IL, United States of America.

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.

Keywords: Bacteriophage; Induction; Lysogens; pH.

Grants and funding

This work was supported by the National Science Foundation (Grant 1661357 to Catherine Putonti). Taylor Miller-Ensminger was supported through Loyola University Chicago’s Carbon Research Fellowship. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.