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When Plaquing Is Not Possible: Computational Methods for Detecting Induced Phages.

Taylor Miller-Ensminger1, Genevieve Johnson1, Swarnali Banerjee2

  • 1Bioinformatics Program, Loyola University Chicago, Chicago, IL 60660, USA.

Viruses
|February 28, 2023
PubMed
Summary

A new tool, Prophage Induction Estimator (PIE), identifies induced phages in microbial DNA sequences. This method helps understand how phages influence bacterial communities by distinguishing between integrated and unintegrated viral stages.

Keywords:
genomicsinductionmetagenomicsprophagetemperate phages

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Area of Science:

  • Microbiology
  • Virology
  • Bioinformatics

Background:

  • High-throughput sequencing reveals diverse phage populations within microbial communities.
  • Phages often integrate into bacterial genomes (lysogenic stage), influencing host behavior.
  • Distinguishing between integrated (lysogenic) and unintegrated (lytic) phages is crucial for understanding phage-bacterial interactions.

Purpose of the Study:

  • To introduce the Prophage Induction Estimator (PIE), a novel computational tool.
  • To enable the identification of induced phages within genomic and metagenomic datasets.
  • To provide statistical confidence in detecting phage induction events.

Main Methods:

  • PIE processes raw sequencing reads and phage predictions.
  • Includes read quality control, assembly, and abundance calculations for phage and non-phage sequences.
  • Utilizes the distribution of non-phage sequence abundances to statistically infer induced phages.

Main Results:

  • PIE successfully detected induction events and phages with small burst sizes (down to 10×) in silico.
  • Induced phages were identified in isolate genome sequencing data.
  • Instances of induced phages were also found in mock community and urinary metagenome datasets.

Conclusions:

  • PIE is a flexible software tool for detecting induced prophages in genomic and metagenomic data.
  • It enhances the utility of sequencing data beyond mere phage discovery and identification.
  • The tool aids in understanding the dynamic role of phages in shaping microbial communities.