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Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins
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Deciphering Active Prophages from Metagenomes.

Kristopher Kieft1,2, Karthik Anantharaman1

  • 1Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA.

Msystems
|March 24, 2022
PubMed
Summary
This summary is machine-generated.

We developed PropagAtE, a new tool to identify active temperate phages (prophages) in microbial communities. This tool reveals distinct prophage activation patterns across environments and links them to microbial community dynamics.

Keywords:
metagenomemicrobiomeprophagesoftwarevirus

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Area of Science:

  • Microbiology and Virology
  • Bioinformatics and Computational Biology
  • Ecology and Environmental Science

Background:

  • Temperate phages (prophages) are viruses that integrate into bacterial genomes, existing in dormant (lysogenic) or active (lytic) states.
  • Active prophages significantly influence microbial communities by affecting bacterial virulence, biogeochemical cycling, and community structure.
  • Current methods lack the ability to accurately determine the activation status of prophages within complex microbial communities.

Purpose of the Study:

  • To develop and validate an automated computational tool, PropagAtE (Prophage Activity Estimator), for distinguishing between lysogenic and lytic prophage states.
  • To assess prophage activity across diverse environmental samples, including human gut, murine gut, and soil microbiomes.
  • To investigate the correlation between prophage activation and specific conditions, such as antibiotic treatment in infants.

Main Methods:

  • PropagAtE utilizes statistical analysis of prophage-to-host read coverage ratios to infer prophage replication status.
  • The tool was tested for speed, accuracy, and sensitivity across various sequencing depths.
  • PropagAtE was applied to 348 complex metagenomes from human gut, murine gut, and soil environments, as well as infant gut samples.

Main Results:

  • PropagAtE accurately and efficiently identifies active prophages, irrespective of induction method or sequencing depth.
  • Murine gut samples exhibited the highest proportion of active prophages, indicating significant spatial and temporal activation signatures.
  • Active prophage populations were identified in infants, with correlations to antibiotic treatment status; some prophages remained consistently present but inactive in human gut time series.

Conclusions:

  • PropagAtE provides a robust method for estimating prophage activity, enabling more accurate representation of viral roles in ecosystems.
  • The study reveals significant variations in prophage activation across different environments and host conditions.
  • This tool will advance our understanding of how viruses shape microbial communities and drive ecological processes.