Phylogenomic analyses and host range prediction of cluster P mycobacteriophages

Abigail A. Howell, Cyril J. Versoza, Gabriella Cerna, Tyler Johnston, Shriya Kakde, Keith Karuku, Maria Kowal, Jasmine Monahan, Jillian Murray, Teresa Nguyen, Aurely Sanchez Carreon, Abigail Streiff, Blake Su, Faith Youkhana, Saige Munig, Zeel Patel, Minerva So, Makena Sy, Sarah Weiss, Susanne P. Pfeifer

Research output: Contribution to journalArticlepeer-review

Abstract

Bacteriophages, infecting bacterial hosts in every environment on our planet, are a driver of adaptive evolution in bacterial communities. At the same time, the host range of many bacteriophages—and thus one of the selective pressures acting on complex microbial systems in nature—remains poorly characterized. Here, we computationally inferred the putative host ranges of 40 cluster P mycobacteriophages, including members from 6 subclusters (P1–P6). A series of comparative genomic analyses revealed that mycobacteriophages of subcluster P1 are restricted to the Mycobacterium genus, whereas mycobacteriophages of subclusters P2–P6 are likely also able to infect other genera, several of which are commonly associated with human disease. Further genomic analysis highlighted that the majority of cluster P mycobacteriophages harbor a conserved integration-dependent immunity system, hypothesized to be the ancestral state of a genetic switch that controls the shift between lytic and lysogenic life cycles—a temperate characteristic that impedes their usage in antibacterial applications.

Original languageEnglish (US)
Article numberjkac244
JournalG3: Genes, Genomes, Genetics
Volume12
Issue number11
DOIs
StatePublished - Nov 2022
Externally publishedYes

Keywords

  • cluster P
  • comparative genomics
  • host range
  • mycobacteriophages
  • phylogenomics

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Genetics(clinical)

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