Next Article in Journal
Transcriptomic Analysis of the Campylobacter jejuni Response to T4-Like Phage NCTC 12673 Infection
Next Article in Special Issue
Bacteriophages of Myxococcus xanthus, a Social Bacterium
Previous Article in Journal
Viral Determinants of Virulence in Tick-Borne Flaviviruses
Previous Article in Special Issue
Analysis of 19 Highly Conserved Vibrio cholerae Bacteriophages Isolated from Environmental and Patient Sources Over a Twelve-Year Period
Article Menu
Issue 6 (June) cover image

Export Article

Open AccessArticle
Viruses 2018, 10(6), 331; https://doi.org/10.3390/v10060331

Pseudomonas PB1-Like Phages: Whole Genomes from Metagenomes Offer Insight into an Abundant Group of Bacteriophages

1
Department of Biology, Loyola University Chicago, Chicago, IL 60660, USA
2
Department of Computer Science, Loyola University Chicago, Chicago, IL 60660, USA
3
Bioinformatics Program, Loyola University Chicago, Chicago, IL 60660, USA
Current Address: Biology Department, New Mexico Institute of Mining and Technology, Socorro, NM 87801, USA.
Current Address: Biology Department, City University of New York, New York, NY 10031, USA.
*
Author to whom correspondence should be addressed.
Received: 15 May 2018 / Revised: 11 June 2018 / Accepted: 11 June 2018 / Published: 16 June 2018
(This article belongs to the Special Issue Bacteriophage Genomes and Genomics: News from the Wild)
Full-Text   |   PDF [1976 KB, uploaded 16 June 2018]   |  

Abstract

Despite the abundance, ubiquity and impact of environmental viruses, their inherent genomic plasticity and extreme diversity pose significant challenges for the examination of bacteriophages on Earth. Viral metagenomic studies have offered insight into broader aspects of phage ecology and repeatedly uncover genes to which we are currently unable to assign function. A combined effort of phage isolation and metagenomic survey of Chicago’s nearshore waters of Lake Michigan revealed the presence of Pbunaviruses, relatives of the Pseudomonas phage PB1. This prompted our expansive investigation of PB1-like phages. Genomic signatures of PB1-like phages and Pbunaviruses were identified, permitting the unambiguous distinction between the presence/absence of these phages in soils, freshwater and wastewater samples, as well as publicly available viral metagenomic datasets. This bioinformatic analysis led to the de novo assembly of nine novel PB1-like phage genomes from a metagenomic survey of samples collected from Lake Michigan. While this study finds that Pbunaviruses are abundant in various environments of Northern Illinois, genomic variation also exists to a considerable extent within individual communities. View Full-Text
Keywords: bacteriophage; Pbunaviruses; Pseudomonas phage PB1; uncultivated phage genomes bacteriophage; Pbunaviruses; Pseudomonas phage PB1; uncultivated phage genomes
Figures

Figure 1

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

Supplementary material

SciFeed

Share & Cite This Article

MDPI and ACS Style

Watkins, S.C.; Sible, E.; Putonti, C. Pseudomonas PB1-Like Phages: Whole Genomes from Metagenomes Offer Insight into an Abundant Group of Bacteriophages. Viruses 2018, 10, 331.

Show more citation formats Show less citations formats

Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Related Articles

Article Metrics

Article Access Statistics

1

Comments

[Return to top]
Viruses EISSN 1999-4915 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top