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Still Something to Discover: Novel Insights into Escherichia coli Phage Diversity and Taxonomy

1
Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
2
Quadram Institute Bioscience, Norwich Research Park, Colney Lane, Norwich NR4 7UQ, UK
3
Departments of Food Science and Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada
4
Protein Analytics Platform, Helmholtz-Centre for Infection Research (HZI), 38124 Braunschweig, Germany
5
Central Facility for Microscopy, Helmholtz-Centre for Infection Research (HZI), 38124 Braunschweig, Germany
6
Department of Macromolecular Structure, Centro Nacional de Biotecnologia CNB-CSIC, 28049 Madrid, Spain
*
Author to whom correspondence should be addressed.
Viruses 2019, 11(5), 454; https://doi.org/10.3390/v11050454
Received: 14 March 2019 / Revised: 29 April 2019 / Accepted: 15 May 2019 / Published: 17 May 2019
(This article belongs to the Special Issue Diversity and Evolution of Phage Genomes)
PDF [10803 KB, uploaded 17 May 2019]

Abstract

The aim of this study was to gain further insight into the diversity of Escherichia coli phages
followed by enhanced work on taxonomic issues in that field. Therefore, we present the genomic
characterization and taxonomic classification of 50 bacteriophages against E. coli isolated from
various sources, such as manure or sewage. All phages were examined for their host range on a set
of different E. coli strains, originating, e.g., from human diagnostic laboratories or poultry farms.
Transmission electron microscopy revealed a diversity of morphotypes (70% Myo-, 22% Sipho-, and
8% Podoviruses), and genome sequencing resulted in genomes sizes from ~44 to ~370 kb.
Annotation and comparison with databases showed similarities in particular to T4- and T5-like
phages, but also to less-known groups. Though various phages against E. coli are already described
in literature and databases, we still isolated phages that showed no or only few similarities to other
phages, namely phages Goslar, PTXU04, and KWBSE43-6. Genome-based phylogeny and
classification of the newly isolated phages using VICTOR resulted in the proposal of new genera
and led to an enhanced taxonomic classification of E. coli phages.
Keywords: bacteriophage; Escherichia coli; taxonomy; diversity; genomics bacteriophage; Escherichia coli; taxonomy; diversity; genomics
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).

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Korf, I.H.E.; Meier-Kolthoff, J.P.; Adriaenssens, E.M.; Kropinski, A.M.; Nimtz, M.; Rohde, M.; van Raaij, M.J.; Wittmann, J. Still Something to Discover: Novel Insights into Escherichia coli Phage Diversity and Taxonomy. Viruses 2019, 11, 454.

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