Still Something to Discover: Novel Insights into <i>Escherichia coli</i> Phage Diversity and Taxonomy
The aim of this study was to gain further insight into the diversity of <i>Escherichia coli</i> phages followed by enhanced work on taxonomic issues in that field. Therefore, we present the genomic characterization and taxonomic classification of 50 bacteriophages against <i>E. col...
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doaj-d4f6e10739c045c69753009b15b2a7382020-11-25T02:08:00ZengMDPI AGViruses1999-49152019-05-0111545410.3390/v11050454v11050454Still Something to Discover: Novel Insights into <i>Escherichia coli</i> Phage Diversity and TaxonomyImke H. E. Korf0Jan P. Meier-Kolthoff1Evelien M. Adriaenssens2Andrew M. Kropinski3Manfred Nimtz4Manfred Rohde5Mark J. van Raaij6Johannes Wittmann7Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, GermanyLeibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, GermanyQuadram Institute Bioscience, Norwich Research Park, Colney Lane, Norwich NR4 7UQ, UKDepartments of Food Science and Pathobiology, University of Guelph, Guelph, ON N1G 2W1, CanadaProtein Analytics Platform, Helmholtz-Centre for Infection Research (HZI), 38124 Braunschweig, GermanyCentral Facility for Microscopy, Helmholtz-Centre for Infection Research (HZI), 38124 Braunschweig, GermanyDepartment of Macromolecular Structure, Centro Nacional de Biotecnologia CNB-CSIC, 28049 Madrid, SpainLeibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, GermanyThe aim of this study was to gain further insight into the diversity of <i>Escherichia coli</i> phages followed by enhanced work on taxonomic issues in that field. Therefore, we present the genomic characterization and taxonomic classification of 50 bacteriophages against <i>E. coli</i> isolated from various sources, such as manure or sewage. All phages were examined for their host range on a set of different <i>E. coli</i> 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 <i>E. coli</i> 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 <i>E. coli</i> phages.https://www.mdpi.com/1999-4915/11/5/454bacteriophage<i>Escherichia coli</i>taxonomydiversitygenomics |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Imke H. E. Korf Jan P. Meier-Kolthoff Evelien M. Adriaenssens Andrew M. Kropinski Manfred Nimtz Manfred Rohde Mark J. van Raaij Johannes Wittmann |
spellingShingle |
Imke H. E. Korf Jan P. Meier-Kolthoff Evelien M. Adriaenssens Andrew M. Kropinski Manfred Nimtz Manfred Rohde Mark J. van Raaij Johannes Wittmann Still Something to Discover: Novel Insights into <i>Escherichia coli</i> Phage Diversity and Taxonomy Viruses bacteriophage <i>Escherichia coli</i> taxonomy diversity genomics |
author_facet |
Imke H. E. Korf Jan P. Meier-Kolthoff Evelien M. Adriaenssens Andrew M. Kropinski Manfred Nimtz Manfred Rohde Mark J. van Raaij Johannes Wittmann |
author_sort |
Imke H. E. Korf |
title |
Still Something to Discover: Novel Insights into <i>Escherichia coli</i> Phage Diversity and Taxonomy |
title_short |
Still Something to Discover: Novel Insights into <i>Escherichia coli</i> Phage Diversity and Taxonomy |
title_full |
Still Something to Discover: Novel Insights into <i>Escherichia coli</i> Phage Diversity and Taxonomy |
title_fullStr |
Still Something to Discover: Novel Insights into <i>Escherichia coli</i> Phage Diversity and Taxonomy |
title_full_unstemmed |
Still Something to Discover: Novel Insights into <i>Escherichia coli</i> Phage Diversity and Taxonomy |
title_sort |
still something to discover: novel insights into <i>escherichia coli</i> phage diversity and taxonomy |
publisher |
MDPI AG |
series |
Viruses |
issn |
1999-4915 |
publishDate |
2019-05-01 |
description |
The aim of this study was to gain further insight into the diversity of <i>Escherichia coli</i> phages followed by enhanced work on taxonomic issues in that field. Therefore, we present the genomic characterization and taxonomic classification of 50 bacteriophages against <i>E. coli</i> isolated from various sources, such as manure or sewage. All phages were examined for their host range on a set of different <i>E. coli</i> 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 <i>E. coli</i> 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 <i>E. coli</i> phages. |
topic |
bacteriophage <i>Escherichia coli</i> taxonomy diversity genomics |
url |
https://www.mdpi.com/1999-4915/11/5/454 |
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