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Article

Metaviromes Reveal the Dynamics of Pseudomonas Host-Specific Phages Cultured and Uncultured by Plaque Assay

1
Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
2
Department of Environmental Science, Aarhus University, 4000 Roskilde, Denmark
3
Department of Food Science, University of Copenhagen, 1958 Frederiksberg C, Denmark
4
COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, 2820 Gentofte, Denmark
*
Authors to whom correspondence should be addressed.
These authors contributed equally to the work presented.
Academic Editors: Jennifer R. Brum and Simon Roux
Viruses 2021, 13(6), 959; https://doi.org/10.3390/v13060959
Received: 26 April 2021 / Revised: 14 May 2021 / Accepted: 18 May 2021 / Published: 21 May 2021
(This article belongs to the Special Issue Viromics)
Isolating single phages using plaque assays is a laborious and time-consuming process. Whether single isolated phages are the most lyse-effective, the most abundant in viromes, or those with the highest ability to make plaques in solid media is not well known. With the increasing accessibility of high-throughput sequencing, metaviromics is often used to describe viruses in environmental samples. By extracting and sequencing metaviromes from organic waste with and without exposure to a host-of-interest, we show a host-related phage community’s shift, as well as identify the most enriched phages. Moreover, we isolated plaque-forming single phages using the same virome–host matrix to observe how enrichments in liquid media correspond to the metaviromic data. In this study, we observed a significant shift (p = 0.015) of the 47 identified putative Pseudomonas phages with a minimum twofold change above zero in read abundance when adding a Pseudomonas syringae DC3000 host. Surprisingly, it appears that only two out of five plaque-forming phages from the same organic waste sample, targeting the Pseudomonas strain, were highly abundant in the metavirome, while the other three were almost absent despite host exposure. Lastly, our sequencing results highlight how long reads from Oxford Nanopore elevates the assembly quality of metaviromes, compared to short reads alone. View Full-Text
Keywords: bacteriophages; viromes; metaviromes; Oxford Nanopore Technologies; Illumina sequencing; plaque-assay; PEG precipitation; phage enrichment; Pseudomonas syringae pv. tomato DC3000 bacteriophages; viromes; metaviromes; Oxford Nanopore Technologies; Illumina sequencing; plaque-assay; PEG precipitation; phage enrichment; Pseudomonas syringae pv. tomato DC3000
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MDPI and ACS Style

Alanin, K.W.S.; Junco, L.M.F.; Jørgensen, J.B.; Nielsen, T.K.; Rasmussen, M.A.; Kot, W.; Hansen, L.H. Metaviromes Reveal the Dynamics of Pseudomonas Host-Specific Phages Cultured and Uncultured by Plaque Assay. Viruses 2021, 13, 959. https://doi.org/10.3390/v13060959

AMA Style

Alanin KWS, Junco LMF, Jørgensen JB, Nielsen TK, Rasmussen MA, Kot W, Hansen LH. Metaviromes Reveal the Dynamics of Pseudomonas Host-Specific Phages Cultured and Uncultured by Plaque Assay. Viruses. 2021; 13(6):959. https://doi.org/10.3390/v13060959

Chicago/Turabian Style

Alanin, Katrine W.S., Laura M.F. Junco, Jacob B. Jørgensen, Tue K. Nielsen, Morten A. Rasmussen, Witold Kot, and Lars H. Hansen. 2021. "Metaviromes Reveal the Dynamics of Pseudomonas Host-Specific Phages Cultured and Uncultured by Plaque Assay" Viruses 13, no. 6: 959. https://doi.org/10.3390/v13060959

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