Metaviromes Reveal the Dynamics of Pseudomonas Host-Specific Phages Cultured and Uncultured by Plaque Assay
| Autor: | Witold Kot, Tue Kjærgaard Nielsen, Morten Arendt Rasmussen, Laura Milena Forero Junco, Lars Hestbjerg Hansen, Jacob Bruun Jørgensen, Katrine Skov Alanin |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
0301 basic medicine
bacteriophages viruses 030106 microbiology Illumina se-quencing Viral Plaque Assay Biology Microbiology Article Host Specificity phage enrichment 03 medical and health sciences plaque-assay Virology Pseudomonas PEG precipitation Pseudomonas syringae Bacteriophages viromes Illumina dye sequencing Host specific Virus quantification Oxford Nanopore Technologies Plaque-assay Strain (chemistry) Virome Host (biology) Illumina sequencing Computational Biology Metaviromes Phage enrichment biology.organism_classification Solid medium QR1-502 Pseudomonas syringae pv. tomato DC3000 030104 developmental biology Infectious Diseases Viromes metaviromes Metagenome Metagenomics Nanopore sequencing Pseudomonas Phages |
| Zdroj: | Viruses, Vol 13, Iss 959, p 959 (2021) Alanin, K W S, Junco, L M F, Jørgensen, J B, Nielsen, T K, Rasmussen, M A, Kot, W & Hansen, L H 2021, ' Metaviromes Reveal the Dynamics of Pseudomonas Host-Specific Phages Cultured and Uncultured by Plaque Assay ', Viruses, vol. 13, no. 6 . https://doi.org/10.3390/v13060959 Alanin, K W S, Junco, L M F, Jørgensen, J B, Nielsen, T K, Rasmussen, M A, Kot, W & Hansen, L H 2021, ' Metaviromes reveal the dynamics of pseudomonas host-specific phages cultured and uncultured by plaque assay ', Viruses, vol. 13, no. 6, 959 . https://doi.org/10.3390/v13060959 Viruses Volume 13 Issue 6 |
| ISSN: | 1999-4915 |
| DOI: | 10.3390/v13060959 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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