Metaviromes Reveal the Dynamics of Pseudomonas Host-Specific Phages Cultured and Uncultured by Plaque Assay
Abstract
:1. Introduction
2. Materials and Methods
2.1. Bacterial Host Strain and Organic Waste Sample Preparation
2.2. Plaque Assay and Isolation of Single Phages
2.3. Virome Spike and Extraction
2.4. DNA Extraction, Purification, and Library Prep
2.5. Quality Control and Assembly
2.6. Viral Identification and Clustering
2.7. Abundance Calculations
2.8. Host Prediction
2.9. Diversity Analysis and Statistics
3. Results
3.1. Viral Contigs Constitute the Majority of Each Assembly
3.2. Differences in Viral Composition Correlates with the Presence/Absence of vOTUs Rather Than High/Low Abundance
3.3. Most Abundant vOTUs Indicate a Population Change
3.4. DrKristoffer, Hovsa, and OtownIsak Cluster Together with Two Contigs from the OW Viromes
3.5. Pseudomonas Phages Are Significantly Enriched When Exposed to DC3000
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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No. of Contigs | % | No. of bp | % | ||
---|---|---|---|---|---|
Total | 131,073 | 100 | Total | 317,732,011 | 100 |
Putative viral | 101,068 | 77.1 | Putative viral | 275,137,398 | 86.6 |
Putative nonviral | 30,005 | 22.9 | Putative nonviral | 42,594,613 | 13.4 |
Phage | Genome Size | Family/Genus | Cluster Representative (CR) | Coverage of CR | Percent Identity to CR |
---|---|---|---|---|---|
DrKristoffer | 98,997 | Myoviridae/Otagovirus | NODE_5 | 91% | 93.61% |
Hovsa | 40,290 | Autographiviridae/Ghunavirus | NODE_16 | 94% | 97.41% |
OtownIsak | 40,331 | Autographiviridae/Ghunavirus | NODE_16 | 100% | 99.99% |
GhostToast | 39,235 | Autographiviridae/Pifdecavirus | - | - | - |
SummerBoyErik | 40,716 | Autographiviridae/Pifdecavirus | - | - | - |
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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
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 StyleAlanin, Katrine Wacenius Skov, Laura Milena Forero Junco, Jacob Bruun Jørgensen, Tue Kjærgaard Nielsen, Morten Arendt Rasmussen, Witold Kot, and Lars Hestbjerg 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
APA StyleAlanin, 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, 13(6), 959. https://doi.org/10.3390/v13060959