Characterization and Genomic Analysis of Novel Vibrio parahaemolyticus Phage vB_VpaP_DE10
Abstract
:1. Introduction
2. Materials and Methods
2.1. Bacterial Strains and Growth Conditions
2.2. Isolation of Phage
2.3. Phage Concentration and Morphological Observation
2.4. Spot Assay
2.5. Efficiency of Plating (EOP)
2.6. Phage Nucleotide Extraction
2.7. Genome Sequencing and Bioinformatics Analysis
2.8. Phage One-Step Growth Curve Assay
2.9. Accession Number
2.10. Statistical Analysis
3. Results
3.1. Isolation, Identification, and General Characterization of Phages
3.2. Host Range
3.3. Genomic Signature of Phage vB_VpaP_DE10
3.4. Phage Taxonomy and Phylogeny Analysis
4. Discussion
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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No. | V. parahaemolyticus Strains | Serotype | Antibiotic Resistance | Spot Test | EOP Value | EOP Rank |
---|---|---|---|---|---|---|
1 | O1-1 | O1 | CN-K-CIP-S-AMP | - | NT | Inefficient |
2 | O1-3 | O1 | K-CIP-S-AMP-C | + | 0.32 | Medium |
3 | O2-5 | O2 | S-AMP | - | NT | Inefficient |
4 | O2-7 | O2 | CIP-S-AMP | - | NT | Inefficient |
5 | O3-8 | O2 | K-CIP-S-AMP | - | NT | Inefficient |
6 | O3-10 | O3 | AMP | - | NT | Inefficient |
7 | O3-11 | O3 | CN-S-AMP-C | - | 2.80 | High |
8 | O4-12 | O4 | CIP-S-AMP | + | 1 | High |
9 | O4-13 | O4 | S-AMP | + | 0.99 | High |
10 | O4-14 | O4 | AMP | + | 0.40 | Medium |
11 | O5-15 | O5 | CN-K-CIP-S-AMP | + | NT | Inefficient |
12 | O6-18 | O6 | K-CIP-S-AMP | + | 0 | Inefficient |
13 | O6-20 | O6 | CIP-S-AMP | + | 0.68 | High |
14 | O8-21 | O8 | S-AMP | + | 0 | Inefficient |
15 | O8-126 | O8 | AMP | - | NT | Inefficient |
16 | O9-24 | O9 | CN-CIP-S-AMP | - | NT | Inefficient |
17 | O10-25 | O10 | S-AMP | - | NT | Inefficient |
18 | O10-26 | O10 | CN-CIP-S-AMP-C | - | NT | Inefficient |
19 | O10-28 | O10 | AMP | - | NT | Inefficient |
20 | O11-29 | O11 | CN-K-CIP-AMP | - | NT | Inefficient |
21 | O11-30 | O11 | S-AMP | - | NT | Inefficient |
22 | O11-31 | O11 | CIP-S-AMP | + | 8.91 | High |
23 | O12-32 | O12 | S-AMP | - | NT | Inefficient |
24 | O12-33 | O12 | CIP-S-AMP | + | 0.065 | Low |
25 | O12-34 | O12 | SXT-CIP-AMP-TE-K | - | NT | Inefficient |
26 | O12-35 | O12 | CN-CIP-S-AMP | - | NT | Inefficient |
Label | Length (nt|aa) | Product | Organism | Identity |
---|---|---|---|---|
ORF2 | 1281|426 | DNA helicase | Vibrio phage vB_VpP_DE18 | 100% |
ORF3 | 234|77 | putative DNA helicase | Vibrio phage vB_VpP_DE18 | 100% |
ORF4 | 2427|808 | DNA-directed DNA polymerase | Vibrio phage vB_VpP_DE18 | 99% |
ORF7 | 597|198 | putative nucleotidyl transferase | Vibrio phage vB_VpaP_KF1 | 98% |
ORF10 | 630|209 | DNA binding protein | Vibrio phage BUCT233 | 98% |
ORF13 | 951|316 | exonuclease | Vibrio phage vB_VpP_DE18 | 99% |
ORF15 | 441|146 | endonuclease | Vibrio phage BUCT233 | 100% |
ORF17 | 585|194 | putative deoxynucleoside monophosphate kinase | Vibrio phage vB_VpaP_KF1 | 80% |
ORF18 | 2451|816 | DNA-directed RNA polymerase | Vibrio phage BUCT233 | 99% |
ORF19 | 420|139 | GNAT family N-acetyltransferase | Vibrio phage vB_VpP_DE18 | 100% |
ORF20 | 246|81 | virion protein | Vibrio phage vB_VpP_DE18 | 100% |
ORF21 | 1533|510 | putative head–tail connector protein | Vibrio phage vB_VpP_DE17 | 99% |
ORF22 | 816|271 | putative scaffolding protein | Vibrio phage vB_VpaP_MGD1 | 99% |
ORF23 | 999|332 | major capsid protein | Vibrio phage vB_VpaP_MGD1 | 99% |
ORF25 | 561|186 | putative tail tubular protein A | Vibrio phage vB_VpaP_MGD1 | 100% |
ORF26 | 2343|780 | putative tail tubular protein B | Vibrio phage vB_VpaP_MGD1 | 99% |
ORF27 | 741|246 | internal virion protein | Vibrio phage vB_VpP_FE11 | 86% |
ORF28 | 2679|892 | internal virion protein | Vibrio phage vB_VpaP_KF1 | 95% |
ORF29 | 3855|1284 | peptidoglycan lytic exotransglycosylase | Vibrio phage vB_VpP_DE18 | 99% |
ORF30 | 612|203 | putative tail fiber protein | Vibrio phage VP93 | 99% |
ORF31 | 2733|910 | putative glycosyl hydrolase | Vibrio phage vB_VpaP_KF1 | 99% |
ORF32 | 300|99 | terminase small subunit | Vibrio phage vB_VpP_DE18 | 98% |
ORF33 | 1920|639 | terminase large subunit | Vibrio phage vB_Vc_SrVc2 | 100% |
ORF37 | 414|137 | peptidase M15A | Vibrio phage vB_VpP_DE18 | 100% |
ORF44 | 2136|711 | putative structural protein | Vibrio phage vB_VpP_DE18 | 98% |
ORF45 | 1092|363 | putative peptidase | Vibrio phage vB_VpP_DE18 | 100% |
Accession Number | Virus Name | Identity (%) |
---|---|---|
MT501516.1 | vB_VpaP_MGD1 | 96.41 |
NC_048035.1 | vB_VpaP_KF1 | 95.97 |
MZ592921.1 | vB_VpP_NS8 | 95.87 |
MZ020222.1 | BUCT233 | 95.64 |
MW331544.1 | vB_Vc_SrVc2 | 95.55 |
LR794124.1 | vB_Vc_SrVc9 | 95.55 |
NC_048036.1 | vB_VpaP_KF2 | 95.21 |
MZ182247.1 | vB_VpP_DE18 | 95.06 |
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Ye, Y.; Chen, H.; Huang, Q.; Huang, S.; He, J.; Zhang, J.; Wu, Q.; Li, X.; Hu, W.; Yang, M. Characterization and Genomic Analysis of Novel Vibrio parahaemolyticus Phage vB_VpaP_DE10. Viruses 2022, 14, 1609. https://doi.org/10.3390/v14081609
Ye Y, Chen H, Huang Q, Huang S, He J, Zhang J, Wu Q, Li X, Hu W, Yang M. Characterization and Genomic Analysis of Novel Vibrio parahaemolyticus Phage vB_VpaP_DE10. Viruses. 2022; 14(8):1609. https://doi.org/10.3390/v14081609
Chicago/Turabian StyleYe, Yuanming, Hanfang Chen, Qiaolan Huang, Shixuan Huang, Jiaxin He, Jumei Zhang, Qingping Wu, Xueling Li, Wenfeng Hu, and Meiyan Yang. 2022. "Characterization and Genomic Analysis of Novel Vibrio parahaemolyticus Phage vB_VpaP_DE10" Viruses 14, no. 8: 1609. https://doi.org/10.3390/v14081609
APA StyleYe, Y., Chen, H., Huang, Q., Huang, S., He, J., Zhang, J., Wu, Q., Li, X., Hu, W., & Yang, M. (2022). Characterization and Genomic Analysis of Novel Vibrio parahaemolyticus Phage vB_VpaP_DE10. Viruses, 14(8), 1609. https://doi.org/10.3390/v14081609