Investigation of Salmonella Phage–Bacteria Infection Profiles: Network Structure Reveals a Gradient of Target-Range from Generalist to Specialist Phage Clones in Nested Subsets
Abstract
:1. Introduction
2. Materials and Methods
2.1. Phages and Bacterial Strains
2.2. Antibiotic Susceptibility Tests
2.3. Bacteriophage Susceptibility Test
2.4. Representation of In Vitro Infection Data in a Phage–Bacterium Infection Matrix
2.5. Assignment of Infection Profiles and Clustering
2.6. Construction of Salmonella Phage–Bacterium Infection Network
2.7. Calculating Nestedness and Modularity
2.8. Statistical Analysis
3. Results
3.1. The Salmonella Phage Target-Range Varies between Clones of Different Taxonomic Lineages and Isolated from Different Environmental Sites
3.2. The Salmonella Phages Are Grouped into Clusters with Different Infection Profiles
3.3. The Genetic Distances of the Salmonella Phages Are Positively Associated to Their Infection Profiles
3.4. The Salmonella Phage–Bacteria Infection Network Is Nested
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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Source | Name | Study id | Tax id | Family | Genus | Taxonomic Clade | Infection Profile | Infected Hosts |
---|---|---|---|---|---|---|---|---|
Mtkari river water | Salmonella phage GEC_vB_B1 | GE_vB_B1 | 2108164 | Myoviridae | Unclassified Ounavirinae | Clade 1 | Cluster 1 | 111 |
Salmonella phage GEC_vB_B3 | GE_vB_B3 | 2108165 | Myoviridae | Unclassified Ounavirinae | Clade 1 | Cluster 1 | 106 | |
Salmonella phage GEC_vB_HIL | GE_vB_HIL | 2108167 | Siphoviridae | Unclassified Jerseyvirus | Clade 4 | Cluster 1 | 82 | |
Salmonella phage GEC_vB_7A | GE_vB_7A | 2108163 | Myoviridae | Unclassified Felixounavirus | Clade 2 | Cluster 2 | 52 | |
Salmonella phage GEC_vB_TR | GE_vB_TR | 2108174 | Podoviridae | Unclassified Lederbergvirus | Clade 5 | Cluster 2 | 57 | |
Salmonella phage GEC_vB_N5 | GE_vB_N5 | 2108171 | Demerecviridae | Unclassified Tequintavirus | Clade 3 | Cluster 3 | 76 | |
Salmonella phage GEC_vB_N8 | GE_vB_N8 | 2108172 | Demerecviridae | Unclassified Tequintavirus | Clade 3 | Cluster 3 | 76 | |
Salmonella phage GEC_vB_N3 | GEC_vB_N3 | 2777377 | Demerecviridae | Unclassified Tequintavirus | Clade 3 | Cluster 3 | 96 | |
Black sea water | Salmonella phage GEC_vB_BS | GE_vB_BS | 2108166 | Myoviridae | Unclassified Ounavirinae | Clade 1 | Cluster 1 | 107 |
Salmonella phage GEC_vB_M4 | GE_vB_M4 | 2108168 | Siphoviridae | Unclassified Jerseyvirus | Clade 4 | Cluster 4 | 33 | |
Salmonella phage GEC_vB_M5 | GE_vB_M5 | 2108169 | Siphoviridae | Unclassified Jerseyvirus | Clade 4 | Cluster 4 | 52 | |
Raw cow milk | Salmonella phage GEC_vB_NS7 | GE_vB_NS7 | 2108173 | Myoviridae | Unclassified Ounavirinae | Clade 1 | Cluster 1 | 97 |
Tbilisi sewage water | Salmonella phage GCE_vB_MG | GE_vB_MG | 2108170 | Myoviridae | Unclassified Seunavirus | Clade 2 | Cluster 2 | 56 |
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Makalatia, K.; Kakabadze, E.; Bakuradze, N.; Grdzelishvili, N.; Stamp, B.; Herman, E.; Tapinos, A.; Coffey, A.; Lee, D.; Papadopoulos, N.G.; et al. Investigation of Salmonella Phage–Bacteria Infection Profiles: Network Structure Reveals a Gradient of Target-Range from Generalist to Specialist Phage Clones in Nested Subsets. Viruses 2021, 13, 1261. https://doi.org/10.3390/v13071261
Makalatia K, Kakabadze E, Bakuradze N, Grdzelishvili N, Stamp B, Herman E, Tapinos A, Coffey A, Lee D, Papadopoulos NG, et al. Investigation of Salmonella Phage–Bacteria Infection Profiles: Network Structure Reveals a Gradient of Target-Range from Generalist to Specialist Phage Clones in Nested Subsets. Viruses. 2021; 13(7):1261. https://doi.org/10.3390/v13071261
Chicago/Turabian StyleMakalatia, Khatuna, Elene Kakabadze, Nata Bakuradze, Nino Grdzelishvili, Ben Stamp, Ezra Herman, Avraam Tapinos, Aidan Coffey, David Lee, Nikolaos G. Papadopoulos, and et al. 2021. "Investigation of Salmonella Phage–Bacteria Infection Profiles: Network Structure Reveals a Gradient of Target-Range from Generalist to Specialist Phage Clones in Nested Subsets" Viruses 13, no. 7: 1261. https://doi.org/10.3390/v13071261