Unveiling Hidden Allies: In Silico Discovery of Prophages in <i>Tenacibaculum</i> Species
Tenacibaculosis, caused by <i>Tenacibaculum</i> species, is a significant disease in aquaculture, leading to high mortality and economic losses. Antibiotic treatment raises concerns about resistance, making phage therapy an interesting alternative. Analyzing phage traces in <i>Tena...
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MDPI AG
2024-12-01
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| author | Carolina Ramírez Jaime Romero |
| author_facet | Carolina Ramírez Jaime Romero |
| author_sort | Carolina Ramírez |
| collection | DOAJ |
| description | Tenacibaculosis, caused by <i>Tenacibaculum</i> species, is a significant disease in aquaculture, leading to high mortality and economic losses. Antibiotic treatment raises concerns about resistance, making phage therapy an interesting alternative. Analyzing phage traces in <i>Tenacibaculum</i> genomes is crucial for developing these bacteriophage-based strategies. Methods: We assessed the presence of prophages in 212 <i>Tenacibaculum</i> genomes/assemblies available in the NCBI repository, comprising several species and global locations, using the PHASTEST program. Then, we focused on those regions classified as intact, evaluating the most common phages found using VICTOR. The protein of interest discovered in the prophages was evaluated using the ProtParam, DeepTMHMM, InterPro, and Phyre2 tools. In addition, we evaluated the presence of antiphage defense systems in those genomes with intact prophages using the DefenseFinder tool. Results: We identified 25 phage elements in 24 out of the 212 <i>Tenacibaculum</i> genomes/assemblies analyzed, with 11% of the assemblies containing phage elements. These were concentrated in <i>T. maritimum</i> and <i>T. mesophilum</i>, which harbored 10 and 7 prophage regions, respectively. Of the identified elements, six were classified as intact, including four in <i>T. maritimum</i>, with the most common phages belonging to the <i>Pippivirus</i> and <i>Siphoviridae</i> families. Bioinformatic analysis showed that the putative endolysin is a stable protein of 432 amino acids and 49.8 kDa, with three transmembrane helices and a CHAP domain, structurally similar to the CHAP lytic domain of <i>S. aureus</i> bacteriophage K. Conclusions: Key prophage elements in <i>Tenacibaculum</i>, especially in <i>T. maritimum</i>, show promise for phage therapy against tenacibaculosis, supporting sustainable, antibiotic-free treatments in aquaculture. |
| format | Article |
| id | doaj-art-2f0095d4cbc74f78bdd8f9880efa79e0 |
| institution | DOAJ |
| issn | 2079-6382 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | MDPI AG |
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| series | Antibiotics |
| spelling | doaj-art-2f0095d4cbc74f78bdd8f9880efa79e02025-08-20T02:55:53ZengMDPI AGAntibiotics2079-63822024-12-011312118410.3390/antibiotics13121184Unveiling Hidden Allies: In Silico Discovery of Prophages in <i>Tenacibaculum</i> SpeciesCarolina Ramírez0Jaime Romero1Laboratorio de Biotecnología de Alimentos, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, El Líbano 5524, Santiago 7830489, ChileLaboratorio de Biotecnología de Alimentos, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, El Líbano 5524, Santiago 7830489, ChileTenacibaculosis, caused by <i>Tenacibaculum</i> species, is a significant disease in aquaculture, leading to high mortality and economic losses. Antibiotic treatment raises concerns about resistance, making phage therapy an interesting alternative. Analyzing phage traces in <i>Tenacibaculum</i> genomes is crucial for developing these bacteriophage-based strategies. Methods: We assessed the presence of prophages in 212 <i>Tenacibaculum</i> genomes/assemblies available in the NCBI repository, comprising several species and global locations, using the PHASTEST program. Then, we focused on those regions classified as intact, evaluating the most common phages found using VICTOR. The protein of interest discovered in the prophages was evaluated using the ProtParam, DeepTMHMM, InterPro, and Phyre2 tools. In addition, we evaluated the presence of antiphage defense systems in those genomes with intact prophages using the DefenseFinder tool. Results: We identified 25 phage elements in 24 out of the 212 <i>Tenacibaculum</i> genomes/assemblies analyzed, with 11% of the assemblies containing phage elements. These were concentrated in <i>T. maritimum</i> and <i>T. mesophilum</i>, which harbored 10 and 7 prophage regions, respectively. Of the identified elements, six were classified as intact, including four in <i>T. maritimum</i>, with the most common phages belonging to the <i>Pippivirus</i> and <i>Siphoviridae</i> families. Bioinformatic analysis showed that the putative endolysin is a stable protein of 432 amino acids and 49.8 kDa, with three transmembrane helices and a CHAP domain, structurally similar to the CHAP lytic domain of <i>S. aureus</i> bacteriophage K. Conclusions: Key prophage elements in <i>Tenacibaculum</i>, especially in <i>T. maritimum</i>, show promise for phage therapy against tenacibaculosis, supporting sustainable, antibiotic-free treatments in aquaculture.https://www.mdpi.com/2079-6382/13/12/1184Tenacibaculosisphage therapy<i>Tenacibaculum</i>endolysinaquaculture |
| spellingShingle | Carolina Ramírez Jaime Romero Unveiling Hidden Allies: In Silico Discovery of Prophages in <i>Tenacibaculum</i> Species Antibiotics Tenacibaculosis phage therapy <i>Tenacibaculum</i> endolysin aquaculture |
| title | Unveiling Hidden Allies: In Silico Discovery of Prophages in <i>Tenacibaculum</i> Species |
| title_full | Unveiling Hidden Allies: In Silico Discovery of Prophages in <i>Tenacibaculum</i> Species |
| title_fullStr | Unveiling Hidden Allies: In Silico Discovery of Prophages in <i>Tenacibaculum</i> Species |
| title_full_unstemmed | Unveiling Hidden Allies: In Silico Discovery of Prophages in <i>Tenacibaculum</i> Species |
| title_short | Unveiling Hidden Allies: In Silico Discovery of Prophages in <i>Tenacibaculum</i> Species |
| title_sort | unveiling hidden allies in silico discovery of prophages in i tenacibaculum i species |
| topic | Tenacibaculosis phage therapy <i>Tenacibaculum</i> endolysin aquaculture |
| url | https://www.mdpi.com/2079-6382/13/12/1184 |
| work_keys_str_mv | AT carolinaramirez unveilinghiddenalliesinsilicodiscoveryofprophagesinitenacibaculumispecies AT jaimeromero unveilinghiddenalliesinsilicodiscoveryofprophagesinitenacibaculumispecies |