Ramírez Carolina, Romero Jaime
Laboratorio de Biotecnología de Alimentos, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, El Líbano 5524, Santiago 7830489, Chile.
Antibiotics (Basel). 2024 Dec 5;13(12):1184. doi: 10.3390/antibiotics13121184.
Tenacibaculosis, caused by 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 genomes is crucial for developing these bacteriophage-based strategies.
We assessed the presence of prophages in 212 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.
We identified 25 phage elements in 24 out of the 212 genomes/assemblies analyzed, with 11% of the assemblies containing phage elements. These were concentrated in and , which harbored 10 and 7 prophage regions, respectively. Of the identified elements, six were classified as intact, including four in , with the most common phages belonging to the and 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 bacteriophage K.
Key prophage elements in , especially in , show promise for phage therapy against tenacibaculosis, supporting sustainable, antibiotic-free treatments in aquaculture.
由 种引起的鱼结核病是水产养殖中的一种重要疾病，会导致高死亡率和经济损失。抗生素治疗引发了对耐药性的担忧，使得噬菌体疗法成为一个有趣的替代方案。分析 基因组中的噬菌体痕迹对于开发这些基于噬菌体的策略至关重要。
我们使用PHASTEST程序评估了NCBI数据库中212个 基因组/组装体中前噬菌体的存在情况，这些基因组/组装体包括多个物种和来自全球各地的样本。然后，我们聚焦于那些被分类为完整的区域，使用VICTOR评估发现的最常见噬菌体。使用ProtParam、DeepTMHMM、InterPro和Phyre2工具评估在前噬菌体中发现的目标蛋白质。此外，我们使用DefenseFinder工具评估那些含有完整前噬菌体的基因组中抗噬菌体防御系统的存在情况。
在分析的212个 基因组/组装体中的24个中，我们鉴定出了25个噬菌体元件，11%的组装体含有噬菌体元件。这些元件集中在 和 中，分别含有10个和7个前噬菌体区域。在鉴定出的元件中，有6个被分类为完整的，其中4个在 中，最常见的噬菌体属于 和 家族。生物信息学分析表明，推定的内溶素是一种稳定的蛋白质，有432个氨基酸，49.8 kDa，有三个跨膜螺旋和一个CHAP结构域，在结构上与噬菌体K的CHAP裂解结构域相似。
中的关键前噬菌体元件，特别是在 中的，显示出用于噬菌体治疗鱼结核病的潜力，支持水产养殖中可持续的无抗生素治疗。
