Anderson Ranee K, Qin Shijie, Carson Rachel M, Nugen Sam R
Department of Food Science, Cornell University, Ithaca, NY, USA.
Phage (New Rochelle). 2025 Jun 4;6(2):81-86. doi: 10.1089/phage.2024.0049. eCollection 2025 Jun.
Genomic sequencing and annotation, morphological characterization, and host range analyses of bacteriophage (phage) isolates are crucial to understanding each phage's unique set of properties and how they can be utilized as effective tools in medicine, environmental monitoring, biotechnology, and agriculture. In this study, we present the fully annotated genome of viral isolate phage Ge15 (GenBank Accession No. PP359696.1), taxonomically identified as unclassified Tequatrovirus, and deposited into our strain collection as sample NRG-P0073. A host range analysis was performed against all 72 isolates of the Reference (ECOR) library and a selection of K-12 single-gene knockouts from the Keio collection in an effort to identify the receptor-binding protein.
Whole genome sequencing, assembly, and evidence-driven annotation using the Center for Phage Technology's Galaxy and Apollo software were performed on NRG-P0073. Double-agar spot tests were performed against the ECOR library and nine K-12 knockouts from the Keio collection to evaluate both the permissive and adsorptive host ranges of the phage. Transmission electron microscopy was utilized to elucidate the phage morphology.
NRG-P0073 was found to have a 170,913 bp genome, coding for 10 tRNAs, 14 terminators, 259 genes, 249 coding sequences, and a GC content of 35.5%. Double-agar spot tests revealed that NRG-P0073 could adsorb 33 of the 72 strains (45.8%), but only 15 of the 72 strains (20.8%) could complete replication to form distinguishable plaques. All nine of the K-12 single-gene knockout strains (100%) supported complete phage replication, suggesting that none of the nine evaluated receptors are solely responsible for facilitating the attachment of NRG-P0073 to the host surface.
This study presents novel and complete genomic data, characterization, and host range analyses for the newly characterized phage NRG-P0073. Further characterization and analysis are required, including the identification of the receptor-binding protein responsible for initial host recognition. This study provides a foundation for future studies to understand more about NRG-P0073 and provides data that can be utilized for future machine-learning studies of phages and their host interactions.
噬菌体分离株的基因组测序与注释、形态学特征分析以及宿主范围分析，对于理解每种噬菌体独特的性质组合，以及它们如何能作为医学、环境监测、生物技术和农业领域的有效工具至关重要。在本研究中，我们展示了病毒分离株噬菌体Ge15（GenBank登录号PP359696.1）的全注释基因组，该噬菌体在分类学上被鉴定为未分类的特夸特罗病毒，并作为样本NRG - P0073保藏于我们的菌株库中。针对参考（ECOR）文库的所有72个分离株以及来自Keio文库的一系列K - 12单基因敲除菌株进行了宿主范围分析，以鉴定受体结合蛋白。
使用噬菌体技术中心的Galaxy和Apollo软件对NRG - P0073进行全基因组测序、组装和基于证据的注释。针对ECOR文库以及来自Keio文库的9个K - 12敲除菌株进行了双层琼脂斑点试验，以评估噬菌体的允许宿主范围和吸附宿主范围。利用透射电子显微镜阐明噬菌体形态。
发现NRG - P0073具有170,913 bp的基因组，编码10个tRNA、14个终止子、259个基因、249个编码序列，GC含量为35.5%。双层琼脂斑点试验表明，NRG - P0073能吸附72个菌株中的33个（占4 . 8%），但在72个菌株中只有15个（占20.8%）能完成复制形成可区分的噬菌斑。所有9个K - 12单基因敲除菌株（100%）都支持噬菌体的完全复制，这表明所评估的9种受体中没有一种单独负责促进NRG - P0073附着于宿主表面。
本研究展示了新鉴定的噬菌体NRG - P0073的新的完整基因组数据、特征分析和宿主范围分析。还需要进一步的特征分析，包括鉴定负责初始宿主识别的受体结合蛋白。本研究为未来更多了解NRG - P0073的研究提供了基础，并提供了可用于噬菌体及其宿主相互作用的未来机器学习研究的数据。
