INfrastructure for a PHAge REference Database: Identification of Large-Scale Biases in the Current Collection of Cultured Phage Genomes
INfrastructure for a PHAge REference Database: Identification of Large-Scale Biases in the Current Collection of Cultured Phage Genomes
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DOI：
10.1089/phage.2021.0007
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发表时间：
2021-12-01
期刊：
影响因子：
--
通讯作者：
Millard, Andrew
中科院分区：
文献类型：
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作者：
Cook, Ryan;Brown, Nathan;Millard, Andrew
背景：随着测序技术的进步和成本的降低，在过去的十年中，已经测序的噬菌体基因组的数量显著增加。材料和方法：我们开发了一个噬菌体基因组自动检索和分析系统(https://github.com/RyanCook94/inphared))，为建立噬菌体基因组和相关元数据参考数据库(INPHARED)奠定基础。INPHARED的数据集主要是感染少数细菌属的噬菌体，75%的噬菌体仅分离于30个细菌属。还有更多的偏见，在我们的数据库中，裂解噬菌体基因组(类似于70%)明显多于温带(类似于30%)。总体而言，这导致54%的温带噬菌体基因组仅来自三个寄主属。随着对携带抗生素耐药基因及其在噬菌体治疗中的潜在安全性的争论越来越多，我们寻找可能的抗生素耐药基因。温带噬菌体携带抗生素耐药基因的频率高于裂解噬菌体。结论：鉴于目前测序的噬菌体基因组存在偏差，我们建议充分了解噬菌体多样性，应努力从更多的宿主中分离和测序更多的噬菌体，特别是温带噬菌体。
Background: With advances in sequencing technology and decreasing costs, the number of phage genomes that have been sequenced has increased markedly in the past decade.Materials and Methods: We developed an automated retrieval and analysis system for phage genomes (https://github.com/RyanCook94/inphared) to produce the INfrastructure for a PHAge REference Database (INPHARED) of phage genomes and associated metadata.Results: As of January 2021, 14,244 complete phage genomes have been sequenced. The INPHARED data set is dominated by phages that infect a small number of bacterial genera, with 75% of phages isolated on only 30 bacterial genera. There is further bias, with significantly more lytic phage genomes (similar to 70%) than temperate (similar to 30%) within our database. Collectively, this results in similar to 54% of temperate phage genomes originating from just three host genera. With much debate on the carriage of antibiotic resistance genes and their potential safety in phage therapy, we searched for putative antibiotic resistance genes. Frequency of antibiotic resistance gene carriage was found to be higher in temperate phages than in lytic phages and again varied with host.Conclusions: Given the bias of currently sequenced phage genomes, we suggest to fully understand phage diversity, efforts should be made to isolate and sequence a larger number of phages, in particular temperate phages, from a greater diversity of hosts.