INfrastructure for a PHAge REference Database: Identification of Large-Scale Biases in the Current Collection of Cultured Phage Genomes

• DOI: 10.1089/phage.2021.0007
• Publication Date: 2021-10-06T20:30:24Z
• Authors: Ryan Cook; Nathan Brown; Tamsin Redgwell; Branko Rihtman; Megan Barnes; Martha Clokie; Dov J. Stekel; Jon Hobman; Michael A. Jones; Andrew Millard
• Keywords: Lytic cycle; Temperateness; Lysogenic cycle; Phage therapy

Background: With advances in sequencing technology and decreasing costs, the number of phage genomes that have been sequenced has increased markedly past decade. Materials Methods: We developed an automated retrieval analysis system for (https://github.com/RyanCook94/inphared) to produce INfrastructure a PHAge REference Database (INPHARED) associated metadata. Results: As January 2021, 14,244 complete sequenced. The INPHARED data set is dominated by phages infect small bacterial genera, with 75% isolated on only 30 genera. There further bias, significantly more lytic (∼70%) than temperate (∼30%) within our database. Collectively, this results ∼54% originating from just three host much debate carriage antibiotic resistance genes their potential safety therapy, we searched putative genes. Frequency gene was found be higher again varied host. Conclusions: Given bias currently genomes, suggest fully understand diversity, efforts should made isolate sequence larger phages, particular greater diversity hosts.