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

Abstract

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 (*70%) than temperate (*30%) within our database. Collectively, this results in *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.

Genomic Diversity of Bacteriophages Infecting the Genus Acinetobacter

“…To provide a snapshot of the relationship between the Acinetobacter phages and the wider phage population, a gene-sharing network of all phage genomes held in GenBank (24 January 2021) was constructed using the INPHARED pipeline [16] and vConTACT2 0.9.19, using DIAMOND v2.0.7.145 was applied for protein clustering and ClusterOne v1.0 for protein and viral cluster analyses. The resulting network was visualised using Cytoscape (version 3.8.2) [17] and annotated with Adobe Illustrator (Adobe Inc., San Jose, CA, USA).…”

Genetically distant bacteriophages select for unique genomic changes in Enterococcus faecalis

“…Comparative genomic analysis of phi47 was performed with all publicly available enterococcal phage genomes using OrthoMCL (Figure 1c ) (Cook et al, 2021 ). This algorithm generates a phylogenetic tree of clustered phage genomes (orthoclusters) based on orthologous proteins (Bolocan et al, 2019 ; Canfield et al, 2021 ; Li et al, 2003 ).…”

“…Enterococcal phage phylogeny was determined using OrthoMCL (Li et al, 2003 ) as described previously (Canfield et al, 2021 ). Enterococcal phage genomes were downloaded from the INPHARED phage genome database (Cook et al, 2021 ). As of July 1, 2021, there were 126 enterococcal phage genome sequences available in addition to our inclusion of the phi47 genome.…”

“…In contrast, conventional antibiotics lack specificity, killing resident bacteria, and the compounds can remain in the patient after the infection has cleared (Langdon et al, 2016 ). There is an ever‐growing repertoire of phages that infect E. faecalis (Cook et al, 2021 ), making these promising candidates for phage therapy.…”

PVJ1 Is Not the First Tailed Temperate Phage Infecting Bacteria from Genus Psychrobacillus. Comment on Liu et al. Isolation and Characterization of the First Temperate Virus Infecting Psychrobacillus from Marine Sediments. Viruses 2022, 14, 108

“…Although the peer-reviewed literature contains some attempts at summarizing the complete phage genome contents of the public databases (i.e., our attempt at doing so [ 11 ]), such studies, logically, provide no more than overview snapshots of the uncovered phage diversity at a given time and are always prone to becoming obsolete in the light of such diversity being ever-growing. To allow following the expansion of GenBank with novel phage entries, recently, a methodological framework that allows taking such “phage diversity snapshots” and even additionally extracting meaningful data for further phage comparative genomics analyses (INPHARED) was developed and published by Cook and colleagues [ 12 ] but requires some command line proficiency from the potential user seeking to run it independently of the (thus far monthly) output updates by the authors, making manual public database searches still a necessity for some researchers.…”