HtPIP: High-Throughput Phage Isolation Platform increases diversity and reduces isolation time using multiple bacteria

Abstract

Bacteriophages are ubiquitous in nature, but relatively few have been isolated and characterized compared to the number of bacterial strains. Phage biotechnology applications benefit from a diverse library of isolated phages to kill or transfer genetic material to a bacterium of interest. However, scaling phage discovery for diverse bacterial hosts can be time consuming and costly. We developed an approach to capture novel phages for multiple bacteria strains in parallel from an environmental sample using commercially available 0.2-micron filter plates. Using this High-throughput Phage Isolation Platform (HtPIP), we isolated twelve novel phages spanning nine diverse bacterial host genera. Eleven of the isolated phages define new phage species with nine also defining new genera. We show the HtPIP can discover both DNA and RNA phages; including a Tectiviridae infecting Pseudomonas putida mt-2 and a Leviviricetes infecting a Microbacterium isolate, which represents the first cultured RNA phage infecting a host outside of proteobacteria. Using a metagenomic approach, we demonstrate that the HtPIP captures a higher proportion of novel phages compared to traditional low-throughput methods.