Novel technologies enable high throughput acquisition of viral phenotypes

Date
2022
Journal Title
Journal ISSN
Volume Title
Publisher
University of Delaware
Abstract
Viruses of bacteria (bacteriophages) are the most abundant biological entities on the planet. Phages shape their ecosystems by regulating host abundance and driving nutrient cycling. Despite the marked increase in phage sequence data, phage phenotypes remain largely uncharacterized due to the labor-intensive and low throughput nature of phage phenotypic assays. It is critical that novel high throughput assays to measure phenotypes of phages be developed to elucidate the impacts of phages in our environment. My research examined three novel approaches for high throughput acquisition of phage phenotypes and their interactions with hosts. Firstly, the utility of microfluidic technology was assessed for the direct observation of host cells and virus particles in microfluidic droplets. Secondly, a comparison was made between phage replication phenotypes obtained from a classic viable count-based one- step growth (OSG) assay with those obtained from a direct count-based OSG assay using a newly developed tool named the Virometer. Validation of the direct count- based OSG assay was performed using both a model system (phage T7 and its host Escherichia coli) and a novel system with Bradyrhizobium as a host, the latter being a nitrogen-fixing symbiont of soybean. In preparation for the examination of the Bradyrhizobium system, the host ranges of lytic phages virulent towards a collection of soybean bradyrhizobia isolated from Delaware soils were determined. Lastly, a lytic phage-host genome to phenome database (G2PDB) was developed as a resource for the prediction of unknown phage phenotypes. These novel methods provide a foundation for the future development of high throughput assays for the acquisition of phage phenotypes.
Description
Keywords
Bacteriophages
Citation