Needle in a Whey-Stack: PhRACS as a Discovery Tool for Unknown Phage-Host Combinations

The field of metagenomics has rapidly expanded to become the go-to method for complex microbial community analyses. However, there is currently no straightforward route from metagenomics to traditional culture-based methods of strain isolation, particularly in (bacterio)phage biology, leading to an...

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Bibliographic Details
Authors: Casey, Eoghan, McDonnell, Brian, White, Kelsey, Stamou, Panagiota, Crowley, Tadhg, O’Neill, Ian, Lavelle, Katherine, Hayes, Stephen, Lugli, Gabriele A., Arboleya, Silvia, James, Kieran, Ventura, Marco, Martínez, Inés, Gueimonde Fernández, Miguel, Bello, Fabio dal, Nally, Ken, Mahony, Jennifer, Sinderen, Douwe van
Format: article
Status:Published version
Publication Date:2022
Country:España
Institution:Consejo Superior de Investigaciones Científicas (CSIC)
Repository:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/295544
Online Access:http://hdl.handle.net/10261/295544
Access Level:Open access
Keyword:Metagenome
Virome
Phageome
Cytometry
Fluorescent
RBP
Fecal
Whey
Fluorescence
Description
Summary:The field of metagenomics has rapidly expanded to become the go-to method for complex microbial community analyses. However, there is currently no straightforward route from metagenomics to traditional culture-based methods of strain isolation, particularly in (bacterio)phage biology, leading to an investigative bottleneck. Here, we describe a method that exploits specific phage receptor binding protein (RBP)-host cell surface receptor interaction enabling isolation of phage-host combinations from an environmental sample. The method was successfully applied to two complex sample types—a dairy-derived whey sample and an infant fecal sample, enabling retrieval of specific and culturable phage hosts. IMPORTANCE PhRACS aims to bridge the current divide between in silico genetic analyses (i.e., phageomic studies) and traditional culture-based methodology. Through the labeling of specific bacterial hosts with fluorescently tagged recombinant phage receptor binding proteins and the isolation of tagged cells using flow cytometry, PhRACS allows the full potential of phageomic data to be realized in the wet laboratory.

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