Needle in a Whey-Stack: PhRACS as a Discovery Tool for Unknown Phage-Host Combinations
Eoghan Casey,
Brian McDonnell,
Kelsey White,
Panagiota Stamou,
Tadhg Crowley,
Ian O’Neill,
Katherine Lavelle,
Stephen Hayes,
Gabriele A. Lugli,
Silvia Arboleya,
Kieran James,
Marco Ventura,
Ines Martinez,
Miguel Gueimonde,
Fabio dal Bello,
Ken Nally,
Jennifer Mahony,
Douwe van Sinderen
Affiliations
Eoghan Casey
School of Microbiology, University College Cork, Cork, Ireland
Brian McDonnell
School of Microbiology, University College Cork, Cork, Ireland
Kelsey White
School of Microbiology, University College Cork, Cork, Ireland
Panagiota Stamou
APC Microbiome Ireland, University College Cork, Cork, Ireland
Tadhg Crowley
APC Microbiome Ireland, University College Cork, Cork, Ireland
Ian O’Neill
School of Microbiology, University College Cork, Cork, Ireland
Katherine Lavelle
School of Microbiology, University College Cork, Cork, Ireland
Stephen Hayes
School of Microbiology, University College Cork, Cork, Ireland
Gabriele A. Lugli
Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
Silvia Arboleya
Microbiota, Food and Health Group, Department of Biochemistry and Microbiology of Dairy Products, Institutode Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas, Villaviciosa, Spain
Kieran James
APC Microbiome Ireland, University College Cork, Cork, Ireland
Marco Ventura
Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
Ines Martinez
Sacco Srl, Cadorago (Co), Italy
Miguel Gueimonde
Microbiota, Food and Health Group, Department of Biochemistry and Microbiology of Dairy Products, Institutode Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas, Villaviciosa, Spain
Fabio dal Bello
Sacco Srl, Cadorago (Co), Italy
Ken Nally
APC Microbiome Ireland, University College Cork, Cork, Ireland
Jennifer Mahony
School of Microbiology, University College Cork, Cork, Ireland
Douwe van Sinderen
School of Microbiology, University College Cork, Cork, Ireland
ABSTRACT 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.
