Tuesday, July 1, 2025 7/1/2025

Receptor-Guided Discovery of Environmental Phages

Award Number: F31AI178993
ORGANIZATION: NATIONAL INSTITUTE OF ALLERGY & INFECTIOUS DISEASES
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: FELLOWSHIP/SCHOLARSHIP/STUDENT LOANS
PERIOD OF PERFORMANCE START DATE: 04/01/2024
PERIOD OF PERFORMANCE END DATE: 03/31/2027

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Receptor-Guided Discovery of Environmental Phages - Project Summary Bacteriophages, phages for short, are extremely abundant and diverse in the environment but also very under sampled and understudied. A major factor limiting the characterization of more phages is the lack of fast and efficient methods to do so. Alghough, techniques have been developed to find the receptor of a given phage on its host cell, no techniques to find phages dependent on a given receptor have been developed. However, this second method may be even more important. Such a technique would allow a user to select a bacterial membrane protein or structure of interest and preferentially select environmental phages that require it for infection. This could be useful for understanding the fluctuations of bacterial membrane structures across different ecological systems or for informing which environmental phages will make the best therapies. This proposal will develop a novel and generalizable assay for receptor-guided discovery of environmental phages using co-culture. The current standard technique includes a classic plaque assay where a single host strain of bacteria is grown in a lawn with an environmental sample of phages. Each phage infecting the host bacteria causes a clearing in the lawn called a plaque, and unique phages are not identifiable based on the appearance of the resulting plaques. The novel assay proposed here adds a new visual signal by co-culturing multiple strains of bacteria in the lawn. Each strain is a single gene knockout and tagged with a unique fluorescent maker. Phages with infection cycles independent of any of the proteins knocked out will lyse every strain on the plate and leave no fluorescent signal in the plaque. Phages of interest will lyse only a subset of the bacterial strains in the lawn, and the fluorescent signal corresponding to the required protein knockout will show through the plaque. In this way the novel assay differentiates plaques by the dependencies of the original infecting phage and allows for targeted isolation of phages of interest in just one experimental step. This project will be completed in a highly interdisciplinary environment where the experimental protocols, computational analysis, and hardware can all be developed with equal rigor. This assay will be developed first in Escherichia coli as a model system and then generalized into Pseudomonas aeruginosa to move towards clinical applications. Knockout proteins will be chosen first to test the limits of the assay and later to search for interactions between phages and bacterial virulence and antibiotic resistance factors. Taken together, this work will develop a novel assay for targeted phage isolation that can be applied to ecological studies, single phage therapies, and construction of phage cocktails.


Issue Date FY	Funding FY	Legal Entity Name	Legal Entity Address	Legal Entity City	Legal Entity State	Legal Entity Zip Code	Legal Entity COUNTY	Legal Entity COUNTRY	Assistance Listing	Award Code	Budget Year	Action Date	Action Type	Action Amount

Issue Date FY: 2025 ( Subtotal = $35,118 )
2025	2025	PRESIDENT AND FELLOWS OF HARVARD COLLEGE	1033 MASSACHUSETTS AVE STE 3	CAMBRIDGE	MA	02138	MIDDLESEX	USA	Allergy and Infectious Diseases Research	000	2	3/7/2025	NON-COMPETING CONTINUATION	$35,118
														Subtotal = $35,118

Issue Date FY: 2024 ( Subtotal = $35,118 )
2024	2024	PRESIDENT AND FELLOWS OF HARVARD COLLEGE	1033 MASSACHUSETTS AVE STE 3	CAMBRIDGE	MA	02138	MIDDLESEX	USA	Allergy and Infectious Diseases Research	000	1	3/25/2024	NEW	$33,838
2024	2024	PRESIDENT AND FELLOWS OF HARVARD COLLEGE	1033 MASSACHUSETTS AVE STE 3	CAMBRIDGE	MA	02138	MIDDLESEX	USA	Allergy and Infectious Diseases Research	002	1	5/15/2024	NEW	$1,280
2024	2024	PRESIDENT AND FELLOWS OF HARVARD COLLEGE	1033 MASSACHUSETTS AVE STE 3	CAMBRIDGE	MA	02138	MIDDLESEX	USA	Allergy and Infectious Diseases Research	001	1	3/25/2024	NEW	$0
														Subtotal = $35,118

Grand Total All Awards = $70,236

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Receptor-Guided Discovery of Environmental Phages

Award Number: F31AI178993

ORGANIZATION: NATIONAL INSTITUTE OF ALLERGY & INFECTIOUS DISEASES

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

AWARD ACTIVITY TYPE: FELLOWSHIP/SCHOLARSHIP/STUDENT LOANS

PERIOD OF PERFORMANCE START DATE: 04/01/2024

PERIOD OF PERFORMANCE END DATE: 03/31/2027

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