Tuesday, September 30, 2025 9/30/2025

Microbiome Based Biomarkers of Wound Healing

Award Number: R33DK133846
ORGANIZATION: NATIONAL INSTITUTE OF DIABETES & DIGESTIVE & KIDNEY DISEASES
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 09/01/2025
PERIOD OF PERFORMANCE END DATE: 08/31/2026

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Microbiome Based Biomarkers of Wound Healing - Abstract Diabetic foot ulcers (DFU) impact over 2 million Americans annually, result in over 130,000 amputations each year, and are associated with high mortality rates. To date, there has been no single infectious agent of DFU identified as a good marker of healing outcome. This is likely because DFUs are host to a diverse community of microbes (i.e., the wound microbiome). Wound microbiomes analyzed at the community-level are promising predictors of wound healing outcomes. We have shown that wounds persisting beyond 12 weeks exhibit high and persistent proportions of mixed-population, anaerobic bacteria within their microbiomes. Additionally, we found a significant increase of anaerobic transcriptional activity in persistent and amputated wounds, even from species identified as being in low abundance by traditional 16S rRNA based gene sequencing. This suggests microbial transcription, and specifically from anaerobic bacteria, are promising biomarkers of wound healing in diabetic patients. The proposed project will identify microbial biomarkers that can be used as prognostic and monitoring tools for DFU wound healing. We hypothesize using RNA instead of DNA will provide a better snapshot of the wound environment and more sensitive biomarkers: specifically, the proportion and transcriptional activity of anaerobes within the wound microbiome can be used as predictors of wound healing outcomes. Using RNAseq to measure the metatranscriptome of the DFU microbiome, we will leverage advances in machine learning approaches to demonstrate the capacity of the anaerobic component of the wound microbiome to serve as a biomarker for wound healing. We have vigorously evaluated the optimal sample collection techniques and methods of detection, determining a simple swab of the ulcer bed is sufficient to characterize the metatranscriptome and will facilitate clinical implementation. We will develop a multiplexed RT-qPCR assay for the panel of candidate biomarker genes we identify and validate the assay sensitivity, specificity, accuracy and precision. We will work closely with the Diabetic Foot Consortium Steering Committee and Data Coordinating Center to test and validate our biomarkers in a multi-site trial with the DFC. Our goal is to develop a multiplexed biomarker assay integrating the complex interactions occurring within the DFU microbiome and tissue microenvironment. It will use a simple swab of the ulcer bed, rely on objective measurements, and is designed to predict healing trajectories at an early time in the clinical course.


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 = $636,359 )
2025	2025	MCMASTER UNIVERSITY	1280 MAIN ST W	HAMILTON	ON			CAN	Diabetes, Digestive, and Kidney Diseases Extramural Research	001	4	8/14/2025	CHANGE OF GRANTEE / TRAINING INSTITUTION / AWARDING INSTITUTION	$434,176
2025	2024	UNIVERSITY OF WISCONSIN SYSTEM	21 N PARK ST STE 6301	MADISON	WI	53715	DANE	USA	Diabetes, Digestive, and Kidney Diseases Extramural Research	002	3	8/15/2025	EXTENSION WITH OR WITHOUT FUNDS	$0
2025	2024	UNIVERSITY OF WISCONSIN SYSTEM	21 N PARK ST STE 6301	MADISON	WI	53715	DANE	USA	Diabetes, Digestive, and Kidney Diseases Extramural Research	000	3	1/16/2025	EXTENSION WITH OR WITHOUT FUNDS	$202,183
														Subtotal = $636,359

Issue Date FY: 2024 ( Subtotal = $458,278 )
2024	2024	UNIVERSITY OF WISCONSIN SYSTEM	21 N PARK ST STE 6301	MADISON	WI	53715	DANE	USA	Diabetes, Digestive, and Kidney Diseases Extramural Research	000	3	8/20/2024	EXTENSION WITH OR WITHOUT FUNDS	$458,278
														Subtotal = $458,278

Grand Total All Awards = $1,094,637

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Microbiome Based Biomarkers of Wound Healing

Award Number: R33DK133846

ORGANIZATION: NATIONAL INSTITUTE OF DIABETES & DIGESTIVE & KIDNEY DISEASES

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

PERIOD OF PERFORMANCE START DATE: 09/01/2025

PERIOD OF PERFORMANCE END DATE: 08/31/2026

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