# Microbial Biomarkers for Diagnosing and Predicting Infections in Kidney Transplant Recipients

> **NIH NIH R01** · WEILL MEDICAL COLL OF CORNELL UNIV · 2024 · $796,319

## Abstract

PROJECT SUMMARY
Kidney transplantation improves survival in patients with end-stage kidney disease. Immunosuppression,
however, leads to infectious complications which cause significant morbidity and mortality in this fragile
population. Infections are mostly diagnosed at the time of clinical presentation and clinical factors do not
adequately anticipate infections. Predicting infectious complications is thus an important goal in kidney
transplantation to prevent significant morbidity and mortality.
The long term goal of this study is to develop comprehensive microbial biomarkers in the stool, blood, and the
urine for diagnosing and predicting infections in kidney transplant recipients. Our objectives are: 1) Develop a
fecal SCFA assay that predicts the risk for infections 2) Develop blood and urine cfDNA assays that can
comprehensively diagnose infections as well as predict the risk for infections. These objectives are
inspired by observations from several recent pilot studies: 1) We have found that the fecal abundance of short-
chain fatty acid (SCFA) producing bacteria is associated with decreased future development of bacterial and
viral infections 2) We have demonstrated that cell-free DNA (cfDNA) profiling in the blood and in the urine can
simultaneously detect changes in the microbiome and virome over time and detect infections in transplant
recipients. Importantly, with respect to cfDNA profiling, we have developed a novel technique called SIFT-seq to
overcome the challenge of environmental contamination in low biomass specimens. By biochemically tagging
the biological specimen prior to downstream DNA isolation, we can bioinformatically remove DNA introduced
during sample preparation and accurately identify the microbiome and virome in low biomass specimens.
In this study, we propose to recruit 300 kidney transplant recipients at the time of transplantation for serial fecal,
urine, and blood specimen collections during the first year after transplantation. We will profile the gut microbiome
using metagenomic sequencing to identify taxa at the species level and using metabolomic SCFA profiling. In
addition, we will profile the blood and urine specimens using our novel technique, SIFT-seq, to identify the blood
and urine microbiome and virome with high sensitivity and specificity. In Aim 1, we will determine the fecal
bacterial and SCFA profiles that predict the risk of infections in kidney transplant recipients. In Aim 2, we will
determine the blood and urine cfDNA profiles that are diagnostic and predictive of infections in kidney transplant
recipients. Significance. Establishing microbial biomarkers as predictive of infections will allow for identifying
kidney transplant recipients at high risk for infections and will allow for future clinical trials involving preemptive
changes in immunosuppression, preemptive antibiotic/antiviral therapies, and/or potential gut microbiota-based
therapies to prevent infections in these high risk individ...

## Key facts

- **NIH application ID:** 10938877
- **Project number:** 1R01AI184528-01
- **Recipient organization:** WEILL MEDICAL COLL OF CORNELL UNIV
- **Principal Investigator:** John Richard Lee
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $796,319
- **Award type:** 1
- **Project period:** 2024-05-24 → 2029-03-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10938877

## Citation

> US National Institutes of Health, RePORTER application 10938877, Microbial Biomarkers for Diagnosing and Predicting Infections in Kidney Transplant Recipients (1R01AI184528-01). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10938877. Licensed CC0.

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