# Functional Genomics Core

> **NIH NIH P01** · UNIVERSITY OF TEXAS HLTH SCI CTR HOUSTON · 2020 · $739,509

## Abstract

ABSTRACT (Functional Genomics Core)
Antimicrobial resistance (AMR) and its impact have been recognized by the WHO, CDC, FDA, and NIH as one
of the most important public health threats facing society today. Vancomycin-resistant enterococci (VRE),
extended spectrum β-lactamase/carbapenemase-producing Enterobacteriaceae (ESBL-E/CRE), and
Clostridiodes difficile are of particular interest as they disproportionately affect immunocompromised and
severely ill patients. The CDC has designated VRE as a serious threat and both ESBL-E/CRE and C. difficile
as urgent threats. Each of these pathogens is able to colonize and infect the gut, with disruption of the
protective gut microbiome by antibiotics a leading risk factor for infection. The overarching hypothesis of the
DYNamics of colonizAtion and infection by Multidrug-resIstant paThogens in immunocompromisEd patients
program (DYNAMITE) is that patient susceptibility to nosocomial acquisition, gut colonization, and subsequent
infection by pathogens is critically dependent on functional microbiota-pathogen interactions that determine
disease progression and clinical outcomes. Importantly, we posit that shotgun metagenomics data coupled
with inferred metabolic potential is not enough to predict and interpret susceptibility to colonization and
infection in a dysbiotic patient, and a combination of genomics, metagenomics, metabolomics, and
metaproteomics is necessary to elucidate the complex interplay between the pathogen, the microbiome, and
the host. To enable this multi-omic approach, the Functional Genomics Core (FGC) will provide a central
resource to all three projects contained within this application, providing facilities and expertise for whole
genome sequencing, metagenomics, metaproteomics, and metabolomics. Additionally, leveraging the robust
bioinformatics infrastructure housed within the FGC, we will provide the application of existing analytical
pipelines and disease classifiers–as well as the development of novel pipelines—that will integrate and
facilitate the comprehensive analyses of the data generated for each individual project. As an example, we
have built a high-throughput pipeline for the generation and annotation of reference-quality fully circularized
bacterial chromosomes and accompanying plasmids, and with accompanying metaproteomics data have
mapped 92% of protein signatures back to the source gene. Overall, to achieve the scientific goals outlined in
this P01 application, the FGC will undertake three aims: i) coordinate the transfer of pure microbiological
isolates and patient stool samples from the study sites to the FGC; ii) complete genomic, metagenomic,
metaproteomic, and metabolomic processes of each project; and iii) assist in the analysis and integration of
the multi-omic data generated under each project. The FGC provides a unique and unparalleled ability to
combine multiple omics data types to create a truly multi-omic assessment of the complex interplay between
VRE, ESBL...

## Key facts

- **NIH application ID:** 10024958
- **Project number:** 1P01AI152999-01
- **Recipient organization:** UNIVERSITY OF TEXAS HLTH SCI CTR HOUSTON
- **Principal Investigator:** Anthony Haag
- **Activity code:** P01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $739,509
- **Award type:** 1
- **Project period:** 2020-08-01 → 2025-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10024958

## Citation

> US National Institutes of Health, RePORTER application 10024958, Functional Genomics Core (1P01AI152999-01). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10024958. Licensed CC0.

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