# A new paradigm for the creation and mining of microbial libraries for drug discovery

> **NIH NIH R01** · UNIVERSITY OF ILLINOIS AT CHICAGO · 2020 · $504,305

## Abstract

A high degree of taxonomic and chemical redundancy is a major limitation in sourcing microbial strain libraries
for drug discovery. Currently, the creation of these libraries relies on outdated and costly methods, namely visual
inspection of morphological differences of colonies from agar plates, or ribosomal RNA gene sequencing
methods that are not indicative of a microbe’s capacity to produce specialized metabolites (SM). Despite the
incredible potential of microorganisms to produce SMs, this redundancy remains a primary barrier to drug
discovery efforts. In order to overcome this, we will develop a rapid, easy to use mass spectrometry (MS)
technique that will maximize both the taxonomic and chemical diversity entering into microbial strain libraries.
This will be coupled to our semi-automated, web-based bioinformatics pipeline that will be made available to the
public. Our platform will employ matrix-assisted laser desorption/ionization time of flight MS (MALDI-TOF MS) to
address a few major obstacles in the drug discovery process. First, we will develop a high-throughput MALDI-
TOF MS method capable of gathering two distinct datasets from single colonies of bacteria from agar-based
diversity plates: a) ribosomal protein fingerprints that are used to putatively identify the genus and species of the
colony, and b) SM fingerprints of each colony to elucidate intra-species differences in SM production (Aim 1).
Importantly, our MALDI-TOF MS platform is capable of processing and analyzing 384 strains in a 4-hour
period, which is a significant advance when compared to other mass spectrometry or genomics-based
profiling approaches. When applied to thousands of bacterial colonies of a cultivatable environmental
microbiome, this platform will serve to maximize the taxonomic and chemical diversity entering a library, while
minimizing the number of strains required to achieve this (e.g. addition of 300 strains as opposed to 3,000).
Second, we will develop a facile fluorescence/MS-detection platform to interrogate the unmined biologically
active chemical space of existing bacterial strain libraries (Aim 2). Using an existing Actinobacteria library as
proof of concept, we will grow each strain under eight different cultivation conditions in 48-well agar plates. We
will then develop and implement a series of antibiotic assays with fluorescent reporter strains of ESKAPE
pathogens, and use MALDI-TOF MS to detect biologically active SMs that exist within zones of inhibition from
each producing actinomycete. This method allows researchers to simultaneously observe growth inhibition via
fluorescence imaging and to identify strains that produce bioactive SMs under single/unique cultivation
conditions. This foregoes laborious liquid cultivation and chromatography steps of inactive bacteria (current
practice). Data analysis will be facilitated through development of a web-based, semi-automated visualization
pipeline that will be freely available to the scientific c...

## Key facts

- **NIH application ID:** 9980959
- **Project number:** 5R01GM125943-03
- **Recipient organization:** UNIVERSITY OF ILLINOIS AT CHICAGO
- **Principal Investigator:** Isabel Cruz
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $504,305
- **Award type:** 5
- **Project period:** 2018-08-10 → 2022-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9980959

## Citation

> US National Institutes of Health, RePORTER application 9980959, A new paradigm for the creation and mining of microbial libraries for drug discovery (5R01GM125943-03). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/9980959. Licensed CC0.

---

*[NIH grants dataset](/datasets/nih-grants) · CC0 1.0*