# Organizing Fungal Strains into a Library of Natural Products and Their Biosynthetic Gene Clusters

> **NIH NIH R43** · ENKAY OMICS, INC · 2022 · $256,061

## Abstract

The natural world has provided humanity with a plethora of molecules enabling major advances
in modern medicine and agriculture. Fungi are one of most prolific providers of such chemicals,
yet represent perhaps the most understudied source of natural products. With often >50 natural
product biosynthetic gene clusters (BGCs) per strain, and only ~3% of fungal natural products
known, fungi contain a wealth of new molecules ready to exploit in research. In this SBIR proposal,
Enkay Omics, Inc. will refine its scalable platform (FungalMGx) to discover novel fungal natural
products through a fruitful union of bioinformatics, genomics and metabolomics. We are
differentiated from the handful of other startups by virtue of a “grow and go” philosophy, wherein
we do not require upfront molecular or synthetic biology approaches yet can uncover hundreds
of new natural scaffolds and the BGCs that produce them. This competitive advantage will be
extended, protected, and used to partner with other companies to accelerate the exploitation of
new natural products in the private sector.
 At the core of FungalMGx is the “metabologenomics” platform, previously applied to
collections of >1000 strains of Actinomycete bacteria. The MGx platform involves prediction of
BGCs from genome sequence data, clustering into gene cluster families (GCFs), collection of
large-scale metabolomics data, and statistical correlation of gene cluster families to metabolites.
However, FungalMGx is more than just applying the metabologenomics platform to fungi –
through the use of our customized fungi-specific informatics tools, we will improve the precision
of bioinformatic tools for BGC and GCF annotation and improve our compound discovery platform
that will be portable to any strain collection of future clients and partners. This will position EnKay
Omics as a leading service provider to regularize fungi into an organized chemical library for
“smart” integration with bioassays conducted by future partners seeking potent “agriphores” for
antifungals, insecticides, and herbicides.
 In this SBIR, we will de-risk the use of combined metabolomics and genomics in fungi, as
this is distinct from implementation in bacteria and not been accomplished to date. Specifically,
we will establish a library of fungal biosynthetic potential through the analysis of 4,000 publicly-
available sequenced fungal genomes (Aim 1). Further, we use the organized set of ~150,000
gene clusters to correlate and score the metabolites detected in extracts of 140 sequenced fungal
strains. In Aim 2, we develop a client-facing interface called Prospect, enabling lead prioritization
and data visualization for diverse genomic and metabolomics datasets. The goal of FUNGALMGX
is to establish correlative NP discovery in fungi as a viable service and position us as efficient
providers of prioritized metabolites to private sector partners such as Varigen Biosciences, Clue
Genetics, and “Big Ag” (e.g., Corteva Agriscience). Once r...

## Key facts

- **NIH application ID:** 10483096
- **Project number:** 1R43GM146580-01A1
- **Recipient organization:** ENKAY OMICS, INC
- **Principal Investigator:** Matthew Thomas Robey
- **Activity code:** R43 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $256,061
- **Award type:** 1
- **Project period:** 2022-05-15 → 2023-11-14

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10483096

## Citation

> US National Institutes of Health, RePORTER application 10483096, Organizing Fungal Strains into a Library of Natural Products and Their Biosynthetic Gene Clusters (1R43GM146580-01A1). Retrieved via AI Analytics 2026-06-01 from https://api.ai-analytics.org/grant/nih/10483096. Licensed CC0.

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