Natural Products Discovery Center
And Natural Products Genomics Resource Center

“The great biosynthetic potential of nature has been explored in a limited way until now. By advancing the technologies needed to sequence large strain collections, such as the one here, we can begin to realize the full potential of this resource to benefit humanity.”

Ben Shen, Ph.D.

Opening nature’s biodiversity to science

More than one-third of all FDA-approved drugs in use today have arisen from natural products. The 125,000-plus specimens now in the Natural Products Discovery Center at The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology offer an invaluable—and irreplaceable—resource for developing more potentially life-saving drugs.

For generations, scientists around the world have been scooping soil, scraping bits of fungus and sampling the marine environment to assemble libraries of natural products for further study.

Recently, The Wertheim UF Scripps Institute was gifted a collection of thousands of bacterial strains gathered over the past 80 years. Many of the specimens can no longer be accessed in their natural environment, making this collection extremely important to human health.

An estimated 3.75 million new natural products await discovery in the sealed glass ampules and frozen specimens now at the Natural Products Discovery Center.

Ben Shen, PhD, an accomplished chemist who has devoted his career to translating natural products into potential new medicines, serves as the director of the Natural Products Discovery Center and the Natural Products Genomics Resource Center, which is developing new methods for exploring the genomes of the collection. Shen and his team have already made discoveries that are upending scientific belief. Thanks to next-generation genomic sequencing, they and others have found that for each chemical expressed by a microbe, there may be as many as 30 silent, new-to-science natural products hiding within its genome. Says Shen, “The biosynthetic potential of a microorganism to produce natural products is massively underestimated based on the compounds we have isolated to date.”

Characterizing and cataloging all 3.7 million potential natural products within the library, then screening them for therapeutic potential, is “daunting,” he says. “But if we can do it, we can change the world.”

The Natural Products Discovery Center and the Natural Products Genomics Resource Center at The Wertheim UF Scripps Institute establishes a resource for scientists across the country, as it comprises a vast, unexplored collection of potential new medicines. Within these specimens lie, most likely, the next generation of antibiotics, anti-cancer drugs, and even answers to agricultural challenges, such as the citrus greening disease threatening Florida’s orange crops.

Information for scientists

The actinobacterial strain collection at the Natural Products Discovery Center (NPDC) at The Wertheim UF Scripps Institute currently contains a total of 125,127 strains, of which at least 62,328 are actinobacteria, 14,465 other bacteria, and 48,334 unidentified. These strains were isolated over the last eight decades, with the majority acquired between 1940s to the 2010s. The wide time range of collection has allowed for capture of chemical diversity based on evolution and environmental cues, which change over time and are impossible to reproduce in laboratory settings today. The 62,328 actinobacteria in the collection, spanning at least 88 different genera, were isolated from 69 different countries with different climate and ecology factors that further increase natural product structural diversity.  Although these statistics, as well as taxonomic data, are incomplete, the fraction of the strains whose information is available provides a glimpse into the vast spatial, temporal, and taxonomic diversity of the entire collection.

The potential number of natural products awaiting discovery from the actinobacterial strain collection at The Wertheim UF Scripps Institute is immense. Estimated on the assumption of ~30 biosynthetic gene clusters (BGCs) per strain, the ~125K strains in the collection could encode more than 3.75 million BGCs, i.e., the potential of producing more than 3.75 million natural products.  In reference to the ~40,000 natural products that have been isolated from bacteria to date, of which about half (~20,000) are from actinobacteria, the current number of known natural products is only ~1% of this value, leaving millions of compounds to be discovered.  Of course, there will be redundancies with many strains producing the same natural products or structurally similar congeners.  However, these redundancies are unlikely to fundamentally reduce the total number of natural products waiting for discovery.  The estimated 3.75 million BGCs will also serve as an unprecedented treasure trove for enzyme and biocatalyst discovery and synthetic biology applications. 

Nature’s pharmacist

A natural products library (NPL) has been constructed at NPDC, consisting of 46,031 crude extracts, 28,739 partially purified fractions, and 650 pure NPs. Of these, the 46,031 crude extracts were made from 14,635 actinobacterial strains that were selected to represent the overall diversity of the strain collection at UF Scripps and were cultured, on average, in three or four different media to maximize natural product production. The 28,739 partially purified fractions were made from crude extracts of large-scale fermentation of 2,366 strains with the richest natural product profiles, which were fractionated by medium-pressure C18 chromatography.  The 650 pure natural products were isolated from 143 selected strains under optimized fermentation conditions.  Based on the estimated ~30 BGCs per strain, the 14,635 actinobacteria could encode biosynthesis of ~440,000 natural products.  

Natural products have been exquisitely tailored via evolution to elicit potent and unique biological activities, rendering them unrivaled in structural complexity and diversity. Accordingly, natural products have served as drug leads for the pharmaceutical industry.  Of the FDA-approved small molecule therapeutics, 67% of anti-infective and 83% of anti-cancer drugs are natural products, natural product derivatives, or inspired by natural products. Therefore, even with realization of only 20% of this potential under the cultured conditions, the NPL could still represent the chemodiversity of ~88,000 natural products, which, in reference to the ~20,000 natural products of actinobacterial origin known to date, provide an unprecedented source of rich and unique natural product chemotypes to target emerging biology.

Natural Products Genomics Resource Center

Over the past two decades, ~23,000 non-pathogenic actinobacterial genomes have been sequenced and made publicly available. We have initiated a large-scale genome sequencing campaign to sequence all actinobacterial strains at NPDC over the next five years, ultimately quintupling the number of actinobacterial genomes currently available.  In collaboration with the Joint Genome Institute (JGI), Department of Energy, we have established the Natural Products Genomics Resource Center (NPGRC) at the Natural Products Discovery Center, and the genomic sequences generated will be used to create the NPGRC database, which, together with the strains, will be made available to the broader scientific community, including academia, not-for-profit, and private sector organizations, through fee-based approaches. 

We will provide bioinformatics and computational tools for the discovery and analysis of BGCs, and enable natural product discovery, characterization, and development for a range of associated applications.

Development of Innovative Technologies

Critical to realizing the full potential of the actinobacterial strain collection at The Wertheim UF Scripps Institute are innovative technologies that enable rapid access to, and identification of, the global diversity of encoded natural products.  We are developing innovative technologies in the next five years (2022-2026), to enable: (i) high-throughput strain culturing, gDNA preparation, and genome sequencing of the entire NPDC strain collection, (ii) benchmarking the taxonomy of NPDC strains against NCBI public database by using GTDB-TK whole-genome taxonomy analysis, (iii) establishing the NPGRC at NPDC for BGC identification, annotation, and comparison, (vi) benchmarking the biosynthetic potential of NPDC strains by measuring the number of distinct BGC groups (GCFs) using BiG-SLiCE, (v) constructing the 2^nd generation NPL by maximizing BGC diversity of fermented NPDC strains, (vi) producing natural products from targeted BGCs by “plug-and-play” synthetic biology, and (vii) correlating natural products to targets, pathways, biology, diseases, and medicine. 

Collaborative R&D and Licensing Opportunities

Our goal is to develop a shared state-of-the-art strain collection and resource center to revitalize natural products discovery.  We look forward to serving the broad scientific community by making the strains, NPL, NPGRC, and associated enabling technologies at NPDC open-access to promote research and development on natural products and associated applications  and to enable partner organizations to commercialize new products without the need of building and maintaining in-house natural product resources.  We envisage broad research initiatives, ranging from fundamental microbiology and evolutionary biology, AI, machine learning, and big data mining, chemistry, enzymology, and structural biology to translational applications such as agricultural products, crop protection, citrus greening diseases, biotherapeutics, animal health products, enzyme discovery and biocatalysis, biofuels, bioproducts, and biomaterials.

References

1.      Kalkreuter, E.; Pan, G.; Cepeda, A. J.; Shen, B. Targeting bacterial genomes for natural product discovery: opportunities, challenges, and strategies. Trends Pharmacol. Sci. 2020, 41, 13-26.

2.      Steele, A. D.; Teijaro, C. N.; Yang, D.; Shen, B. Leveraging a large microbial strain collection for natural product discovery. J. Biol. Chem. 2019, 194, 16567-16576.

3.      Yan, X.; Chen, J.-J.; Adhikari, A.; Yang, D.; Crnovcic, I.; Wang, N.; Chang, C.-Y.; Rader, C.; Shen, B. Genome mining of Micromonospora yangpuensis DSM 45577 as a producer of an anthraquinone-fused enediyne. Org. Lett. 2017, 19, 6192-6195.

4.      Pan, G.; Xu, Z.; Guo, Z.; Hindra; Ma, M.; Yang, D.; Zhou, H.; Gansemans, Y.; Zhu, X.; Huang, Y.; Zhao, L.-X.; Jiang, Y.; Cheng, J.; Van Nieuwerburgh, F.; Suh, J.-W.; Duan, Y.; Shen, B. Discovery of the leinamycin family of natural products by mining actinobacterial genomes. Proc. Natl. Acad. Sci. USA 2017, 114, E11131-E11140. 

5.      Yan, X.; Ge, H.; Huang, T.; Hindra; Yang, D.; Teng, Q.; Crnovčić, I.; Li, X.; Rudolf, J. D.; Lohman, J. R.; Gansemans, Y.; Zhu, X.; Huang, Y.; Zhao, L.-X.; Jiang, Y.; Van Nieuwerburgh, F.; Rader, C.; Duan, Y.; Shen, B. Strain prioritization and genome mining for enediyne natural products. mBio 2016, 7, e2104-16.

6.      Hindra; Huang, T.; Yang, D.; Rudolf, J.D.; Xie, P.; Xie, G.; Teng, Q.; Lohman, J.R.; Zhu, X.; Huang, Y.; Zhao, L.-X.; Jiang, Y.; Duan, Y.; Shen, B. Strain prioritization for natural product discovery by a high-throughput real-time PCR method. J. Nat. Prod. 2014, 77, 2296-2303.

7.      Xie, P.; Ma, M.; Rateb, M.E.; Shaaban, K.A.; Yu, Z.; Huang, S.-X.; Zhao, L.-X.; Zhu, X.; Yan, Y.; Peterson, R.M.; Lohman, J.R.; Yang, D.; Yin, M.; Rudolf, J.D.; Jiang, Y.; Duan, Y.; Shen, B. Biosynthetic potential-based strain prioritization for natural product discovery – a showcase for diterpenoid producing actinomycetes. J. Nat. Prod. 2014, 77, 377-387.