Environment

Natural Commercial Products with Bacterial Origin

Uncovering secondary metabolites with potential agricultural & pharmaceutical applications

With warm and long sunny days, the call of summer beckons gardeners to come outside and tend to their plants. To keep pests at bay, you may be keeping organic pesticides in your arsenal. Chances are that your insecticide might contain spinosyns.

Why it’s important

Spinosyns are macrolides derived from aerobic fermentation of Saccharopolyspora spinosa. S. spinosa strain A83543.1 (ATCC^® 49460™) was first collected from soil samples around an abandoned sugar mill rum still in the Virgin Islands by a scientist on vacation.^1,2 It was quickly recognized as a new species in the Saccharopolyspora genus—an understudied bacteria genus known for other commercial secondary metabolites such as the antibiotic erythromycin.^3,4

Research into S. spinosa strain A83543.1 resulted in the discovery of spinosyn, a metabolite with a favorable effect on insect pests and extremely low toxicity on mammals.⁵ A mixture of two forms of spinosyns, known as spinosad, has been investigated as a potent insecticide against mosquito larvae,⁶ parasitic mites,⁷ and agricultural pests.⁸ The low toxicity of spinosad in mammals has led to the development of a United States Food & Drug Administration (FDA)-approved spinosad topical suspension to control head lice in children.⁹

As a natural product, spinosyn has achieved critical commercial success and is a notable example of a novel unique product generated by the diversity of nature.¹⁰ Since its discovery, spinosyn and its derivatives have won 3 Presidential Green Chemistry Challenge Awards (1999, 2008, and 2010) from the United States Environmental Protection Agency (EPA).

How we can help

The ATCC collection holds numerous Saccharopolyspora species along with other genera such as Streptomyces¹¹ that are known to produce useful secondary metabolites. Many of these strains are undergoing whole-genome sequencing for the ATCC Genome Portal. The genomes of the spinosyn-producing S. spinosa (ATCC^® 49460™), erythromycin-producing S. erythraea (ATCC^® 11635™) and avermectin-producing Streptomyces avermitilis (ATCC^® 31267™) are already available on the ATCC Genome Portal and can provide insights into novel pharmaceutical or agricultural research for useful secondary metabolites.

In bacteria, the genes that encode for secondary metabolites are arranged together in operons known as biosynthetic gene clusters (BGCs). By analyzing genomes for BGCs, researchers can identify strains of interest without utilizing conventional wet lab approaches. These various BGCs have conserved protein domains that can be characterized directly from genomes via bioinformatic tools such as antiSMASH.¹² Utilizing high-quality reference genomes provided by the genome portal, scientists can determine which sequenced ATCC strains have the potential to produce promising compounds without the need for traditional screening methods, which saves both time and money. As more items in ATCC’s collection are sequenced and their genomes become available on the ATCC Genome Portal, bioinformatic insights on these organisms can perhaps provide knowledge on the next great green commercial product or novel therapeutic.

Did you know?

There are over 3,400 reference-quality genomes on the ATCC Genome Portal, and it is continuing to grow each month.

Meet the authors

Scott V. Nguyen, PhD

Senior Biocuration Scientist, ATCC

Dr. Nguyen is a Senior Biocuration Scientist in the Sequencing and Bioinformatics Center at the ATCC. He previously worked as a molecular microbiologist in the USDA-ARS at the U.S. Meat Animal Research Center in Nebraska. He then worked as a bioinformatician at the Centre for Food Safety in University College Dublin, Creme Global in Dublin, Ireland, and at the Washington DC Public Health Laboratory. He has focused on the comparative genomics and taxonomy of human pathogens in his career. Dr. Nguyen has described several novel microbial species and identified multiple new SARS-CoV-2 variants including the Delta-Omicron recombinant XD variant popularly known as 'Deltacron'. In his free time, Dr. Nguyen is an avid hiker and storm chaser. Dr. Nguyen holds a doctorate in microbiology and immunology from the University of Oklahoma Health Sciences Center.

Noah Wax, MS

Biologist, ATCC

Noah Wax is a Biologist in the Sequencing and Bioinformatics Center at ATCC. His work focuses on the extraction of nucleic acids from the various organisms and cell lines found within ATCC’s collection. Noah plays a vital role in supporting two significant initiatives: the ATCC Genome portal and ATCC Cell Line Land. The latter is an ongoing partnership between ATCC and QIAGEN aimed at providing authenticated reference RNA-seq data for all ATCC cell lines. Prior to joining ATCC, Noah received his master’s degree in biology from Virginia Tech where his work focused on utilizing comparative genomic approaches to study amphibian skin microbes.

Check out our featured resources

Concentric circles with purple, orange and yellow markers for DNA sequencing.

Discover the ATCC Genome Portal

The ATCC Genome Portal is a rapidly growing ISO 9001–compliant database of high-quality reference genomes from authenticated microbial strains in the ATCC collection. Through this cloud-based platform, you can easily access and download meticulously curated whole-genome sequences from your browser or our secure API. With high-quality, annotated data at your fingertips, you can confidently perform bioinformatics analyses and make insightful correlations.

Brown and white, rod-shaped Escherichia coli bacteria cluster.

Bacteriology and Archaea

ATCC offers a variety of bacterial and archaeal strains with applications in a variety of research and industrial applications. Our growing portfolio includes antimicrobial-resistant strains, quality control organisms for commercial identification systems, a wide selection of extremophile strains, and genomic and synthetic DNA.

Brown, rod-shaped Pseudomonas aeruginosa bacteria.

Biocontrol

ATCC offers a broad spectrum of fungi and bacteria that can be used in the biological control of microbes and pests that destroy agricultural plants.

Mertz FP, Yao RC. Saccharopolyspora spinosa sp. nov. isolated from soil collected in a sugar mill rum still. International Journal of Systematic and Evolutionary Microbiology 40: 34-39, 1990.
Thompson GD, Dutton R, Sparks TC. Spinosad – a case study: an example from a natural products discovery programme. Pest Management Science 56: 696-702, 2000.
Sayed AM, et al. Saccharopolyspora: an underexplored source for bioactive natural products. Journal of Applied Microbiology 128; 314–329, 2020.
Oliynyk M, et al. Complete genome sequence of the erythromycin-producing bacterium Saccharopolyspora erythraea NRRL23338. Nature Biotechnology 25: 447-453, 2007.
Santos VSV, Pereira BB. Properties, toxicity and current applications of the biolarvicide Spinosad. Journal of Toxicology and Environmental Health, Part B, 23(1): 13-26, 2020.
Hertlein MB, et al. A review of spinosad as a natural product for larval mosquito control. J Am Mosq Control Assoc 26(1): 67-87, 2010.
Fernando DD, Fischer K. Spinosad topical suspension (0.9%): a new topical treatment for scabies. Expert Rev Anti Infect Ther 20(9): 1149-1154, 2022.
Sarfraz M, Dosdall LM, Keddie BA. Spinosad: A Promising Tool for Integrated Pest Management. Outlooks on Pest Management 16(2): 78-84(7), 2005.
Devore CD, Schutze GE. Head Lice. Pediatrics 135 (5): e1355–e1365, 2015.
Kirst H. The spinosyn family of insecticides: realizing the potential of natural products research. Journal of Antibiotics 63: 101–111, 2010.
Õmura S, et al. Genome sequence of an industrial microorganism Streptomyces avermitilis: Deducing the ability of producing secondary metabolites. PNAS 98(21): 12215-12220, 2001.
Blin K, et al. Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters. Briefings in Bioinformatics 20(4): 1103-1113, 2019.