Mining the ATCC Genome Portal: Genomic Insights into Unsequenced Taxa and Rare Historical Strains in the American Type Culture

The ATCC Genome Portal (AGP) was launched in 2019 to serve as an authenticated reference genome database for strains within the ATCC. Strains that are commonly used in the research community or serve as important standards were prioritized for sequencing for the AGP. While the ATCC is one of the world’s largest and most diverse biorepository, many strains in the collection are understudied, reflecting a history of scientific deposits from the last 100 years. 

In the last year, there was an initiative to sequence strains from taxa in which there are few to no publicly available genomes and type strains with no assemblies in public genome databases. Additionally, we searched through depositors’ records within the ATCC archives for keywords related to novel antibiotics, antitumor compounds, or other microbial natural products to identify strains for sequencing.

As a result of sequencing these understudied strains, many have been reclassified to their correct taxonomy. For example, Pseudomonas sp. ATCC 31571, initially deposited for its production of a novel antitumor antibiotic, is now reclassified as Burkholderia sp. A mycorrhizal fungus, ATCC 36554, a source of a novel potent antibiotic, is now identified as a Lachnum sp. This effort has also produced genomes of genera that have never been sequenced before, expanding the known genomic catalog available to the scientific community. The AGP will provide researchers with a valuable resource for mining biosynthetic gene clusters and serve as references for rare strains.