Why is ATCC producing whole-genome sequencing data when similar data already exist? For two particularly important reasons. The first is to confirm the identity of the organism in the vial with the most current technologies and processes available. ATCC is almost 100 years old and methods used to authenticate organism(s) decades earlier have been vastly improved upon. As such, ATCC now completes whole-genome sequencing on all newly accessioned bacteria, fungi, and viruses. Secondly, it is our mission to ensure that accurate and reproducible data for our strains is available to the scientific community. Other databases may contain genomes identified as “ATCC;” however, the AGP is the only authenticated reference genome database for ATCC microbes.
Given that the ATCC microbial collection exceeds 75,000 organisms that were collected over the last 100 years, sometimes we are even surprised by what is revealed with our own whole-genome sequencing data. For instance, we recently sequenced ATCC 2601 thinking we would assemble and annotate the genome for Saccharomyces cerevisiae. After sequencing, we discovered that ATCC 2601 was not just Saccharomyces cerevisiae—as believed at the time of deposit—but is instead a naturally occurring hybrid genome of Saccharomyces cerevisiae AND Saccharomyces kudriavzevii.
Similarly, ATCC 49014 was originally deposited as Enterobacter agglomerans. When we sequenced and assembled the genome, we reclassified it as Enterobacteriaceae sp. as it had no matches to any known genus in the Enterobacteriaceae family nor did it produce digital DNA-DNA hybridization (dDDH) values significant to any described species. We will have more updates to ATCC 49014 in the coming months.
Additionally, the AGP has over 100 novel genomes that are not published anywhere else in the world; examples of these include Anaerosinus glycerini (ATCC 51177), Epidermophyton floccosum (ATCC 9646), and Colwellia arctica (ATCC BAA-2609). The number of never-before-published genus-level or species-level genomes will continue to grow as we publish our quarterly releases. To learn more about the AGP, please visit our Discover The ATCC Genome Portal page or visit us at booth #912 at ASM Microbe from June 13-17, 2024.
Did you know?
With a Supporting Membership to the ATCC Genome Portal, you will have full access to our available reference genomes on the portal and will benefit from our secure REST-API, Discrepancy Reports, and our other extended capabilities.
Meet the authors
Briana Benton, BS
Technical Manager, ATCC
Briana Benton is a Program Manager for ATCC’s Sequencing and Bioinformatics department. Her current focus is on the ATCC Genome Portal and expanding the collection of published reference genomes. Briana previously worked on the development of mock microbial communities for microbiome research and synthetic molecular standards for molecular diagnostics assays. Prior to joining ATCC, she developed molecular diagnostic assays for the Henry M. Jackson Foundation.
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.
Joseph Petrone, PhD
Bioinformatician, Sequencing & Bioinformatics Center, ATCC
Joseph Petrone received his PhD from the University of Florida’s Department of Microbiology and Cell Sciences with a focus in bacterial genomics and metagenomic microbiome analysis. Joseph’s interest in curating authentic genomic databases and developing new bioinformatic software led him to join ATCC in 2023, where he now works as a bioinformatician for the Sequencing and Bioinformatics Center. His current focus is the continual development and curation of the ATCC Genome Portal. In his free time, you will find Joe either caring for his exotic plant collection or modifying and racing cars at the local dragstrip.
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