The ATCC Genome Portal: The Genomics Database of a 100-year-old Culture Collection
IAFP 2025 Annual Meeting
Cleveland, Ohio, United States
July 29, 2025Abstract
Introduction: The ATCC Genome Portal (AGP, https://genomes.atcc.org/) is a reference database of authenticated and traceable whole genome sequence assemblies generated directly from strain vials from one of the largest and most diverse culture collections in the world.
Purpose: The AGP initiative provides a resource to the scientific community as many genomes that are in public genomic databases may represent sequences from strains that have been passed between laboratories, are mislabeled, or have accumulated genetic drift arising from laboratory domestication.
Methods: AGP sequences are hybrid high quality de novo assemblies with data generated from Illumina and Oxford Nanopore platforms. These genomes are assembled under standardized conditions to ensure reproducibility for the research community. Genomic sequences are reviewed for post assembly quality control metrics and checked for contamination before being published to the AGP. These genomes are paired with curated metadata from depositors’ accessioning records, historical internal records, and undergo taxogenomic checks.
Results: Thousands of foodborne pathogens and food related microbes have been deposited into the collection, with isolates representing over a century of research. Currently, there are over 5750 reference quality genomes of prokaryotes, fungi, viruses, and protists available with new additional assemblies each quarter.
Significance: A majority of assemblies in AGP are of higher quality than equivalent assemblies in public genomic databases. Additionally, some of these assemblies represent strains and/or species that have no representation in public genomic databases. The AGP is a unique and authenticated resource for reference genomes.
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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.
Reference-quality sequences
Through the ATCC Genome Portal, you can easily search, access, and analyze thousands of reference-quality genome sequences. Our optimized methodology is designed to achieve complete, circularized (when biologically appropriate), and contiguous genomic elements by using short-read (virology collection) and hybrid (bacteriology, mycology, and protistology collections) assembly techniques. We then take our workflow one step further by accompanying each stage of the process with rigorous quality control analyses that ensure the highest quality data. Only the data that passes all quality control criteria are published to the ATCC Genome Portal. Visit the portal today to find the high-quality data you need for your research.
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