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.
Download the poster to learn how the ATCC Genome Portal can support food safety.
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Scott V. Nguyen, PhD
Senior Biocuration Scientist, Sequencing & Bioinformatics Center, ATCC
As a Senior Biocuration Scientist in ATCC’s Sequencing & Bioinformatics Center, Dr. Nguyen helps lead the ATCC Genome Portal—a cloud resource of authenticated, traceable microbial genomes. Dr. Nguyen’s work spans microbial genomics, comparative genomics, and data provenance, with recent projects covering Yarrowia lipolytica strain sequencing, pangenomics, and structural variation. He has authored conference posters, application notes, and manuscripts advancing standardized hybrid assembly and ISO‑compliant workflows for reference genomes. Earlier in his career, Dr. Nguyen’s identified multiple SARS‑CoV‑2 variants, including the Delta–Omicron recombinant XD (“Deltacron”), and held research roles at USDA‑ARS, University College Dublin, and the DC Public Health Laboratory. He earned his PhD in Microbiology & Immunology from the University of Oklahoma Health Sciences Center. Dr. Nguyen’s current focus is enabling reliable, engineering‑grade genomic data for bioprocessing and industrial biotechnology.
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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