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The ATCC Genome Portal: Authenticated Microbial Reference Genomes

Purple, fragmented DNA double helix strand on a black background.

ASM Microbe 2024

Atlanta, Georgia, United States

June 16, 2024


The ATCC Genome Portal, launched in 2019, is an initiative to produce high-quality reference genomes for ATCC’s entire microbial collection. Monthly releases of genome assemblies for newly sequenced strains are disseminated to the research community through the ATCC Genome Portal or a recently implemented REST-API. This API streamlines mass data access, fostering large-scale comparative genomics studies. Currently, the portal includes fully authenticated and annotated genome assemblies for over 4,079 microbes, encompassing 3,476 bacterial, 317 viral, 282 fungal, and 4 protist genomes. All data is publicly accessible, meticulously curated, and linked to physical materials in ATCC's collection. As the sole ISO 9000-compliant reference database for ATCC microbial strains, the portal ensures full end-to-end data provenance and authentication. Notably, public databases like GenBank and RefSeq lack the authentication and traceability that is provided by resources such as the ATCC Genome Portal. This gap in data provenance potentially complicates downstream bioinformatics applications and research objectives (Yarmosh DA et al., 2022). Additionally, bacterial, fungal, and protist genomes underwent sequencing using both short-read (Illumina) and long-read (Oxford Nanopore) technologies, while viral genomes were exclusively sequenced with Illumina. This presentation outlines the ATCC Genome Portal's expansion, highlights novel strains not previously sequenced by any research group, and updates efforts to integrate historical metadata from ATCC's document repository. Accessible for research purposes, the ATCC Genome Portal and its data can be explored online ( or through an authenticated REST-API.

Download the poster to learn about our latest update to the ATCC Genome Portal.



Joseph Petrone.jpg

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.

DNA rods with bacteria.

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.

Visit the portal