The ATCC Genome Portal: Authenticated Microbial Reference Genomes

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 (https://genomes.atcc.org) or through an authenticated REST-API.