The ATCC Genome Portal – An Updated Resource for Authenticated Microbial Reference Genomes

The traceability and authentication of microbial genome assemblies to physical biological materials is typically poorly documented and not a requirement for many public genome databases. The availability and reliability of this data is, however, essential for most microbiological research. The tension between genomic data reliability and its traceability to source materials is a growing area of concern that has significant real-world impacts on public health epidemiology, drug discovery, and environmental biosurveillance research. While databases such as NCBI’s RefSeq database have leveraged the scalability of crowd sourcing for growth, they have done so at the expense of including some unreliable, incomplete, or incorrect genomes, which have persisted in the database for decades. While the introduction of consequential data provenance policies may potentially mitigate these issues, public databases largely do not have these requirements. This creates substantial risk in the trustworthiness of individual genome assemblies, and in aggregate, for several important genomic database resources. The ATCC Genome Portal was created to reestablish the trustworthiness, reliability, and accuracy of genome assemblies associated with ATCC microbial strains. Currently, it includes over 2,000 high-quality ATCC Standard Reference Genomes (ASRGs), all produced in-house by ATCC from authenticated materials sourced directly from ATCC’s biorepository. The collection of annotated ASRGs, updated monthly, currently represents strains for 1,706 bacteria, 119 fungi, and 175 viruses. Each bacterial and fungal genome is sequenced on both Illumina and Oxford Nanopore platforms, resulting in a “hybrid-assembly” incorporating both sequencing technologies. To date, viral genomes have been produced using only Illumina sequencing. Each genome entry is provided with sequencing and assembly quality metrics, annotation metrics, and additional metadata for each strain such as antibiotic susceptibility, geographical origins, and phenotypic data. Here, we describe our laboratory and bioinformatics methods, the diversity of the current contents of the ATCC Genome Portal, it’s current capabilities, and new features for use by the research community. As we continue to carry out whole-genome sequencing of ATCC’s microbial collection, the number of reference genomes in the ATCC Genome Portal will continue to grow every month for the foreseeable future, and we encourage the research community to contact us with suggestions on taxa to prioritize in our pipeline. The ATCC Genome Portal and the data contained therein is available for research-use and is accessible online (https://genomes.atcc.org) or via an authenticated REST-API.