In this episode, David Yarmosh and Briana Benton discuss the future of the ATCC Genome Portal, focusing on upcoming data types and platform enhancements. Benton reveals that by the end of 2025, researchers will gain access to methylation data for the bacteriology collection with future plans to annotate virology genomes, integrate antimicrobial susceptibility data, and enable advanced search features such as taxonomy browsing and gene-based queries. As the portal evolves into a dynamic “digital twin” platform, it will offer more than genome sequences, incorporating valuable metadata like microscopy images and QC results. Benton underscores the pivotal role of customer feedback in driving these innovations and highlights ATCC’s Supporting Membership, which expands data accessibility to researchers beyond those purchasing physical products. With a vision to establish the portal as a trusted, comprehensive reference for authenticated microbial data, ATCC continues to advance reproducibility and innovation in biological research.
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Episode 29: From IRAD to Impact
In this episode, David Yarmosh and Briana Benton revisit the origins and evolution of the ATCC Genome Portal, tracing its journey from an ambitious research concept in 2017 to a groundbreaking resource for high-quality, traceable genomic data. Benton shares how early internal research proposals—including her push for long-read sequencing and Dr. Marco Riojas’ vision for sequencing ATCC’s collection—laid the foundation for the portal. Their work, along with challenges in microbiome research where public genome assemblies failed to match known inputs, underscored the need for a reliable genomic resource. Launched in 2019 with just 250 genomes and basic sequencing tools, the portal has since expanded to over 5,500 genomes, backed by automation, a larger team, and advanced sequencing capabilities. The portal is continually evolving and now includes data from bacteriology, virology, mycology, and protistology collections, all accessible via a secure REST-API. Looking ahead, ATCC plans to enhance the portal with methylation data, expanded annotations, and additional QC-related metadata, striving to create a comprehensive “digital twin” of each organism to reinforce scientific reproducibility and informed decision-making.
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Episode 28: Ground Truth Genomics
In this episode, Briana Benton presents the ATCC Genome Portal, which was launched in 2019 to offer researchers high-quality, traceable genome data directly associated with physical materials in the ATCC collection. Benton explained that each genome published on the portal is produced entirely in-house, adhering to ISO 9001 standards from strain cultivation to final genome assembly. With over 5,500 genomes currently available and new additions made quarterly, the portal aims to eventually encompass ATCC’s entire collection. The portal’s distinctive value lies in its unparalleled traceability, including documentation of storage conditions and equipment used, which ensures scientific reproducibility and reliability. While the portal does not provide analytical tools, Benton emphasized that ATCC’s mission is to supply authenticated, reproducible data, enabling researchers to utilize their preferred tools for analysis.
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Episode 27: MicroQuant™- Modernizing Quality Control Testing
In this episode, Dr. Nilay Chakraborty discusses the newly launched MicroQuant portfolio by ATCC, which consists of quantitated microbial reference materials designed to simplify quality control testing. These materials are essential for ensuring the safety and efficacy of products across various industries, including food, cosmetics, and pharmaceuticals. The portfolio includes 12 products that meet stringent regulatory requirements, focusing on ease of use and delivering consistent results in terms of colony-forming units (CFU). They highlight the importance of regulatory guidelines and how the portfolio addresses both known pathogens and adventitious agents. The conversation emphasizes the engineering innovation behind MicroQuant, which reduces preparation time from two weeks to less than a minute, offering significant cost savings and logistical benefits. The portfolio is designed to reduce genetic drift risks and ensure consistency in QC testing, with potential for future expansion based on customer input.
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Episode 26: ThawReady™- Transforming Cryopreservation for Instant Cell Functionality
Dr. Chakraborty continues his discussion on cryobiology, focusing on the innovative ThawReady™ Assay Ready Cells that his group developed. He explains that traditional cryopreservation methods cause cellular injuries that manifest when cells are thawed, leading to delayed functionality. ThawReady™ Assay Ready Cells are designed to minimize these injuries, allowing immediate use after thawing and reducing the time and effort required for cell culture. Dr. Chakraborty goes on to discuss the strategic approach ATCC took, leveraging advanced omics technologies to understand and mitigate cellular injuries. The conversation also covers the broader implications of this technology, including cost savings and enhanced efficiency. Dr Chakraborty concludes the discussion by highlighting the importance of compatibility with new characterization technologies and the need for standardization.
Colombia