Episode 113: Global Microbial Identifier conference with Ruth Timme

In this episode of the microbinfie podcast, the hosts discuss the Global Microbial Identifier (GMI) conference with Dr. Ruth Timme, exploring critical challenges in microbial genomics data submission and standardization.

Location: Vancouver, Canada

Day 3 Highlights:

Catch up with Dr. Ruth Timme:

Lee and Andrew engaged in insightful discussions with Dr. Ruth Timme, a prominent figure at the Global Microbial Identifier conference. The conference is focused on the latest advancements in microbiological research and technologies.

Key Points Discussed:

• Microbial Genomics: Dr. Timme emphasized the importance of microbial genomics in understanding pathogen evolution and disease outbreaks.

• Metagenomics: The use of metagenomics was showcased as a powerful tool for studying microbial communities and their roles in various environments.

• Bioinformatics: Advances in bioinformatics are critical for processing large sequences of genomic data effectively.

• Collaboration and Networking: The conference provided an excellent platform for researchers and scientists to collaborate and foster new partnerships for future projects.

Dr. Ruth Timme's insights at the conference were invaluable for advancing the goals of the Global Microbial Identifier initiative, aimed at improving global public health responses.

For more updates and detailed proceedings from the conference, keep following the GMI13 events.

Extra notes

• Genome Tracker Program: Ruth Timme from the U.S. Food and Drug Administration (FDA) runs the Genome Tracker Program, which is focused on genomic epidemiology for foodborne pathogens like Listeria and Salmonella.

• Data Submission Challenges: There are complexities in submitting genomic data to public repositories such as the INSDC. Different pathogens have various submission standards, causing difficulties in data retrieval and uniformity.

• Pathogen Data Object Model (DOM): A proposed solution is the Pathogen Data Object Model (DOM), which aims to standardize the submission and storage of whole genome sequence data for pathogens. This model seeks to unify data formats, making it easier for third-party applications to access and utilize this data without needing pathogen-specific standards.

• Inter-agency and International Collaboration: The FDA works with multiple agencies including the CDC and USDA, and internationally with organizations like PAGE, to align genome data submission standards globally.

• Current Practices: Previously, genome submissions involved complex and varied metadata storage, often resulting in disjointed data sets. The COVID pandemic highlighted gaps in viral genome data submission due to inconsistent standards, especially concerning metadata integration.

• GMI and Standards Implementation: The GMI (Global Microbial Identifier) is noted as a platform for discussing and setting standards, focusing on real-world application and uptake by different governments. It collaborates closely with organizations such as WHO and FAO.

• Technical and Political Roles: There's a recognized distinction between PHAGE, which handles technical aspects like producing specifications and functional code, and GMI, which addresses political and intergovernmental concerns, facilitating discussions and collaboration for implementing standards.

• Expectation for Improvement: There is a consensus that standards like the DOM model are overdue and that there are lessons to be learned for handling future pandemics with better data submission standards.