Episode 111: Global Microbial Identifier with Finlay Maguire and Emma Griffiths

In this episode of the microbinfie podcast, host Andrew Page and Lee Katz explore microbial genomics and data sharing with guest Dr. Finlay Maguire at the Global Microbial Identifier Conference in Vancouver, Canada.

Location: Vancouver, Canada

Attendees: Andrew, Lee, Dr. Finlay Maguire, Dr. Emma Griffiths

First Day Highlights

• Discussion Topics:
  • Microbial Genomics: An exploration of the advancements and current research in the field of microbial genomics.
  • Tim Hortons: A casual conversation about the popular Canadian coffee and donut franchise.

Both Dr. Finlay Maguire and Dr. Emma Griffiths shared their insights into the world of microbial genomics, contributing to the broader dialogue on how these scientific advancements can impact global health.

Extra notes

• Microbial Bioinformatics Background: The discussion features Finlay McGuire, an Assistant Professor at Dalhousie University with a background in microbiology, who currently specializes in pathogenomics and bioinformatics. He has affiliations in both Community Health and Epidemiology within the Faculty of Computer Science, engaging in computational and bioinformatics work to distance himself from wet lab activities.

• Conference Participation and Interests: Finlay attended the Global Microbial Identifier (GMI) Conference thanks to Dr. Emma Griffiths. His academic interests include making genomic data usable for clinical decision-making and developing tools to support public health policy, ranging from individual patient care to global health initiatives.

• Data Sharing and Standards: A significant focus is on the challenges of global data sharing, especially the operationalization of data sharing principles articulated by health organizations like WHO. The discussion underscores the importance of integrating various data sources, including plant pathogens, into the One Health framework, which encompasses animal and human health.

• Tools and Methodologies: There is an emphasis on practical bioinformatics work within working groups like Phage, with a focus on creating pipelines that include multiple AMR (antimicrobial resistance) detection tools, and ensuring these tools are actionable and useful through implementations like Python scripts.

• Challenges in Microbial Data Sharing: The integration of human and agricultural data is highlighted as problematic due to tighter restrictions and legal barriers on agricultural data compared to human clinical data. There are divergent models for data sharing, such as the restrictive GISAID model versus the open access INSTC model, reflecting tensions between open data and data ownership.

• Technological and Analytical Barriers: An example is provided of inadequacies in processing genetic data due to limitations on data mobility and the availability of proper analytical technology, as illustrated by the past issues with food contamination detection and the retarded progress due to technical and legal constraints.

• Global Strategy and Practical Work: There's a tension between focusing on broader global strategies and engaging in detailed practical work necessary for bioinformatics progress, emphasizing the need for clear protocols and well-structured data sharing methodologies.

Overall, the podcast reflects on the complex landscape of microbial bioinformatics, from the integration of diverse datasets to the implementation of practical bioinformatics tools and methodologies, while addressing challenges like data sharing, technology use, and international collaboration in the field.

Key Points

1. Microbial Genomics and Data Sharing

• Challenges in global data sharing across human, animal, and plant health domains
• Tensions between open data principles and data ownership models
• Importance of operationalizing WHO data sharing guidelines

2. One Health and Interdisciplinary Research

• Integration of plant, animal, and human pathogen research
• Zoonotic disease tracking, including SARS-CoV-2 transmission between deer and humans
• Complex interactions between different biological ecosystems

3. Bioinformatics Tools and Methodologies

• Development of practical bioinformatics pipelines
• Focus on creating actionable tools for clinical and public health decision-making
• Challenges in processing and analyzing genomic data across different sectors

Take-Home Messages

• Effective global health research requires interdisciplinary collaboration
• Data sharing models must balance openness with institutional constraints
• Practical, implementable tools are crucial for advancing microbial genomics