Episode 135: Assembling ATCC bacterial strains

In this episode of the Micro Binfie podcast, host Andrew Page is joined by Nikhita Puthuveetil, Senior Bioinformatician at the American Type Culture Collection (ATCC). They delve into ATCC's ambitious project of sequencing a vast array of organisms from their renowned collection, tackling the challenges of assembling complex genomes from bacteria, viruses, fungi, and more.

Discover how Nikhita and her team navigate through genomic roadblocks, leverage cutting-edge sequencing technologies, and work to ensure accurate data provenance. Whether it's large viral genomes or evolving taxonomy, this episode offers a deep dive into the fascinating world of microbial bioinformatics and genomic curation.

Key Points

1. ATCC Genome Sequencing Project

• Sequencing over 5,000 genomes across multiple organism types
• Using both short-read and long-read sequencing platforms
• Focusing on challenging organisms like extremophiles and complex viruses

2. Genome Assembly Challenges

• Developing flexible assembly pipelines for diverse genomic compositions
• Addressing issues with repetitive regions in herpes viruses
• Manually curating difficult genome assemblies

3. Taxonomic and Metadata Verification

• Comparing deposited sequences with their own assembled genomes
• Tracking data provenance and metadata carefully
• Collaborating with other culture collections to validate strain information

Take-Home Messages

• Genomic sequencing requires flexible, adaptive approaches
• Metadata and provenance are crucial for reliable scientific resources
• Taxonomy is a continuously evolving field requiring constant verification