119 The Challenges of Microbial Taxonomy - Conversations with Titus Brown

In this episode, Andrew Page and Lee Katz continue their chat with Titus Brown, focusing on taxonomy assignment in metagenomics: Topics discussed: Dealing with contamination and low quality genomes in reference databases Sourmash as a versatile search tool, not a curated database The need for high confidence in taxonomic assignment in public health Most microbial assignment tools have low specificity or sensitivity Possible ways to achieve perfect species classification (in theory) The challenges around defining species based on small genomic differences Interesting cryptography concept of 'unicity' distance for classification Conveying the nuances and uncertainties in taxonomic assignment The conversation highlights the difficulties around taxonomic classification, especially at the species level, but explores ideas for improving accuracy. Overall it emphasizes the complexities of biology and need for transparent conveyance of uncertainties. Papers: Spacegraphcats - https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02066-4 Sourmash - https://www.biorxiv.org/content/10.1101/2022.01.11.475838v2 IBD exploration - https://dib-lab.github.io/2021-paper-ibd/