LINgroups as a principled approach to compare and integrate multiple bacterial taxonomies

Mazloom, Reza and Pierce-Ward, Tessa and Sharma, Parul and Pritchard, Leighton and Brown, C Titus and Vinatzer, Boris and Heath, Lenwood (2024) LINgroups as a principled approach to compare and integrate multiple bacterial taxonomies. IEEE/ACM Transactions on Computational Biology and Bioinformatics. ISSN 1545-5963 (https://doi.org/10.1109/TCBB.2024.3475917)

[thumbnail of Mazloom-etal-IEEE-ACM-TCBB-2024-LINgroups-as-a-principled-approach-to-compare-and-integrate]
Preview
 Text. Filename: Mazloom-etal-IEEE-ACM-TCBB-2024-LINgroups-as-a-principled-approach-to-compare-and-integrate.pdf
Accepted Author Manuscript
License: Creative Commons Attribution 4.0 logo
Download (10MB)| Preview

Abstract

Traditional taxonomy provides a hierarchical organization of bacteria and archaea across taxonomic ranks from kingdom to subspecies. More recently, bacterial taxonomy has been more robustly quantified using comparisons of sequenced genomes, as in the Genome Taxonomy Database (GTDB), resolving down to genera and species. Such taxonomies have proven useful in many contexts, yet lack the flexibility and resolution of a more fine-grained approach. We apply our Life Identification Number (LIN) approach as a common, quantitative framework to tie existing (and future) bacterial taxonomies together, increase the resolution of genome-based discrimination of taxa, and extend taxonomic identification below the species level in a principled way. We utilize our existing concept of a LINgroup as an organizational concept for microorganisms that are closely related by overall genomic similarity, to help resolve some of the confusions and unforeseen negative effects of nomenclature changes of microbes due to genome-based reclassification. Our results obtained from experimentation demonstrate the value of LINs and LINgroups in mapping between taxonomies, translating between different nomenclatures, and integrating them into a single taxonomic framework. Our results also reveal the robustness of LINs to hyper-parameter changes in the assignment process when considering within-species taxonomic groups.

ORCID iDs

Mazloom, Reza, Pierce-Ward, Tessa, Sharma, Parul, Pritchard, Leighton ORCID logoORCID: https://orcid.org/0000-0002-8392-2822, Brown, C Titus, Vinatzer, Boris and Heath, Lenwood;
CORE (COnnecting REpositories)