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bioRxiv · 10.64898/2025.12.09.693184

BacTaxID: A universal framework for standardized bacterial classification

Fernandez-de-Bobadilla, M. D.·Lanza, V. F.
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Abstract

Bacterial strain typing is key to surveillance, outbreak investigation and microbial ecology, yet current systems remain species-specific, reference-dependent and lack a universal, interpretable metric of genomic relatedness. Here, we introduce BacTaxID, a fully configurable, whole-genome k-mer-based framework that encodes each genome as a numeric sketch and organizes strains into hierarchical clusters with user-defined similarity thresholds. BacTaxID distances are strictly proportional to Average Nucleotide Identity (ANI), providing a direct quantitative link between vectorial typing and genome-wide divergence. Applied to 2.3 million genomes from "All the Bacteria" database across 67 genera, BacTaxID demonstrates universal concordance species and sub-species classification systems, while capturing finer strain-level diversity than traditional reference-based approaches. In simulated surveillance and real outbreak datasets, BacTaxID reproduces SNP and cgMLST-based definitions while enabling rapid, scalable screening. Precomputed genus-level schemes and an open implementation provide a practical, genus-agnostic alternative to classical typing systems for standardized bacterial classification.

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Fernandez-de-Bobadilla, M. D., Lanza, V. F.. 2025-12-11. BacTaxID: A universal framework for standardized bacterial classification. https://doi.org/10.64898/2025.12.09.693184

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