Sequence‐identical microbial genomes with disparate taxonomy: A large‐scale redundancy analysis in NCBI genome database

Public microbial genome repositories (such as NCBI) contain thousands of sequence-identical genome assemblies assigned to different taxonomic lineages, potentially inflating microbial diversity and introducing bias into comparative genomics, metagenomics, and pathogen surveillance. By systematically screening 729,559 NCBI prokaryotic genomes using assembly metadata filtering followed by MD5 hash-based sequence validation, we identified 3334 sets of completely identical genome assemblies with taxonomic inconsistencies. We propose a simple redundancy-aware genome submission workflow that combines assembly-level screening with cryptographic sequence identity checks to flag identical submissions, harmonize metadata, and strengthen the accuracy, transparency, and reliability of public genomic databases.