Database size positively correlates with the loss of species-level taxonomic resolution for the 16S rRNA and other prokaryotic marker genes

• DOI: 10.1371/journal.pcbi.1012343
• Publication Date: 2024-08-05T17:52:10Z
• Authors: Seth Commichaux; Tu Luan; Harihara Subrahma...; Mihai Pop
• Keywords: Bacterial taxonomy; Marker gene; Taxonomic rank

For decades, the 16S rRNA gene has been used to taxonomically classify prokaryotic species and profile microbial communities. However, criticized for being too conserved differentiate between distinct species. We argue that inability is not a unique feature of gene. Rather, we observe gradual loss species-level resolution other nearly-universal marker genes as number sequences increases in reference databases. This trend was strongly correlated with how represented taxonomic group database indicates that, at gene-level, boundaries many might be fuzzy. Through our study, any approach relies on single distinguish bacterial taxa fraught even if some markers appear discriminative current