Database size positively correlates with the loss of species-level taxonomic resolution for the 16S rRNA and other prokaryotic marker genes
Fig 2
Clustering analysis for simulated databases created by randomly sampling sequences from the 16S rRNA SILVA database and the 120 marker gene Genome Taxonomy Database (GTDB).
Each simulated database was clustered at 95%, 97%, 99%, and 100% identity requiring that shorter sequences fully align to longer ones. The 16S rRNA gene is denoted by a star in all subplots. A) The relationship between the number of genes in the simulated databases, the number of clusters, the number of multi-species clusters, and the number of sequences in multi-species clusters. For GTDB, each curve is for one of the 120 marker genes. B) The rate at which sequences were recruited to multi-species clusters as the database grows. Each point represents one of the 120 marker genes in the GTDB. C) The percentage of species with sequences in multi-species clusters. D) The relationship between the number of multi-species clusters that a species belongs to and the species richness of its genus (i.e., the total number of species from that genus) in the simulated database. This data was only taken from the final iteration of the simulated databases. The results were aggregated across all 120 marker genes in the GTDB.