Fig. 1

The mOTUs3 database enables species-level profiling across diverse environments. a The database of the previous major release of mOTUs (version 2) [14] was updated to version 2.5 to account for the current release of the progenomes2 database [26]. Based on version 2.5, the mOTUs3 database was constructed by adding universal, single-copy phylogenetic marker genes (MGs) from 605,653 genomes (metagenome-assembled genomes (MAGs) and a smaller number of isolate and single amplified genomes (SAGs)). This addition resulted in the extension of the database by 19,358 new species-level, MG-based operational taxonomic units (ext-mOTUs). Genomes already represented by ref- and meta-mOTUs in version 2.5 were not added (gray lines). b Breakdown by the three types of mOTUs shows that mOTUs3 enables the reference genome-independent profiling of a substantial fraction of microbial diversity across different environments. The numbers below the ring charts represent: First, the number of metagenomes analyzed (with “n=”), second the total number of mOTUs that were detected per environment considering only species with a prevalence of 0.1% and finally the median number of mOTUs per sample that were detected after downsampling to 5000 inserts