Fig. 5

Species-level resolution increased and then tended to decrease in human-associated metagenomes amidst RefSeq growth. Fraction of metagenomic reads classified at different taxonomic levels, regardless of accuracy, using Kraken against nine bacterial RefSeq databases. The human oral metagenome (a) exhibited patterns seen in the simulated metagenome (Fig. 3): an increase in species-level classifications, followed by an increase in genus-level classifications. The human gut metagenome (b) exhibited a different trend, as species- and genus-level classifications fluctuated and classifications at the family level, and beyond, increased