Fig. 2

Taxonomic assignment of control mixtures by different bioinformatics tools. A Abundance (y-axis) of each genus (see color legend) in synthetic-community mixtures. Data for expected values are plotted next to results (average of 10 replicates) from analyses by Bracken, Kraken2, Metaphlan3, and Metaphlan4 classifiers. B, C Distance between the abundance profile for each classifier compared to the expected composition (n = 10 replicates). B L2 abundance distances for each taxonomic classifier compared to the expected composition, assessed for each genus. Genera are differentiated by point shape. C L2 abundance distances for each taxonomic classifier compared to the expected composition, assessed for each synthetic-community mixture. Synthetic-community mixtures are differentiated by point-shape. D, E Principal coordinate analysis of all synthetic-metagenomic mixture replicates’ (n = 10) (D) calculated organism abundances and (E) assigned number of operational taxonomic units. Mixtures are differentiated by colour. Point shape denotes classification method. The percentage in parentheses on each axis gives the estimated contribution of each principal coordinate to the total variance