Figure 4.

Accuracy of PICRUSt prediction compared with shotgun metagenomic sequencing at shallow sequencing depths. Spearman correlation (y-axis) between either PICRUSt predicted metagenomes (blue lines) or shotgun metagenomes (dashed red lines) using 14 soil microbial communities subsampled to the specified number of annotated sequences (x-axis). This rarefaction reflects random subsets of either the full 16S OTU table (blue) or the corresponding gene table for the sequenced metagenome (red). Ten randomly chosen rarefactions were performed at each depth to indicate the expected correlation obtained when assessing an underlying true metagenome using either shallow 16S rRNA gene sequencing with PICRUSt prediction or shallow shotgun metagenomic sequencing. The data label describes the number of annotated reads below which PICRUSt-prediction accuracy exceeds metagenome sequencing accuracy. Note that the plotted rarefaction depth reflects the number of 16S or metagenomic sequences remaining after standard quality control, dereplication, and annotation (or OTU picking in the case of 16S sequences), not the raw number returned from the sequencing facility. The number of total metagenomic reads below which PICRUSt outperforms metagenomic sequencing (72,650) for this dataset was calculated by adjusting the crossover point in annotated reads (above) using annotation rates for the soil dataset (17.3%) and closed-reference OTU picking rates for the 16S rRNA dataset (68.9%). The inset figure illustrates rapid convergence of PICRUSt predictions given low numbers of annotated reads (blue line).