Fig. 4

The Human microbiome pool probe set can effectively deplete rRNAs found in vaginal and oral microbiome samples to generate metatranscriptomic profiles. Percentage of reads mapping to eukaryotic and prokaryotic rRNAs vs. coding sequences following depletion of vaginal and tongue samples using Ribo-Zero Plus ± pan-microbiome HMv1 probes. A rRNA depletion efficiency of vaginal samples using the Ribo-Zero standard probe set (DP1) ± pan-microbial HMv1 probe set. Non-rRNA host RNA content can be prominent in vaginal samples. ND = Non depleted controls. B rRNA depletion efficiency of representative tongue microbiome samples (T1 & T2) using the Ribo-Zero Plus standard probe set (DP1) ± pan-microbiome HMv1 probe set. Boxed bar plots on top in panels A and B represent remaining bacterial rRNA (LSU & SSU) for indicated samples with a dashed line at the 50% mark. C Alpha diversity (Shannon index) and metatranscriptomic taxonomic profiles for Ribo-Zero Plus (DP1 or DP1 + HMv1) depleted vaginal microbiome samples. D Alpha diversity (Shannon index) and metatranscriptomic taxonomic profiles for Ribo-Zero Plus (DP1 + HMv1) depleted oral microbiome samples