Fig. 2: Pathway-level contributional diversity and species transcriptomal activity of oral microbiome.

a Overall contributional species richness represented in metagenomic (DNA) and metatranscriptomic (RNA) pathway profiles determined across all paired samples. Only pathways expressed (RNA) by at least two species were plotted. b Relationship between pathway relative abundance and contributional species diversity (Shannon diversity index) in metagenomic (DNA) and metatranscriptomic (RNA). Each point represents a pathway and depicts its sample abundance as well species diversity (Shannon diversity index) potentially contributing (DNA) or actively contributing (RNA). We found that pathway abundance and contributional species diversity quite correlate in metagenomes (DNA) while some pathways clearly exhibited overexpression (RNA). Some highly expressed pathways which are not necessarily expressed by highly diverse communities. Pathway code was display for pathway with Abundance > 0.045 or shannons_div < 0.03. c Differences in per-pathway metagenomic (DNA) versus metatranscriptomic (RNA) contributions of top bacterial species as described in Fig. 1c. Each point represents the overall species transcriptional activity averaged within samples from different sites from the same Subject and across patients. Some species exhibited an overall tendency for overtranscription or undertranscription, whereas others displayed pathway-specific activity patterns. Boxplots display first quartile, median, and third quartile and whiskers represent 1.5 times the interquartile range from the first and third quartiles. d Pathway-level transcriptomal activity of species found to be differentially abundant between healthy and patients with periodontitis (see Supplementary Fig. 1A). The activity of each species is average within sample (average of pathways detected within paired metagenomes and metatranscriptomes).