Bacterial community structure and function. (A) The distribution of all mapped mRNA reads for each taxon per sample. The two samples that were considered healthy (N4 and N30) are dominated by Lactobacillus crispatus with lesser amounts of L. iners and L. jensenii detected. The two samples having bacterial vaginosis (BV) have a lower relative proportion of lactobacilli and large proportions of Prevotella amnii, Gardnerella vaginalis, Megasphaera, and other anaerobic organisms. (B) Selected subsystem 2 and subsystem 3 categories showing enriched subsystem 4 functions under N or BV conditions. Each point represents a specific subsystem 4 function, and the magnitude of change in expression is plotted on the x-axis relative to the BV condition. Points are colored blue (non-BV) or red (BV) if significantly differentially expressed between conditions, whereas grey points are not differential between the conditions. (C) Representation of the fractional taxon contribution to functions significantly upregulated in BV (red points in B). Pairs of bars represent the two samples (B27 and B31) and each color is the fraction of reads for that function contributed by a particular taxon. Butyrate kinase, as part of the Acetyl-CoA fermentation to Butyrate subsystem, is highlighted to show the relationship between the differential functions in 1B and the taxonomic composition of the function in 1C. Gly, Glycerol; Gly-3P, Glycerol-3-phosphate; GL, Glycerolipid; GPL, Glycerophospholipid.