Fig 1.
Overview of experimental design.
Schematic showing how samples were processed for 16S rRNA amplicon sequencing.
Fig 2.
Box and whisker plot showing DNA yield obtained by each pretreatment lysis method.
Boxes extend from the lower quartiles to the upper quartiles with median values indicated by the line within each box. Whiskers represent maximum and minimum values, excluding any outliers (values indicated by circles which lie outside 1.5 times the interquartile range). Significant differences between methods are starred (* P <0.05; ** P ≤0.01; *** P ≤0.001).
Fig 3.
Heat map showing most abundant operational taxonomic units (OTUs) with sample extracts arranged by hierarchical clustering.
All OTUs that were present at 1% or higher in at least one sample are shown. Extracts are named according to the sample of origin followed by the pretreatment lysis method used and are arranged by Unweighted Pair Group Method with Arithmetic Mean (UPGMA) clustering on the Bray-Curtis dissimilarity matrix. The coloured bar indicates which extracts have clustered most closely with all other extracts from the same sample (green) and those that have not (red). Reads have been assigned to OTUs based on 97% sequence similarity of the V3–V4 region. Note that in some cases this has resulted in multiple OTUs with the same taxonomic species identifier, which is most likely due to a high degree of intraspecies variability in this region of the gene, or incorrect base calling. Lactobacillus species that could not be identified to species level at the 97% cut-off have been assigned to genus subgroups: L. gasseri group (including L. gasseri and L. johnsonii), L. acidophilus group (including L. acidophilus, L. helveticus, L. gallinarum, L. crispatus, L. jensenii and L. delbruekii), L. vaginalis group (including L. vaginalis and L. reuteri) and L. coleohominis group (including L. coleohominis and L. pontis).
Fig 4.
Principal coordinate analysis ordination of a Bray-Curtis dissimilarity matrix.
Extracts are coloured by sample of origin. Extracts cluster closely with other extracts originating from the same sample and there is no observable effect of pretreatment lysis method. Extracts from samples that are dominated by Lactobacillus iners with variable proportions of Gardnerella have clustered on the left, extracts from samples that are dominated by L. acidophilus group have clustered on the bottom right and extracts from high diversity samples that contained a mixture of strict and facultative anaerobes cluster towards the top.