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1.
Figure 8

Figure 8. Cell Membrane Degradation.. From: A Multi-Omic Systems-Based Approach Reveals Metabolic Markers of Bacterial Vaginosis and Insight into the Disease.

Shown is a diagram depicting classical components of a cell membrane that is depleted in either of the metabolome profiles of the two symptomatic BV types.

Carl J. Yeoman, et al. PLoS One. 2013;8(2):e56111.
2.
Figure 5

Figure 5. Venn Diagram of Discriminative Metabolites.. From: A Multi-Omic Systems-Based Approach Reveals Metabolic Markers of Bacterial Vaginosis and Insight into the Disease.

Shown is a Venn diagram of the numbers of unique and shared metabolites that delineate high Nugent scoring (≥7), Type I symptomatic BV or Type II symptomatic BV from other samples.

Carl J. Yeoman, et al. PLoS One. 2013;8(2):e56111.
3.
Figure 1

Figure 1. Richness and Diversity of Each Sample.. From: A Multi-Omic Systems-Based Approach Reveals Metabolic Markers of Bacterial Vaginosis and Insight into the Disease.

Rarefaction curves showing the richness of microbiomes for all samples colored by Nugent score (A; green = 0–3, orange = 4–6, red = 7–10) or Amsel classification (B; red = positive, green = negative) are presented along with Shannon diversity indexes (C), with samples grouped by Nugent score or Amsel criteria and colored as in rarefaction curves.

Carl J. Yeoman, et al. PLoS One. 2013;8(2):e56111.
4.
Figure 2

Figure 2. Heatmap of Taxonomic Enrichment by Sample.. From: A Multi-Omic Systems-Based Approach Reveals Metabolic Markers of Bacterial Vaginosis and Insight into the Disease.

Shown is a heatmap of the relative enrichment of the most abundant thirty microbial genera across the entire sample set and the relationships among samples. Highly abundant genera tend toward bright green, while less abundant genera tend toward blue, as shown in the key. Dendrograms show the relationship among samples. Red bars in the dendrogram show the relationship of samples with symptomatic BV. Nugent scores are presented beneath the dendrogram.

Carl J. Yeoman, et al. PLoS One. 2013;8(2):e56111.
5.
Figure 7

Figure 7. SBVII Sub-Network View of Linear Relationships among Variables.. From: A Multi-Omic Systems-Based Approach Reveals Metabolic Markers of Bacterial Vaginosis and Insight into the Disease.

Pearson's (between parametric data) and Spearman's (between non-parametric and either parametric or non-parametric data) correlations >0.6 (green) or <−0.4 (red) are shown as edges connecting patient metadata relating to demographics, hygiene and sexual behaviors and sexual practices, OTUs, microbial genera, metabolites and patient symptoms. Figures presented represent sub-networks of the complete network (Fig S2). Node identities are listed or described in the key. The identities of numbered metabolites are listed in Table S2.

Carl J. Yeoman, et al. PLoS One. 2013;8(2):e56111.
6.
Figure 6

Figure 6. SBVI Sub-Network View of Linear Relationships among Variables.. From: A Multi-Omic Systems-Based Approach Reveals Metabolic Markers of Bacterial Vaginosis and Insight into the Disease.

Pearson’s (between parametric data) and Spearman's (between non-parametric and either parametric or non-parametric data) correlations >0.6 (green) or <−0.4 (red) are shown as edges connecting patient metadata relating to demographics, hygiene and sexual behaviors and sexual practices, OTUs, microbial genera, metabolites and patient symptoms. Figures presented represent sub-networks of the complete network (Fig S2). Node identities are listed or described in the key for figure 7. The identities of numbered metabolites are listed in Table S2.

Carl J. Yeoman, et al. PLoS One. 2013;8(2):e56111.
7.
Figure 3

Figure 3. Nonmetric Multidimensional Scaling Analyses.. From: A Multi-Omic Systems-Based Approach Reveals Metabolic Markers of Bacterial Vaginosis and Insight into the Disease.

Shown are nMDS plots of the 16S rRNA reads clustered by genus for all taxa (A), or for just Gardnerella and Lactobacillus (B), or metabolite profiles (C). Samples from patients determined by Amsel criteria to have BV are shown in red, while samples determined by Amsel to be healthy are shown in green. Samples with a high (7–10; up-pointing triangles), moderate (4–6; diamonds) and low (0–3; down-pointing triangles) are indicated. The two metabotypes are delineated by hollow (type I) and solid (type II) symbols.

Carl J. Yeoman, et al. PLoS One. 2013;8(2):e56111.
8.
Figure 4

Figure 4. Heatmap of Metabolite Enrichment by Sample.. From: A Multi-Omic Systems-Based Approach Reveals Metabolic Markers of Bacterial Vaginosis and Insight into the Disease.

Shown is a heatmap of the relative enrichment of each metabolite across the entire sample set and the relationships among samples and among metabolites. Highly abundant metabolites tend toward red, while less abundant metabolites tend toward blue. Dendrograms show the relationship among samples (top) and among metabolites (left). The two BV metabotypes observed (I and II) are labeled at their branching point. Red bars in the top dendrogram show the relationship of samples with symptomatic BV. Nugent scores are shown for each sample. Metabolite mentioned in-text are labeled, others are numbered as in Table S2.

Carl J. Yeoman, et al. PLoS One. 2013;8(2):e56111.

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