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Results: 9

1.
Figure 5

Figure 5. A comparison of prediction scores using different OTU picking methods.. From: A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets.

Prediction strength scores were calculated with JSD at 2 clusters using either OTUs generated using a reference-based approach or de novo.

Omry Koren, et al. PLoS Comput Biol. 2013 January;9(1):e1002863.
2.
Figure 9

Figure 9. HMP fecal samples are slightly enriched in Bacteroides abundances compared to community samples.. From: A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets.

The projection from Fig. 8C, right panel, is colored to show if samples originate from the HMP (blue) or community (yellow), and all PC combinations are shown. See Fig. 8 for description of the axes.

Omry Koren, et al. PLoS Comput Biol. 2013 January;9(1):e1002863.
3.
Figure 6

Figure 6. Prediction scores for enterotypes in fecal samples using WGS data.. From: A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets.

Prediction strength scores calculated using 3 distances metrics for (A) HMP, (B) MetaHIT and (C) HMP + MetaHIT data. The thresholds for significance of clustering scores are indicated as dashed lines on the plots. Bars are standard errors.

Omry Koren, et al. PLoS Comput Biol. 2013 January;9(1):e1002863.
4.
Figure 7

Figure 7. Gradients of OTU abundances are evident in the combined dataset of fecal samples.. From: A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets.

HMP and community fecal samples are shown in a PCoA of weighted UniFrac distances. Samples are colored according to (A) putative cluster membership and by their abundances (0–1, see legend inserts) of (B) Bacteroides, (C) Faecalibacterium and (D) Prevotella.

Omry Koren, et al. PLoS Comput Biol. 2013 January;9(1):e1002863.
5.
Figure 2

Figure 2. A positive control of cluster structure recovered from lognormally distributed synthetic community data containing four clusters.. From: A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets.

Presence of enterotypes was tested using: (A) prediction strength, (B) silhouette index and (C) Caliński-Harabasz combined with BC, JSD and rJSD distance metrics. Bars are standard errors.

Omry Koren, et al. PLoS Comput Biol. 2013 January;9(1):e1002863.
6.
Figure 4

Figure 4. Enterotypes in mid vaginal samples in both the HMP and the Ravel . From: A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets.

Prediction strength scores calculated using 5 distances metrics for HMP mid vaginal samples at the genus level (A), Ravel et al. mid vaginal samples at the genus level (B). HMP mid vaginal samples at the species level (C) and Ravel et al. mid vaginal samples at the species level (D). The thresholds for significance of clustering scores are indicated as dashed lines on the plots. Bars are standard errors.

Omry Koren, et al. PLoS Comput Biol. 2013 January;9(1):e1002863.
7.
Figure 3

Figure 3. Clustering scores for enterotypes in fecal samples using 16S rRNA data.. From: A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets.

(A) Prediction strength scores, (B) Caliński-Harabasz and (C) average silhouette scores calculated using 5 distances metrics for HMP data only, adult community data, and combined HMP and adult community data. The thresholds for significance of clustering scores are indicated as dashed lines on the plots. Bars are standard errors.

Omry Koren, et al. PLoS Comput Biol. 2013 January;9(1):e1002863.
8.
Figure 1

Figure 1. Bacterial diversity clusters by body habitat.. From: A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets.

A–C: All body sites. The two principal coordinates from the PCoA analysis of the unweighted UniFrac distances are plotted for (A) HMP data; (B) community data (see Table S1 for list of studies), (C) both datasets combined. Symbol colors correspond to body sites as indicated on panel A. Panel D shows gut samples (majority are fecal) divided into infants (green), children (blue), adults (black) and elderly (orange) samples. The variance explained by the PCs is indicated in parentheses on the axes.

Omry Koren, et al. PLoS Comput Biol. 2013 January;9(1):e1002863.
9.
Figure 8

Figure 8. The fecal microbiota exhibit a smooth gradient of Bacteroides abundances across samples from the HMP and community studies.. From: A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets.

Bacteroides abundances are mapped onto the first two principal coordinates of the weighted UniFrac PCoA analysis for HMP data (A), community data (B), and combined HMP and community data (C). Left panels: 3D plots showing kernel density estimates mapped onto PC1 and PC2; Right panels: contours indicate sample densities, sample colors indicate Bacteroides relative abundances ranging from 0–1, where 1 = 100% Bacteroides; color levels are determined by quantiles to allow visual comparison of any distribution of relative abundances (e.g., 0% of samples fall below the first threshold, 20% below the second threshold, 40% below the third, etc.)

Omry Koren, et al. PLoS Comput Biol. 2013 January;9(1):e1002863.

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