Interactive visualization explorer of the diarrheal microbiome in young children from low-income countries

Diarrhea is a major cause of mortality and morbidity in young children from developing countries, leading to as many as 15% of all deaths in children under 5 years of age.

Among the discoveries of our study are the effectiveness of quantitative PCR as an alternative to culture in characterizing Shigella infections, as well as the potential of members of the Streptococcus genus to cause diarrhea. The data underlying our study is presented in part through these interactive plots.


Explore the data in the tabs above!

We welcome you to explore the data on this site through the tabs above. Data was filtered (for server speed) at each level to include only bacteria present in over 20 samples. Additionally, only OTU sequences present in over 20 samples are shown. Examples of the interactive plots are shown below.

Bacterial Abundance

Manhattan plots of the bacterial abundances at various levels of the tree stratified by sample health status, age, and country of origin. Scroll through your favorite bacteria and display your country/age of interest.

Heatmap

Heatmap of the bacterial abundances filtered by either the most variable bacteria or those with the largest median absolute deviation scores. Trend in abundance due to age (above). warning: takes a few seconds

PCA/MDS

PCA or MDS plots (methods for dimensionality-reduction). Projecting samples onto two dimensions and coloring the samples by phenotype. warning: takes a few seconds

Diversity

Shannon diversity index boxplots of the various stratified samples.

Rarefaction

Operational taxonomic unit (OTU) richness as a function of sequencing depth.

OTU Description

OTU representative sequence annotations.


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Data comes from the molecular characterization of the diarrheal microbiome in young children from low-income countries

Visualization code by Joseph N. Paulson
Manhattan plots of bacterial abundances where each bar represents the abundance in a sample.



*OTU sequence centers for OTUs present in > 20 samples
              OTU ID and sequence center for OTU above:
              
              OTU ID and sequence centers for bacteria above:
              
Heatmap of the top N bacteria.

Warning: takes a few seconds
PCA or MDS to project samples, using the 200 most variable bacteria, onto 2 dimensions.

Warning: takes a few seconds
Boxplots of Shannon diversity indexes. Both cases and controls exhibited higher mean Shannon diversity index scores at higher age groups compared to lower age groups. The diversity of healthy samples is higher than diseased samples
The linear effect depth of coverage has on the number of bacteria detected. Including each of the three factors in a linear model, the adjusted R^2 is 0.912