Figure 1

Gut and salivary microbiota dynamics in two subjects over 1 year. (A) Stream plots showing OTU fractional abundances over time. Each stream represents an OTU and streams are grouped by phylum: Firmicutes (purple), Bacteroidetes (blue), Proteobacteria (green), Actinobacteria (yellow), and Tenericutes (red). Stream widths reflect relative OTU abundances at a given time point. Sampled time points are indicated with gray dots over each stream plot. (B) Horizon graphs of most common OTUs’ abundance over time. Horizon graphs enable rapid visual comparisons between numerous time series [21]. Graphs are made by first median-centering each OTU time series and dividing the curve into colored bands whose width is the median absolute deviation (Inset, step 1). Next, the colored bands are overlaid (step 2) and negative values are mirrored upwards (step 3). Thus, warmer regions indicate date ranges where a taxon exceeds its median abundance, and cooler regions denote ranges where a taxon falls below its median abundance. Colored squares on the vertical axis correspond to stream colors in (A). Time series in both the stream plots and horizon graphs were smoothed using Tukey’s running median. Lower black bars span Subject A’s travel abroad (days 71 to 122) and Subject B’s Salmonella infection (days 151 to 159).