Fig. 3

a Nonmetric multidimensional scaling plots generated using the vegan package in R [76], using MetaPhlAn2 classifications of data from Lewis et al. [61]. Each point is colored by the cluster in which it was annotated in the Lewis et al. metadata—cluster 2 (red) is the dysbiotic cluster, while cluster 1 (blue) is the healthy-like cluster. b Inverse Simpson diversity by absolute latitude calculated using the vegan package in R from the Kraken classification output of Sunbeam for Bahram et al. [63]. Points are colored by habitat. The polynomial regression line is shown in black. c Boxplots of unique Anelloviridae taxa in each sample from McCann et al. [64]. Each point corresponds to a single sample. d Heatmap from shallow shotgun analysis colored by proportional abundance. Each row corresponds to a bacterial taxon; each column represents a different reagent combination. Columns are grouped by time point, then by subject (top). All plots were generated using the ggplot2 R package [77]