Dynamics of major OTU clusters across major perturbations. Highly abundant OTUs were clustered by their dynamics across Subject A’s travel period (A-D) and Subject B’s acute enteric infection (E-H). Clusters were produced separately for the two environments; see Methods for more details. (A,E) Taxonomic composition of major clusters (fractional abundance exceeds 10% for more than 3 days). (B,F) Cluster abundances over time (shaded points) and trend lines (solid) fit using LOESS smoothing, colored using the same scheme as in (A,E). Subject A’s travel abroad (days 71 to 122) and Subject B’s enteric infection (days 151 to 159) are shaded in gray. (C,G) Median log10(abundance) of OTUs in each cluster before and after perturbation. OTUs are colored by cluster membership, except for uncolored OTUs belonging to clusters not plotted in (A,E). OTU detection limits were set to the minimum fractional abundance observed in each subject’s time series (1e-5.8 for Subject A and 1e-5.6 for Subject B). (D,H) Cartoon of microbiome state models, in which microbiota are considered to be balls in a landscape shaped by environmental factors . Subject A’s travel-related microbiota shift is consistent with a model where environmental disturbances cause state changes (D), while Subject B’s infection-related shift is consistent with state transitions caused by direct community perturbations (H).