Fig. 3.

PCoA of unweighted UniFrac distances, a phylogenetically aware measure of intersample (β) diversity. A covers the period encompassing the first Cp, with samples before Cp (pre-Cp), during the first Cp course (first Cp), during the first week post-Cp (first WPC), and in the interim period between Cp courses (interim) progressing from darker to lighter shades. B covers the second Cp period, with interim samples in the darkest shades and the second Cp course, second WPC, and post-Cp periods becoming progressively lighter. Data points from A are also shown on B with small gray symbols to facilitate comparisons between the two parts of the experiment. Numbers adjacent to some samples track the Cp perturbation by indicating the number of days elapsed since the start of Cp administration; missing numbers indicate that samples were not collected on those days.