Fig. 2

FMT treatment timeline and PCoA visualization. A Timeline of treatment process with FC levels. B PCoA based on gene expression profile of each sample. In A, sampling time points are indicated with the following: < No. FMT > _ < days since this FMT > . ABT is the timepoint for the antibiotic treatment. FMT1/2/3 indicates the timepoint for the corresponding FMT, while DKS or DSS in the bracket shows the donor used for this FMT. The height of the bars indicates the FC level. In B, each dot represents a sample, and the number in the dot indicates the number of days since the latest FMT. A negative number indicates the sample was taken before the first FMT. The trajectory lines show the timepoints across different FMT treatments. The start of each FMT is indicated in italic label. The donor sample used by each FMT is marked and colored in green, and the samples before treatment are in red, before FMT after ABT in orange, and after FMT in blue. To be able to compute the distance metric and visualize the data, only the top 200,000 expressed genes which account for 92% total mapped reads were taken into account