Detection of virulence factors in stool DNA by qPCR are shown for FMT donors, patients prior to FMT, and patients at various time points after FMT (2–10 weeks, 10–20 weeks, and >27 weeks) (n = 11 patient/donor pairs). Virulence factors B. fragilis bft (A), E. coli clbB (B), and F. nucleatum fadA (C). Left panels indicate whether there was evidence for transmission/expansion; middle panels, clearance/reduction; right panels, neutral/other changes in the levels of bacterial virulence factors. Colors denote the source of the FMT donor stool, with familial donors in shades of blue/purple (P1–P7) and commercial stool bank donors shown in shades of green (P8–P11). Undetectable data points were assigned a value of 1 for display purposes on the log10 scale.