Fig. 4: Propagation of HGT segments in the gut community is mediated by both HGT and strain replacement.

a Comparison of HGT prevalence at baseline (blue) and follow-up (green) (two-sided Wilcoxon Signed Rank Tests, n = 338). Box plots show the median (center line), the 25th and 75th percentiles (box), and whiskers extending to points within 1.5 × IQR. Violin plots indicate data distribution. b Distribution of HGT segment prevalence at baseline (blue, 338 individuals, n = 7581) and follow-up (green, 338 individuals, n = 7581). c, Prevalence of HGT Segment 35 at baseline and follow-up. d Phylogenetic tree of Agathobacter rectalis (112) (SGB4933) for individuals in selected clusters at baseline and follow-up (see Figure S6). e As in (d) but with individuals hosting the same A. rectalis strain at baseline and follow-up highlighted in red. f As in (d) but highlighting individuals with different A. rectalis strains at baseline and follow-up. Samples with A. rectalis with the HGT segments are indicated in yellow. Samples with A. rectalis without the HGT segments are indicated in green. Red dashed lines indicate the strain replacement direction of individuals who gained HGT segments at follow-up. Blue dashed lines indicate individual loss of HGT segments at follow-up. In (d−e), the tag _B indicates a baseline sample and _F indicates a follow-up sample.