Fig. 3

Strain profiling reveals a variety of competition dynamics for conspecific microbial strains. a Phylogenetic tree of different Bacteroides faecis strains, one of the species enriched post-FMT. Bacteroides faecis strains were present in 138 fecal metagenomes as determined by SNP haplotyping. Scale bar signifies difference in sequence similarity between SNP haplotypes. b Distribution of median normalized DNA distances for conspecific strain pairs. Recipient strains (pre-FMT, post-FMT, and placebo) were compared against donor strains from the corresponding treatment batch. Because we had multiple stool samples for each donor, we also compared intra-donor strains (plotted in red). This allowed us to set a universal strain threshold of 0.2 median normalized DNA distance for calling identical strains, as indicated by the vertical dashed line. c Proportions of strains identified as being either unique to recipient (matching recipient’s baseline strain) or unique to donors (matching any of the contributing donor strains). Strains that were newly detected, or that did not match the recipient’s baseline strain or any contributing donor strains were designated as “Novel”. d Proportion of longitudinal strain profiling scenarios by treatment group. Differences between FMT and placebo proportions for each scenario were tested by proportion test with significance denoted by *p < 0.05, ***p < 0.0005, n.s. not significant