2. Microbiome outcomes.

Study	Methods and main findings of microbiome analysis
Hota 2017	Diversity indices were analyzed using Student t‐tests interrogating the V4 hypervariable region of the 16S ribosomal RNA locus of bacterial DNA in samples from 19 donors and 3 recipients with successful outcomes. Fecal microbiota composition and diversity of the 19 donors were consistently high, with no significant difference between those associated with recipient success or failure of resolution of rCDI. Increased fecal microbiota diversity was found post‐FMT in the analysis of 3 recipients who had resolution of rCDI after FMT.
Kelly 2016	DNA extraction, 16S ribosomal RNA gene amplification, and sequencing were performed on donors and participants ≥ 5 days before and 2 and 8 weeks after FMT. Shannon indices and abundance‐based coverage estimate parameters were calculated to assess alpha diversity, while beta diversity and abundances of genera were analyzed using analysis of similarity and Kruskal–Wallis analysis. All participants had marked dysbiosis prior to FMT. This persisted in those who received autologous FMT while those receiving donor FMT had a restoration of alpha diversity, a pattern seen in those who had success with rescue FMT after initial failure of treatment. This study had 2 sites, and analysis showed differences in the pre‐FMT microbiomes between sites in both donors and recipients pre‐FMT.
van Nood 2013	The study used paired‐samples Student t‐tests to examine statistical significance of a change in microbiota diversity. Wilcoxon signed‐rank tests were performed to determine microbial groups in fecal samples before and after FMT infusion. The Simpson's Reciprocal Index of 9 pre‐FMT patients was low (mean 57, SD 26) and increased within 2 weeks after infusion to 179, SD 42 (P < 0.001), which became indistinguishable from the diversity level of the donors (mean 172, SD 54). This persisted throughout the follow‐up period for those who completed follow‐up testing. A principal component analysis indicated a major shift in the participants' microbiota after FMT towards that of the donors. There was a statistically significant change in multiple groups of intestinal bacteria (P < 0.05).

FMT: fecal microbiota transplantation; rCDI: recurrent Clostridioides difficile infections; RNA: ribonucleic acid.