Extended Data Fig. 3: Diet-dependent changes in the microbiome are maintained following transplantation to GF mice.

a, Distribution of weight loss in diet intervention participants identified the five individuals that lost the most weight for transplantation of stool samples to GF C57BL/6J mice. b, Experiment design and microbiota sampling times. c, Differential 16S rRNA ASV abundances in human donors and recipient mice demonstrate 58 candidate effectors of the weight-loss phenotype (zero-inflated beta regression model with random effects (ZIBR), FDR Q < 0.1, Supplementary Table 6). Note: taxonomy assigned using SILVA 123 with Peptoclostridium difficile synonymous for C. difficile. d, Functional differences between pre- and post-diet recipient communities by enrichment of KEGG functional pathways based on inferred gene content from amplicon sequencing (PICRUSt, Supplementary Table 7). Comparison of groups predicts altered amino acid, carbohydrate, and SCFA metabolic function. Central nodes represent KEGG pathways significantly enriched by their constituent significant differentially abundant KOs, shown with fold-change (colour) and FDR value (size) indicated (FDR Q < 0.1, LMM). e, Detection of C. difficile and TcdA/TcdB by endpoint PCR, ELISA, and selective and differential culture demonstrates active toxin production in post-diet mice at time of death.