Extended Data Fig. 9: Metabolomic profiling of the five participants who lost the most weight supports a working model for the effect of caloric restriction on colonization resistance.

a, b, BCAAs (a) and SCFAs (b) were decreased during VLCD and CONVD relative to baseline in the five participants who lost the most weight (n = 5 individuals per time point; mean ± s.e.m.). c, Significant differences in bile acid levels between baseline and VCLD phases in these individuals implicate altered bile acid profiles in permissibility to C. difficile (n = 5 individuals per time point). a–c, LMM with Tukey’s two-sided all-pair comparison. d, Working model for the complex interactions between caloric restriction, the gut microbiome, and C. difficile. We propose that caloric restriction decreases host production of primary bile acids, including cholic acid, while also lowering total gut microbial colonization and altering the gut microbial community structure. Together, these effects lead to decreased production of the C. difficile-inhibitory deoxycholic acid, which allows expansion of C. difficile, which, in turn, disrupts host energy balance. Notably, our data also support the existence of C. difficile-independent mechanisms for weight loss owing to the restructuring of the gut microbiome following caloric restriction. e, Representative culture plate showing presumptive C. difficile colonies with characteristic yellow appearance and filamentous edges.