Plasma and fecal samples assayed for acylcarnitine levels as well as rectal biopsies for colonoid primary cell line generation were obtained from the Food and Resulting Microbial Metabolite (FARMM) study (47). The FARMM study recruited healthy volunteers ages 18–60. Stool, urine, blood, and rectal biopsies were collected throughout the 15-day inpatient study designed to determine the impact of diet on the gut microbiome, fecal, and plasma metabolome. The samples used for this study were obtained at the baseline timepoint at the beginning of the study. The fecal metabolomic analysis in pediatric CD, shown in Figure 7 and Supplemental Figure 6, was performed as part of the PLEASE study that has been previously described (34). Briefly, stool samples from pediatric patients with CD and healthy controls were used for a prospective cohort study to assay metabolites such as acylcarnitines and measure calprotectin and human DNA. Both the FARMM and PLEASE studies received approval from the University of Pennsylvania IRB.

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