Abstract
BACKGROUND: Preclinical literature and behavioral human data suggest that diet profoundly impacts the human gut microbiome and energy absorption-a key determinant of energy balance. To determine whether these associations are causal, domiciled controlled feeding studies with precise measurements of dietary intake and energy balance are needed. Metabolomics can serve as a readout of microbiome function, helping to identify putative mechanisms mediating these effects. We previously demonstrated that a high-fiber microbiome enhancer diet (MBD) limited in processed foods and fed at energy balance decreased energy absorption and increased microbial biomass relative to a calorie-matched, fiber-poor, highly processed Western diet (WD). OBJECTIVES: We aimed to identify metabolomic signatures distinguishing MBD from WD feeding and potential mechanisms mediating the MBD-induced negative energy balance. METHODS: We deployed global metabolomics in feces, serum, and urine using samples collected at the end of a randomized crossover controlled feeding trial delivering 22 d of an MBD and a WD to 17 persons without obesity. Samples were collected while participants were domiciled on a metabolic ward and analyzed using ultra-HPLC-tandem mass spectroscopy. Linear mixed-effects models tested metabolite changes by diet. Weighted gene network correlation analysis identified metabolite modules correlated with energy balance phenotypes. RESULTS: Numerous metabolites were consistently altered by MBD relative to WD feeding in the feces, fasting serum, and urine. Fecal diet-microbiota cometabolites decreased by an MBD correlated with reduced energy absorption and increased microbial biomass. An MBD shifted the urinary metabolome from sugar degradation to ketogenesis-evidence of negative energy balance. CONCLUSIONS: Precisely controlled diets disparate in microbiota-accessible substrates led to distinct metabolomic signatures in feces, fasting serum, and/or urine. These diet-microbiota cometabolites may be biomarkers of a "fed" (MBD) or "starved" (WD) gut microbiota associated with energy balance. These findings lay the foundation for unveiling causal pathways linking diet-microbiota cometabolism to energy absorption. This trial was registered at clinicaltrials.gov as NCT02939703 (https://clinicaltrials.gov/study/NCT02939703?term=NCT02939703&rank=1).