Description:To investigate the functional changes of gut microbiota, we collected feces (2-3 pellets) from Sle1.Yaa lupus-prone mice treated with Faecalibacterium prausnitzii strain UT1 versus PBS (every other day for 3 months). The untargeted fecal metabolomes of the two groups of mice were analyzed by LC-MS. Data demonstrated that UT1 treatment induced profound metabolic changes of the gut microbiota, leading to sustain activities of pentose phosphate pathway and tryptophan metabolism. These data were integrated with metagenomics and metatranscriptomics data of the same fecal samples to correlatively elucidate the functional programming of the microbiota by probiotic UT1 bacterium.