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Intestinal microbiota confers susceptibility to diet-induced obesity yet many probiotic species that synthesize tryptophan (trp) actually attenuate this effect, however the underlying mechanisms are unclear. We monocolonized germ-free (GF) mice with a widely consumed probiotic Lacticaseibacillus rhamnosus GG (LGG) under trp-free or -sufficient dietary conditions. We obtained untargeted metabolomics from the mouse feces and serum using liquid chromatography-mass spectrometry and obtained intestinal transcriptomic profiles via bulk-RNA sequencing. When comparing LGG-monocolonized mice with GF mice, we found a synergy between LGG and dietary trp in markedly promoting the transcriptome of fatty acid metabolism and -oxidation. Upregulation was specific and was not observed in transcriptomes of trp-fed conventional mice and mice monocolonized with Ruminococcus gnavus. Metabolomics showed that fecal and serum metabolites were also modified by LGG-host-trp interaction. We developed an R-Script based MEtabolome-TRanscriptome Correlation Analysis (METRCA) algorithm and uncovered LGG- and trp-dependent metabolites that were positively or negatively correlated with fatty acid metabolism and -oxidation gene networks. This high throughput metabolome-transcriptome correlation strategy can be used in similar investigations to reveal potential interactions between specific metabolites and functional or disease-related transcriptomic networks.