Using the SHIME (an in vitro simulator of the human gut microbiome) we studied changes in the gut metabolome that occurred in response to the administration of the Laticaseibacillus rhamnosus strain GG (LGG). Using fecal inoculum from three healthy human donors, reactors were established representing three colonic regions and both the luminal and mucosal microbiome in those regions. Samples were collected before, during, and after inoculation of the reactors with LGG. This dataset includes untargeted metabolomics data. Shallow shotgun metagenomic sequencing data can be found in the NCBI Sequence Read Archive associated with BioProject PRJNA893635 : https://www.ncbi.nlm.nih.gov/bioproject/PRJNA893635. Resources in this dataset: Resource Title: Batch normalized metabolite peak area data File Name: metabolites_individual_samples_batch_norm_non_imputed.csv Resource Title: Sample metadata File Name: LGG2_metadata.csv

Using the SHIME (an in vitro simulator of the human gut microbiome) we tracked the fate of the probiotic Lacticaseibacillus rhamnosus GG (LGG) over time and across colonic regions. Using fecal inoculum from three healthy human donors, reactors were established representing three colonic regions and both the luminal and mucosal microbiome in those regions. Community composition before, during, and after inoculation of the reactors with LGG as well as short chain fatty acid concentrations representing microbiome metabolic outputs. This dataset includes short-chain fatty acid concentrations and qPCR-based cell concentrations. Raw 16S rRNA amplicon sequencing of the V1-V2 regions can be found in the NCBI Sequence Read Archive associated with BioProject PRJNA893635: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA893635. Resources in this dataset: Resource Title: Short Chain Fatty Acid concentrations File Name: LGG_SCFA_data.csv Resource Title: LGG qPCR concentrations File Name: LGG_qPCR_data.csv Resource Title: Sample metadata File Name: LGG_16S_metadata.csv