Multi-targeted polar metabolomics data from murine fecal samples is included. Data is in the form of normalized signal intensities Data was filtered via a missing value of 50 % cut-off and a coefficient of variance on the QC samples of 30 % or lower. Data was total sum normalized to and auxillary datasets were stitched to the core dataset via shared signals for metabolites. Further information, incuding methods references, can be found in the associated manuscript.