The experimental design of the animal study and the sanitary challenge model used have been described by Van der Meer et al. (2020). Pigs were divided into high sanitary condition (HSC) or to low sanitary condition (LSC), for details please see the original publication by Van der Meer et al. (2020). At the dissection day, three pigs per room were euthanized to collect blood and digesta samples for further analysis. We used colon digesta and blood samples from pigs in this study that received a diet with a basal amino acid (AA) ratios (indicated as “diet AA-B” in the paper of van der Meer et al. 2020) and a protein content of CP 168 g/kg; LSC (n=18) and HSC (n=18). These samples were analyzed by Nuclear Magnetic Resonance (NMR) and by Triple Quad Mass Spectrometry (TQMS). The details of these laboratory analysis are described in the journal article entitled "Sanitary conditions affect the colonic microbiome and the colonic and systemic metabolome of female pigs" (doi: will update accordingly). The data uploaded here are by the format of the Joint Committee on Atomic and Molecular Physical Data (JCAMP). Moreover the metadata file shows the link between the samples and their corresponding group, i.e. HSC or LSC, and other characteristics.