Although known to play a vital role in nutrient digestion and absorption and immune function, the small intestinal microbiota (SIM) is often overlooked due to difficulty accessing the anatomical site and known variability between donors. In this study, an in vitro model of the SIM was designed and used to develop the microbiota of four unique donors. Shotgun sequencing was used to determine community structure and genomic representation. Short chain fatty acid (SCFA) analysis, bile acid quantification, and untargeted metabolomics were combined to determine community function. Combining the results of metagenomics and metabolomics revealed that despite variation in taxonomic structure there was a core set of genes shared among the communities that correlated with a relatively consistent metabolomic signature.
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