An in vitro model of the small intestinal microbiota provides key insights into interindividual variability in structure and function.

UNLABELLED: Although there is clear evidence demonstrating the importance of the small intestinal microbiota (SIM) for nutrient utilization within the upper gastrointestinal tract, research is limited by difficulties accessing this community in vivo. Additionally, the high level of interindividual variability in taxonomic structure, which is well documented for the SIM, raises the question of how such divergent communities fill the same physiological roles. Here, we designed and evaluated an in vitro model of the terminal ileum representative of four unique donors and utilized it to interrogate interindividual variability. Shotgun sequencing confirmed that the in vitro communities were representative of their specific inocula and composed of facultative and obligate anaerobic taxa typical of the SIM, such as Klebsiella, Escherichia, Streptococcus, and Enterococcus. Untargeted metabolomics revealed a high degree of similarity between communities in terms of which metabolites were produced. Combining metagenomics and metabolomics, a core set of genes, features, and metabolites was found shared across all communities despite the high degree of structural variability observed. These results indicated that while the taxonomic structure of the SIM was variable between individuals, there were similarities in functional outcome due to underlying gene representation in the microbiome. Moving forward, this model system may serve as a starting point to further elucidate the role of the SIM in nutrition and health.

IMPORTANCE

The small intestinal microbiota (SIM) plays a pivotal role in nutrient digestion and absorption and immune function, with researchers continuing to find connections between this community and human health. Expanding on the currently available methods within the field to study this community, here, an in vitro model of the SIM was developed and designed to mimic the terminal ileum. Metagenomic and metabolomic analysis confirmed that this model recapitulated the unique communities of four different donors while maintaining the interindividual variability canonical of the SIM. Despite variation in taxonomic structure, in-depth analysis found that there was a core set of genes shared among the four in vitro communities that correlated with a relatively consistent metabolomic signature. These significant findings provided unique insight into the relationship between structural and functional variability for the SIM and furthered the field's understanding of how such structurally variable communities have such similar physiological outcomes.