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

An in vitro model of the terminal ileum was designed and evaluated as representative of four unique donors to study the small intestinal microbiota.

• The model was specifically designed to mimic the terminal ileum environment.
• Four unique donors were used as inocula to capture interindividual variability canonical of the SIM.
• The model system was evaluated for its ability to recapitulate the unique communities of each donor.
• The study positioned this model as a starting point to further elucidate the role of the SIM in nutrition and health.

Shotgun sequencing confirmed that the in vitro communities were representative of their specific inocula and composed of taxa typical of the small intestinal microbiota.

• Metagenomics confirmed the in vitro communities recapitulated the unique communities of four different donors.
• The communities were composed of facultative and obligate anaerobic taxa typical of the SIM.
• Characteristic taxa identified included Klebsiella, Escherichia, Streptococcus, and Enterococcus.
• Interindividual variability in taxonomic structure was maintained across the four in vitro communities.

Untargeted metabolomics revealed a high degree of similarity between the four in vitro communities in terms of which metabolites were produced.

• Metabolomic analysis was performed using an untargeted approach.
• Despite divergent taxonomic structures across donors, the metabolomic signatures were relatively consistent.
• A core set of metabolites was found shared across all communities despite the high degree of structural variability observed.
• The similarity in metabolomic output was observed across all four donor-representative communities.

A core set of genes, features, and metabolites was identified as shared across all four in vitro communities despite high taxonomic structural variability.

• Combined metagenomics and metabolomics analysis was used to identify the core shared elements.
• The core set included shared genes, metabolomic features, and metabolites.
• The core gene representation in the microbiome was identified as the underlying explanation for similar functional outcomes.
• These findings indicated that while taxonomic structure was variable between individuals, there were similarities in functional outcome due to underlying gene representation.

The high level of interindividual variability in taxonomic structure of the small intestinal microbiota does not preclude similar physiological functional outcomes.

• The study addressed the question of how divergent communities fill the same physiological roles.
• Structural variability was high across the four donor communities, consistent with what is well documented for the SIM in vivo.
• Functional similarity was attributed to underlying gene representation shared across structurally different communities.
• The findings provided 'unique insight into the relationship between structural and functional variability for the SIM.'

Research on the small intestinal microbiota is limited by difficulties in accessing this community in vivo, motivating the development of in vitro models.

• The SIM plays a pivotal role in nutrient digestion and absorption and immune function.
• Researchers continue to find connections between the SIM community and human health.
• High interindividual variability in taxonomic structure is well documented for the SIM.
• The in vitro model was developed to expand on currently available methods within the field to study this community.