Small intestine is not colon: a new in vitro model of the human ileum microbiome integrating the mucosal microenvironment and feeding status

The small intestinal microbiota plays a key role in human health but is understudied due to the invasiveness of sampling. There is no available model of the human ileal microbiome simulating the key nutritional and physicochemical parameters shaping this ecosystem, which has been fully validated based on in vivo data. Here, the Mucosal Artificial Ileum (M-ARILE) was set up to reproduce the pH, transit time, anoxic conditions, dynamics of feeding and microenvironments (luminal versus mucosal) found in a healthy human mid-ileum. To validate the newly developed in vitro system, nine-day fermentations were performed under either ileal or colonic conditions using the same fecal inoculum (n = 3 adult volunteers). The gut microbiota composition and metabolic activities were monitored daily. Distinct microbial signatures and metabolite profiles were obtained between in vitro ileum and colon conditions. In accordance with in vivo data, Peptostreptococcaceae, Clostridiaceae and Enterococcaceae were enriched in the ileum and associated with lower short-chain fatty acid production but higher O₂ percentages. Interestingly, the abundances of key populations, such as Akkermansiaceae, and bile acid profiles were dependent on the feeding status of the M-ARILE. This new model provides a powerful platform for mechanistic studies on the role of ileal microbes in human nutrition and health considering inter-individual variabilities.