Development of a dynamic in vitro Food Digestion SIMulator (FooDSIM) - A platform for studying synthetic gut microbiota dynamics.

In vitro digestion and fermentation model systems are invaluable tools for understanding the complexities of human digestion outside the body, offering critical insights into gastrointestinal processes and advancing research in human health. Despite their importance, many existing in vitro digestion and fermentation systems are proprietary and inaccessible for academic research, creating a gap in the availability of open-access, reproducible tools. To address this gap, this study introduces FooDSIM, a dynamic in vitro digestion and fermentation model system specifically designed for academic research. FooDSIM consists of four linked bioreactors in series representing the stomach, upper small intestine, lower small intestine, and colon, each simulating the key physicochemical parameters of the corresponding regions of the human gastrointestinal tract. In this study, the lower small intestine and colon compartments were inoculated with a defined gut microbiota consortium, and the system was operated for 12 days. Microbial stability, as indicated by consistent cell density, and functional stability, measured by acetate production, were achieved after 5 days of operation. Reproducibility of results was confirmed through three independent biological replicates, demonstrating consistent microbial dynamics and acetate production across runs. In conclusion, FooDSIM replicates critical physicochemical parameters of the gastrointestinal tract while producing reproducible microbial and functional results. By providing an open-access, dynamic in vitro digestion and fermentation system, FooDSIM addresses the need for accessible tools in academic research, paving the way for future studies on gut microbial behaviour and host-microbe interactions.