The Mini Colon Model (MiCoMo): a benchtop multi-bioreactor system to investigate the gut microbiome

In vitro fermentation systems allow for the investigation of gut microbial communities with precise control of various physiological parameters while decoupling confounding factors from the human host. Current systems, such as the SHIME and Robogut, are large in footprint, lack multiplexing, and have low experimental throughput. Alternatives which address these shortcomings, such as the Mini Bioreactor Array system, are often reliant on expensive specialized equipment, which hinders wide replication across labs. Here, we present the Mini Colon Model (MiCoMo), a low-cost, benchtop multi-bioreactor system that simulates the human colon environment with physiologically relevant conditions. The device consists of triplicate bioreactors working independently of an anaerobic chamber and equipped with automated pH, temperature, and fluidic control. We conducted 14-day experiments and found that MiCoMo was able to support a stable complex microbiota community from individual fecal samples after only 3-5 days of inoculation. MiCoMo also retained inter-sample microbial differences by developing closely-related communities unique to each donor, while maintaining both minimal variations between replicate reactors and day-to-day variations after this short stabilization period. Together, these results establish MiCoMo as an accessible system for studying gut microbial communities with high throughput and multiplexing capabilities.