Comparative analysis of the gut microbiota cultured in vitro using a single colon versus a 3-stage colon experimental design

The importance of the gut microbiota in human health, and its association with the progression of disease, makes it a target for research in both the biomedical and nutritional fields. To date, a number of in vitro systems have been designed to recapitulate the gut microbiota of the colon that range in complexity from the application of a single vessel to cultivate the community in its entirety, to multi-stage systems that mimic the distinct regional microbial communities that reside longitudinally through the colon. While these disparate types of in vitro designs have been employed previously, information regarding the similarities and differences between the communities that develop within was less defined. Here, a comparative analysis of the population dynamics and functional production of short chain fatty acids was performed using the gut microbiota of the same donor cultured using a single vessel and a 3-stage colon system.