In vitro modeling of colonic fermentation, challenges and solutions

Abstract: A complex relationship occurs in the intestine between the gut microbiota, the diet, and the host. Different in vitro and in vivo strategies have been applied to elucidate mechanisms or functions of dietary compounds on the gut microbiota, health, and physiology of humans. In vitro gut fermentation modeling has gained momentum in recent years as a powerful strategy to isolate and investigate factors of the gut microbiota, independent of the host (1). In vitro models allow the application of a highly controlled environment and the study of mechanistic effects of dietary, microbial, drug and physiological factors on gut microbiota at levels that cannot be reached in in vivo setup. In vitro models are particularly well suited for screening, for example, prebiotics or probiotics for special functions in the gut, before moving to in vivo investigation s of effective conditions, while reducing in vivo animal testing. The human colon is inhabited by a multitude of multitude of mostly strict anaerobic microbes. A range of systems have been developed to model fermentation of the colon, which harbors the highest density of microbes: from simple anaerobic batch culture systems in flasks to multistage continuous flow models, which are different with respect to conditions and output (2). Selection of the most suitable model should be done carefully, considering their features and limits in relation with the scientific question addressed. In particular, most models do not reproduce the sessile state bacterial populations in the colon and do not reach bacterial density and microbial competition akin to the gut. To solve these limits we developed a process of fecal microbiota immobilization in polysaccharide beads. Different continuous intestinal fermentation models of the PolyFermS platform inoculated with fecal beads were set for mimicking healthy and diseased human gut microbiota (from young infant to elder) (3). PolyFermS models expanded to various configurations for different colon sections, allow the accurate comparison of treatments with a parallel control in blocked experiments (4). Features of the PolyFermS model platform, eventually combined with cellular models, will be illustrated in mechanistic studies and for cultivating and profiling gut microbiota.