1 | INTRODUCTION
The gut microbiota is a diverse and complex community of bacteria, archaea, fungi and viruses. The characteristics of its species composition and function have garnered great interest of researchers in recent years. The microbial community is an integral part of the gastrointestinal tract as it provides the host with an extended set of metabolic, structural and protective functions (O’Hara & Shanahan, 2006). In recent times, dysbiosis of the gut microbiota has been associated with a variety of diseases, such as inflammatory bowel diseases, diabetes, obesity, cancers, and even some behavioral disorders (Musso et al., 2011; Manichanh et al., 2012; Zhu et al., 2013; Vuong et al., 2017). It is now accepted that the gut microbiota has a strong influence on host health.
Due to the complex nature of the host-microbial interaction, it is difficult to infer specific mechanistic aspects of this interaction using conventional in vivo models and thus highlights the need for facile in vitro systems to help understand the complex interactions between the host and its gut microbiota (de Vos & de Vos, 2017). The currently available in vitro gut models vary in their complexity (Molly et al, 1993; Minekus et al., 1999; Makivuokko & Nurminen, 2006; Payne et al., 2012; Tanner et al., 2014; Moon et al., 2016; Card et al., 2017; von Martels et al., 2017; Dupont et al., 2019). Batch culture models are simple closed fermentation systems, that usually operate for less than two days. In continuous culture models, which might be single or multi-stage in design, fresh culture medium, supplemental growth factors or any other additives, are added continuously, while wastes and toxic byproducts are prevented from accumulating excessively by continuous dilution of the spent medium with fresh culture medium (Moon et al., 2016). The addition of fresh medium can be scheduled at specified time intervals as in the semi-continuous model EnteroMix (Makivuokko & Nurminen, 2006), or continuously supplied as in the Simulator of the Human Intestinal Microbial Ecosystem (SHIME) model (Molly et al, 1993). Some models, such as the TNO Gastro-Intestinal Model TIM1 and TIM2 systems (Minekus et al., 1999), permit simulation of intestinal tract processes like digestion and absorption. Other models permit incorporation of intestinal tissues by employing co-culturing techniques (von Martels et al., 2017). Different gut models have been developed for in vitro study of complex microbial communities associated with various physiological and pathological states, or from the digestive tracts of humans and animals (Tanner et al., 2014; Card et al., 2017).
Since most of the in vitro gut models in existence were designed to simulate a specific digestive tract or condition, their designs inherently make it difficult to study different conditions or applications using the one device. Here we describe the design and implementation of a modular bioreactor. The novel bioreactor design serves as a new platform that features unparalleled functional flexibility for the culturing of mono- and mixed bacterial cultures in vitro. In particular, the bioreactors can operate either as single static batch cultures or connected in series to dynamically simulate the environments of the various segments of the gastrointestinal tract.