Physical complexity shapes the abundance and diversity of organisms in a community. One model system for studying the role of physical complexity is the mammalian gastrointestinal (GI) tract, which contains trillions of bacteria that prime the immune system, prevent pathogen colonization, and synthesize vitamins essential for nutrition. Two aspects of physical complexity likely important to the GI tract are residence time, or the time particles spend in a system, and habitat structure, or the abundance and diversity of folds, crypts, and villi in the gut, yet little is known about how they influence the ecology of the gut microbiome. We developed stochastic individual-based models (IBMs) to explore how aspects of gut physical complexity affected the abundance, diversity, and productivity of host microbiomes. To test our model predictions, we propose a novel 3D printed system of gut bioreactors to examine how physical characteristics of the GI tract (i.e., habitat structure, residence time) influence the diversity, functioning, and stability of host-associated microbiomes.
Results/Conclusions
We have developed a gut bioreactor model using computer-aided design (CAD) based on a sine-wave design. This bioreactor model can be easily modified to change dimensions and geometry of these bioreactors (e.g., volume, length, diameter) as well as degrees of folding and villi that characterize another aspect of physical complexity of a gut segment. We iteratively improved our design to allow sampling of outflow and biofilm formation within the bioreactors. We have also 3D printed these bioreactors with varying levels of habitat structure and have fed the bioreactors a GI medium. This GI medium is controlled by a multi-channel peristaltic pump, which is used to supply the bioreactors with an immigrant microbial population. Preliminary results reveal that abundance of the bioreactors reached a steady state, and this steady state abundance varies between levels of physical complexity. Our findings suggest that we can use this 3D printed bioreactor system to address questions of the role that physical complexity plays in community composition, function and structure of gut microbiomes.