Fecal Inocula in a Chemostat-Based Gut Model Culture Developed into Three Subsets of Gut Microbes, Forming a Pseudo-Ecosystem

A stable gut microbial community (SGMC) created by the culture of fecal samples in a chemostat-based gut model is a physiologically relevant, reproducible tool for ecological research on the gut microbiome. It is also a subject of continuous improvement for the model to better mimic the in vivo system. In this research, compositions of fecal homogenates and the derived SGMC were analyzed based on shotgun metagenomic sequencing. It was found that taxa in the fecal inocula could be divided into resilient or sensitive types according to their response to environmental factors; taxa were sorted into three subsets—shared, emerged, and lost—by how they were represented in the established communities. The first two subsets consisted of resilient species, constituting an SGMC, which was suitable for long-term, ecological research. In contrast, species of the lost subset were sensitive to the new environmental conditions and were missing from the SGMC. However, these lost species may carry host-dependent information that is useful or even critical for drug and functional foods development or nutrition research. The differentiation between the three subsets reveal the community shift and metabolic profile along with SGMC formation and could serve as a diagnosis for understanding the extent to which the SGMC mimics, or differs from, the actual ecosystem in vivo or the donor’s fecal samples, which may be useful in work to upgrade in vitro models.