The limitations surrounding the mechanistic study of the gut ecosystem have motivated the development and use of multiple in vitro models. These models include batch cultures and bioreactors that simulate some of the features of the gut environment, which can open access to the microbial “dark matter”. Multiple bioreactors capable of sustaining reproducible microbial communities have been developed. However, there is a lack of studies describing and comparing the microbial diversity cultivated in these devices.
We describe and compare the microbial diversity of 1,619 samples from 19 studies in which batch cultures and various bioreactor models were used to cultivate faecal microbiota. The comparison of the community structure between samples (β-diversity) using t-SNE and the Hellinger distance showed that the community structure differed between projects. The main driver of these differences was the inter-individual variation between the donor faecal inocula. Studies with more than one donor showed higher variations than those with pooled samples. Moreover, there was no overlap between the microbial profiles of samples from studies that used the same bioreactor model.
In addition, the diversity profiles based on Hill numbers of the samples within the projects (α-diversity) showed that the diversity inside highly complex bioreactors was not higher than that found in more simple designs. Nevertheless, further analyses of the samples of five projects showed Amplicon Sequence Variants (ASVs) enrichment in the bioreactors compared to the faecal inoculum. Finally, a comparative analysis of the taxonomy of the families detected in the projects and those observed in the GMRepo database revealed 30 families only found in the bioreactor models, highlighting the potential of bioreactors to enrich the presence of low-abundance microorganisms and to evaluate their contribution to unveiling the gut microbial “dark matter”.