Quantitative differences in synthetic gut microbial inoculums do not affect the final stabilized in vitro community compositions Raw sequence reads
In vitro studies of synthetic gut microbial communities (SGMCs) can provide valuable insights into the ecological structure and function of gut microbiota. However, the importance of quantitative composition of an SGMC inoculum and its effect on the eventual stable in vitro microbial community have not been studied. To address this, we constructed two 114-member SGMCs differing only in their quantitative composition - one reflecting average human fecal microbiome and another mixed in equal proportions. We inoculated each in an automated anaerobic multi-stage in vitro gut fermentor simulating two different colonic conditions mimicking proximal and distal colons. We replicated this set up with two different nutrient media, periodically sampled the cultures for 27 days and profiled their microbiome compositions using 16S rRNA gene amplicon sequencing. While nutrient medium explained 36% of the variance in microbiome composition, initial inoculum composition failed to show a statistically significant effect. Under all four conditions, paired fecal and equal inoculums converged to reach stable community compositions resembling each other. Our results have broad implications in simplifying in vitro SGMC investigations.