The Simulator of Human Microbial Ecosystem (SHIME) is used across the literature to study the response of human microbiota to various interventions. However, studies comparing the behaviour of the microbiota of a given person in the simulator and in its natural environment are very scarce. Here, we have run a parallel experiment where a 39-year-old female volunteer who donated a sample of feces for SHIME and the microbiota established in the simulator was subjected to dietary and probiotic intervention. Although collected data showed that shifts in the microbial community differed depending on whether it was cultured in vitro or in vivo, all recorded changes were typical of those reported in the earlier literature. Thus, the utility of the SHIME system as a reliable platform to study the fate of human microbiota was confirmed once more. On the other hand, a growing interest in precision nutrition research points to a need for developments that would allow studying the response of an individual microbiota in vitro. Detailed data description was contained in the Readme File.txt. This research was funded by the National Science Centre, Poland 2021/05/X/NZ4/01613. This dataset was used for the needs of a publication entitled "Comparison of the response of the human intestinal microbiota to probiotic and nutritional intervention in vitro and in vivo"