A Comparison of the Response of the Human Intestinal Microbiota to Probiotic and Nutritional Interventions In Vitro and In Vivo—A Case Study

Background/Objectives: With increasing knowledge of the role of the microbiota in health and disease, the need for the reliable simulation of its behavior in response to various factors, such as diet and probiotic administration in in vitro conditions, has emerged. Although many studies utilize developed systems, data on how accurately these systems represent individual microbiota responses are scarce. Methods: In the present study, the Simulator of Human Intestinal Microbial Ecosystem (SHIME®) was exposed to experimental conditions mimicking the application of probiotics and dietary changes in the study participant. Next-generation 16S rRNA sequencing was used to reveal the structure of the microbial communities in the analyzed samples. Results: Analysis of 17 samples revealed that predominantly diet and, to a lesser extent, probiotics had a divergent effect on the microbiota’s fluctuations dependent on the culture environment. Despite this, results from both in vitro and in vivo conditions aligned well with previously published data on the expected impact of dietary changes on the intestinal microbial community. Conclusions: The anecdotal evidence presented in this study suggested that current in vitro technology enables the reproduction of some of the microbiota responses that are well known from in vivo research. However, further work is required to enable simulations of an individual microbiota.