The intestinal microbiota has recently become the focus of research and is credited with numerous positive effects on human health. In addition, the microbial population of the lower gastrointestinal tract is increasingly associated with the etiology of various diseases such as Clostridium difficile infection, inflammatory bowel disease and obesity. To treat such pathological conditions, fecal microbial transplantation has recently been used as an alternative to already established methods of treatment. Given the numerous shortcomings of fecal transplantation, the aim of this study was to cultivate the intestinal microbiota in vitro and compare it with the native feces from which it originates (inoculum) in order to determine whether it is possible to obtain a stable and sufficiently diverse community of microorganisms in such controlled conditions. Alpha and beta diversity as well as the taxonomic profile of the intestinal microbiota of the samples were determined by 16S rRNA sequencing and data processing was performed using the QIIME 2 program. According to the results of this work, a decrease in the bacterial diversity of fecal samples cultivated in the bioreactor and changes in the taxonomic representation of bacterial species compared to the inoculum were observed. Nevertheless, in vitro cultivation of fecal samples could serve as a basis for fecal microbial transplantation treatment with additional research required.