Possible applications of the Simulator of Human Microbial Ecosystem (SHIME) have been broadly discussed in the literature. However, so far, its reliability in providing data on the microbiota diversity mirroring humans has not been evaluated in detail. Our study aimed to provide sequencing data in order to allow such evaluation. A human (donor of a faecal microbiota sample for SHIME) was subjected to dietary (28 days) and probiotic (14 days) intervention in parallel with the system. Samples of microbiota from SHIME: both luminal and mucosal setup and faeces were collected and sequenced. We have found a rather low resemblance of the microbiota between SHIME (regardless of mucosal or luminal setups) and the donor. This could have been caused by several factors of which, probably most significant were the use of a standard protocol for the initial stabilisation of microbiota in SHIME and discrepancies between food residues that could reach the colon of a human and SHIME. The relative abundance of Lactobacillus sp. was low and hence, probiotic Lactobacillus rhamnosus GG, contained in the intervention did not consistently appear in SHIME and human microbiota samples throughout 14 days of the supplementation. 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 publication entitled "CHANGES IN THE MICROBIOME OF A HUMAN AND IN THE SIMULATOR OF HUMAN INTESTINAL MICROBIAL ECOSYSTEM (SHIME®) IN RESPONSE TO A DIET AND PROBIOTIC SUPPLEMENTATION " DOI: 10.15193/zntj/2023/134/437