The use of modern sequencing methods enables us to determine the taxonomic biodiversity of various bacterial communities. Specifically, it allows to assess the diversity of bacterial strains that are not cultured. At present, there are two generations of sequencing technologies that enable the determination of microbial community diversity: 2nd generation (represented by Illumina and BGI) and 3rd generation (Nanopore and PacBio). However, as these technologies use different approaches to sequencing, there is a question of reproducibility of the results. This research revealed that using Illumina and Nanopore sequencing methods differs in terms of diversity indices and taxonomic diversity. This data emphasizes the requirement to develop advanced methods for sample preparation and DNA sequencing to achieve an unequivocal microbial community profile.