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Introduction . The concept of heterogeneity in obesity depending on the risk of developing cardiometabolic complications has garnered attention in recent decades, since not everyone with obesity goes on to develop metabolic dysfunction. The aim of the work is to study specific characteristics of colonic microbial communities in patients with different obesity phenotypes and in healthy individuals by employing metagenomics methods. Materials and methods . A total of 265 individuals (44 men and 221 women; mean age 47.1 ± 4.8 years) were enrolled in the study. They were further divided into clinical groups: Healthy normal-weight individuals (n = 129); patients with obesity (n = 136), including metabolically healthy obesity (n = 40) and metabolically unhealthy obesity (n = 55). Quantitative and qualitative assessment of the intestinal microbiome was based on metagenomic analysis. Fecal samples were used to isolate DNA and perform sequencing of the variable v3-v4 region of the 16S rRNA gene. Results . The study revealed statistically significant (p < 0.05) differences between quantitative and qualitative variables in studied phylotypes of colonic microorganisms in healthy individuals without obesity and in patients with different obesity phenotypes. Discussion . Patients with obesity had higher levels of Bacteroidetes, Proteobacteria and lower levels of Actinobacteria, Firmicutes, TM7 (Saccharibacteria), Fusobacteria, and more frequently detected phyla Tenericutes, Planctomycetes and Lentisphaerae compared to healthy individuals. Metabolically healthy obese patients had more rarely detected phylum Lentisphaerae in their colonic microbiome, increased numbers of Firmicutes and reduced numbers of Bacteroidetes compared to metabolically unhealthy obese patients. Conclusion . The findings demonstrate alterations in the colonic microbiome in patients with different obesity phenotypes.