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Periodontal diseases are considered to be among the most prevalent diseases (up to 95%) in patients of dental clinics. The involvement of the oral microbiota in the development of this pathology, the insufficient number of studies of the state of the oral cavity and colon microbiocenoses in periodontitis, as well as the potential therapeutic benefits of probiotics in the in prevention and treatment of periodontitis have determined the relevance of this work. The objective of the present study was to investigate in-depth the oral cavity and colon microbiota of patients with chronic generalized periodontitis and to develop an algorithm of the use of probiotic dietary supplement probiotic complex of bifidobacteria and lactobacilli based on 6 strains belonging to the species Bifidobacterium bifidum, Bifidobacterium longum, Lactobacillus plantarum, Lactobacillus fermentum on enterosorbent zeolite in the combined therapy of periodontal diseases. To study the species composition of the microbial communities of these loci, we used a bacteriological method for isolating pure cultures, followed by the identification of microorganisms by MALDI TOF mass spectrometry. The hygiene index, the Muhleman bleeding index, and the associated periodontal index were used for clinical assessment of the periodontal condition. To correct the microbiota in both biotopes, the author’s probiotic containing Lactobacillus and Bifidobacterium species immobilized on zeolite was used. As a result of the conducted research, we discovered, identified and determined the count of a wide range of oral bacteria, including periodontopathogens, such as orange complex bacteria: in 10.3% of patients Prevotella nigrescens in the amount of 10 3-10 7 CFU/ml, in 45.8% - Fusobacterium nucleatum in an amount of 10-1 -10.5 CFU/ml. It was found that chronic generalized periodontitis of moderate severity is accompanied by pronounced (48.5%) and most pronounced (25%) oral microbiota dysbiosis as well as dysbiotic changes in the colon of the first (50%) and second (33.3%) degrees. After the treatment according to our proposed algorithm, we recorded an improvement in clinical (decreased bleeding, good hygiene) and microbiological parameters in the main group - the typical orange complex periodontopathogens ceased to be isolated, normalization of the microbiocenoses of the oral cavity and colon occurred in 73.5% cases versus 15.7% in the comparison group. The proposed therapy method is protected under patent No. 2789345 dated 02.01.2023 “Method of treatment of chronic generalized periodontitis of moderate severity in patients with comorbid pathology”.