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Introduction. Probiotics are well-known adjuvants, used as complementary therapeutic agents in health (e.g. gastrointestinal or metabolic) disorders, considering their beneficial role on gut microbiota, and their support in immunity. The objective of the study was to evaluate the impact of probiotic supplementation on abundance of Bacteroides spp. in intestinal microbiome of patients with Crohn’s disease (CD). Materials and methods. The comparative evaluation was conducted over a 6-month period, on 49 subjects diagnosed with CD, who were separated into two groups, as follows: the study group (probiotics associated with allopathic treatment) and the control group (only allopathic treatment). All patients were evaluated at baseline and at 6 months. Demographic characteristics, associated pathology, and the evolution of intestinal microbiome and faecal pH were followed. Results. In this research, the microbiome of patients with CD showed changes in the abundance of bacterial species. The combination of probiotic treatment led to the following changes: Escherichia coli ​(from 5.77×107 to 4.15×107, p=0.006) and Enterobacter spp. ​(from 1.92×104 to 1.17×104, p=0.009) values decreased significantly and Faecalibacterium prausnitzii (from 3.73×108 to 4.55×108, p=0.003), Bifidobacterium spp. (from 4.76×106 to 4.92×106, p