Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 12 3 2020 05 29 231 241 Yuliia Bukina Department of Microbiology, Virology and Immunology, Zaporizhzhya State Medical University, Zaporizhzhya, Ukraine Marina Thyhonovska Department of Normal Physiology, Zaporizhzhya State Medical University, Zaporizhzhya, Ukraine Mariya Koval Department of General Chemistry, I. Horbachevsky Ternopil National Medical University, Ternopil, Ukraine Mariya Marushchak Department of Functional and Laboratory Diagnostics, I. Horbachevsky Ternopil National Medical University, Ternopil, Ukraine Inna Krynytska Department of Functional and Laboratory Diagnostics, I. Horbachevsky Ternopil National Medical University, Ternopil, Ukraine Aleksandr Kamyshnyi Department of Microbiology, Virology and Immunology, Zaporizhzhya State Medical University, Zaporizhzhya, Ukraine 2020 01 21 2020 05 06 Background and Objectives: Intestinal microbiota is involved in the development and maintenance of immune homeostasis. This study was conducted to investigate the levels of key immunoregulatory bacteria in the intestinal wall-associated microflora and its effect on the transcriptional activity of the Foxp3 and RORyt genes in the gut-associated lymphoid tissue (GALT) of rats with Salmonella-induced inflammation, both untreated and treated with vancomycin and Bacteroides fragilis. Materials and Methods: To determine the levels of immunoregulatory bacteria in GALT of rats Q-PCR was used to identify them by species-specific 16S rDNA genes. Transcriptional activity of Foxp3 and RORyt genes was determined using Q-PCR with reverse transcription. Results: In animals treated with both vancomycin and Salmonella, the levels of segmented filamentous bacteria (SFB) increased while Akkermansia muciniphila and Faecalibacterium prausnitzii decreased. In rats that received pretreatment with vancomycin and then were infected with S. Enteritidis and S. Typhimurium, the levels of SFB increased, and the number of Bacteroides-Prevotela group, A. muciniphila, Clostridium spp. clusters XIV, IV, and F. prausnitzii significantly decreased, decreasing Foxp3 and increasing Rorγt mRNA expression. Administration of B. fragilis to animals treated with S. Enteritidis or S. Typhimurium and pre-treated with vancomycin caused a decrease in SFB and Rorγt mRNA levels and conversely, increased the numbers of the Bacteroides-Prevotela group, Clostridium spp. clusters XIV, IV, A. muciniphila, F. prausnitzii and Foxp3 gene expression in GALT. Conclusion: Our results suggest that the commensal microorganism B. fragilis may provide a protective role against the development of experimental colitis, which has to be taken into consideration for further clarification of the effective therapeutic strategy of inflammatory bowel diseases, irritable bowel syndrome and necrotising colitis. https://ijm.tums.ac.ir/index.php/ijm/article/view/2461 https://ijm.tums.ac.ir/index.php/ijm/article/download/2461/1246