Background: Pathophysiology of rheumatoid arthritis (RA) is an undetermined complex mechanism which include interaction between genetic, environmental and immunological factors. Recent studies suggest a possible role for gut microbiome in the pathogenesis. Objectives: To assess the alteration of fecal Bacteroids, Lactobacilli, and Prevotella genera among RA patients. Methods: Stool samples were collected from 25 patients newly diagnosed as RA (RA group) and 25 healthy controls (control group) for quantitation of Bacteroids, Lactobacilli, and Prevotella genera by real time PCR. Results: The intestinal microbiome of RA group was significantly altered. We reported a significant enrichment of the bacterial Lactobacilli genus in RA patients (16.206% vs 1.5%; P<0.001). Bacteroids and Prevotella genera showed lower percentages in RA patients compared to the controls (1.113% vs 2.7 %: 3.157% vs 17% respectively, P= 0.018, P<0.001 respectively). Conclusion: Predominance of Lactobacilli genus with the lower levels of Bacteroids and Prevotella, in recently diagnosed RA patients, could indicate the role of gut dysbiosis in the pathoghysiology of RA.