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<h3>Background</h3> Growing attention has been given to the effects of dysbiosis in the gastrointestinal tract that possibly modulate intestinal permeability. This will trigger the secretion of pro-inflammatory cytokines that induces inflammation. Thus, probiotics are suggested to reverse the mechanism by promoting the growth of good bacteria that participate in the modulation of intestinal epithelial defense responses. We aimed to evaluate the effects of probiotics on gut microbiota composition in non-alcoholic fatty liver disease (NAFLD) patients. <h3>Methods</h3> This is a randomized, double-blind, controlled clinical trial. Twenty-nine patients were randomly assigned into probiotics and placebo groups. Multi-strain probiotics containing six different Lactobacillus and Bifidobacterium species at the concentration of 30 billion CFU were administered during the 6-month study. Anthropometric measurements like body mass index (BMI) and waist circumference (WC) were recorded. The duodenal biopsies from pre-and post-intervention were analyzed for microbiota compositions using amplicon sequencing based on the V3 region of 16s rRNA. <h3>Results</h3> The average mean age of recruited patients was 52 ± 13 years. Both groups displayed the same BMI and WC at the baseline and after the intervention. The 16s rRNA analysis revealed three main prokaryotic phyla, namely Actinobacteria, Proteobacteria, and Firmicutes, with genera Streptococcus, Methylobacterium, Cutibacterium, and Prevotella being particularly common after intervention for both groups. Beta-diversity analysis of the probiotics group disclosed a significant change of gut microbiota composition upon intervention procedures (<i>p<0.05</i>). Notably, the probiotics group also presented a decrease of Firmicutes/Bacteroidetes (F/B) ratio upon 6-month of intervention. Conversely, the placebo group illustrated a stable diversity upon intervention procedures as Alpha and Beta-diversity analyses showed no significant difference. <h3>Conclusions</h3> We anticipated a potential pattern of dysbiosis among NAFLD patients through the high prevalence of Streptococcus in core microbiome analysis for both groups. Interestingly, we managed to obtain a decrease in Firmicutes/Bacteroidetes ratio in the probiotics group which suggested a balance of microbial compositions through the presence of Lactobacillus and Bifidobacterium species. Hence, probiotics could be adopted as a potent preventive strategy in NAFLD patients