Background: The gut microbiome is thought to produce metabolites that are widely investigated to play a role in various disease pathophysiologies. Aim: This study aims to identify the differences in gut microbiome diversity and profile between nonalcoholic fatty liver disease (NAFLD) and healthy individuals. Methods: This was a cross-sectional study. We collected 21 fecal specimens from NAFLD subjects and 13 controls. The gut microbiota from all samples were profiled by using 16s ribosomal RNA next-generation sequencing. Statistical analysis was done using SPSS version 25.0 software. Results: NAFLD subjects had a greater body mass index. Hypertension, diabetes, and dyslipidemia were found in 19%, 28.6%, and 81%, respectively, in NAFLD subjects. There was a lower diversity of gut microbiota in NAFLD compared to the control group. At the phylum level, Firmicutes was found more in the control than the NAFLD group (42.24% vs. 54.01%, P = 0.037). At the genus level, the percentage of Enterobacter was more abundant in the NAFLD group compared to the control group (0.517% vs. 0%, P = 0.001). At the genus level, there was a negative correlation between Bifidobacterium and NAFLD fibrosis score (NFS) (r = −0.532, P = 0.013). Conclusion: The diversity of the gut microbiota in NAFLD group was less than in control group. Firmicutes was found to be less prevalent in NAFLD patients compared to control. Enterobacter was found to be more abundant in NAFLD patients. The amount of Bifidobacterium was inversely correlated to the severity of NAFLD based on NFS.