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Abstract This is a prospective study conducted on 30 NAFLD patients and 10 healthy volenteers. They were subjected to clinical history taking and examination, laboratory tests, Abdominal ultrasound, Needle liver biopsy for NAS and SAF scoring and stool sample collection for relative quantification of Bacteroidetes and Colostridium coccoides by real time PCR. Results There is a significant decrease in fecal Bacteroidetes in patients with NAFLD with a P value of 0.028, however there was no significant decrease among NAFLD subgroups ( simple steatosis and NASH) although fecal Bacteroidetes among the NASH patients had the least value. There was no significant difference in fecal Clostridium coccoides between NAFLD and control, and between the subgroups of NAFLD, although fecal Clostridium coccoides were lower among NAFLD and the lowest among NASH patients. There was no statistical significance between fecal Bacteroidetes or Clostridium coccoides and the stage of fibrosis in histopathological examination although both were lower in patients with severe fibrosis (F>2). The non hypertensive NAFLD group showed a significantly lower relative quantity of Bacteroides and a lower but statistically insignificant relative quantity of the Clostridium coccoides when compared to the control. There was no significant difference in the delta CT values for Bacteroidetes and Clostridium coccoides among the studied NAFLD patients with its subgroups and normal control in relation to different BMI grades, and presence of Diabetes |