Background <p>Obesity, as a growing health problem, has been associated with dysbiosis. Intestinal bacterial balance has been correlated with diet. Since the bacteria residing in the gut are affected by race, genetics, and geographical region, the present study was designed to investigate the relationship between daily calorie and macronutrient’s intake with the dominant bacterial phylum in metabolically healthy obese individuals living in Iran.</p> Study design <p>A cross-sectional study was conducted.</p> Methods <p>Eighty metabolically healthy adults with obesity (BMI ≥ 30&#xa0;kg/m2), aged 18–50 years were enrolled. A validated food frequency questionnaire (FFQ) was used and fecal Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria were determined by genomic DNA extraction from stool samples and quantified using 16&#xa0;S rRNA gene–specific qPCR.</p> Results <p>The mean age, BMI and waist circumferences of participants were 36.8 ± 0.92 yrs., 31.7 ± 0.35&#xa0;kg/m², and 103.3 ± 1.02&#xa0;cm, respectively. Dietary protein (<i>P</i> = 0.04) and fiber (<i>P</i> = 0.04) showed a significant inverse correlation with the population of Bacteroidetes. Physical activity showed a statistically notable inverse correlation with the gut Bacteroidetes (<i>P</i> = 0.01) and Firmicutes (<i>P</i> = 0.04). Firmicutes to Bacteroidetes ratio showed a tendency toward significance correlation with dietary carbohydrate (<i>P</i> = 0.05). Age showed a trend toward significance inverse correlation with Actinobacteria population (<i>P</i> = 0.05).</p> Conclusions <p>Dietary carbohydrate correlated with an increase in Firmicutes to Bacteroidetes ratio, as a marker of obesity. Further studies with larger sample size and multicenter designed are needed to confirm these results.</p>