In the current study, we aimed to investigate the association between gut microbiome composition and two physiological factors, BMI and age. We did not observe a significant relationship between occurrence of gut bacteria with BMI or age alone. On the other hand, we observed BMI and age together played an important role in impacting gut microbiota composition. Comparison of the microbiota of normal and obese subjects for the each of 20s and 50s group revealed 13 gut bacteria that show significantly different relative abundance in the two groups. We observed that certain organisms show opposite trends within the two age groups. Haemophilus parainfluenzae relative abundance was found to be increased in obese-20s group while reduced in obese-50s group. Relative abundance of organisms such as Mitsuokella jalaludini and Blautia obeum were reduced in obese-20s group while increased in obese-50s group as compared to the normal subjects of respective age group. On the other hand, a reduction in the average relative abundance of both M. jalaludini and B. obeum for obese group as compared to the normal in pan-India only BMI-based group comparison. While studying obesity-related gut microbiota changes, it is critical to consider multiple factors such as age and geography into the study design.