From the earlier to modern times, the human populations passed through stages of subsistence such as foraging, rural farming and industrialized urban life. Till date various tribal people are living in geographically isolated areas depending on their traditional (gathering/rural farming) food sources. The long term cultural practices and food habits shaped the gut microbiome composition in these populations and contributed to health. However, the population-level study of the gut microbiota in Indian tribes with representative sampling across its geography and subsistence are limited. So, it is important to understand the complexity and diversity of the gut microbiome in healthy tribal populations, studied so far, to explore relationship among food, gut microbiome and health. Here, we reviewed gut microbiome studies which included 21 Indian tribal populations from different geographical regions to understand the role of food, ecology and cultural habits on variation of gut microbiota.