Recents studies of the human microbiome have demonstrated the growing significance that the microbial world has to human health. But most of these studies have been done in Western societies, where environments are relatively new to humans and microbes, as rapid evolution in the way we live and eat has occurred in the past few decades. Changes in how we live occur from the very first contact to the external world, our birth, has changed dramatically in comparison to how we used to be born decades ago. In addition, we have changed how and what we eat, how we treat diseases, how we practice hygiene, how we build our houses and the materials we use for them, even the time we spend indoors. The main objective of this thesis is to characterize the changes in the microbial communities due to all the changes the human go through when shifting from rural to urban. To do this, we studied both human and built environment microbiota in different localities ranging from very rural to very urban settings. Chapter 1 of this dissertation provides a broad introduction of what is the microbiome and some evidence of how important it is for our health. Chapter 2 portrays changes in the BMI and nutritional transition that occurs in the process from rural to urban environments in the Amazon Basin. Chapter 3 compares the structure of the human microbiome in different body sites across the urbanization gradient in the Amazon Basin. Chapter 4 compares the microbial communities in the built environment, in houses of families across the urbanization gradient in the Amazon Basin. Chapter 5 presents a general discussion and future perspectives on this field of study.