The global trend towards industrialization and urbanization has led to ever more people living and working indoors. Some studies estimate that humans in industrialized countries spend as much as 90% of their lives inside. Thus, for billions of humans the built environment (BE) now represents the modern ecological habitat of Homo sapiens sapiens. In this talk, I will review our groundbreaking studies using molecular tools and bioinformatics to explore BEs such as therapy pools, offices, hospitals and airplanes. I will then discuss our experimental time-series 16S and metagnomic analysis of bacterial and viral community that demonstrated rapid ecological succession and stabilization of communities on restroom surface. Finally, I will describe the SourceTracker program, inspired by our BE studies, which determines how many different communities have contributed to contaminated environment.