Many people believe that microorganisms, including viruses, bacteria, and microscopic fungi, are dirty and dangerous pollutants to be avoided at all costs. But advances in biotechnology and data science have led scientists to challenge this misperception. Scientists, and also clinicians, now recognize that many of the microorganisms in, on and around us are critical to our health and well-being. This essay reviews how scientific understanding of the microbial world has radically shifted since the germ theory of disease was established in the 19th century. Specifically, the text explores what is currently known about microbial exposure and human health. First, the world of infectious disease, allergies and asthma are considered, with a focus on how exposure to some microorganisms may actually protect humans from getting sick. Next is a discussion of how microorganisms are exchanged between the environment (air, surfaces, water) and humans. Finally, the essay highlights new collaborations between biologists and architects, which have the desired outcome of managing microbial exposure through design. These collaborations include research focused on the following question: how do the buildings and cities where we live, work and play impact our health through their impact on microbial ecology?