To think about inequalities is ultimately to think about health—wellbeing in its broadest sense. Today, health is increasingly understood in terms of the microbiome: the trillions of microbes that inhabit us, feed us, maintain us, and defend us. Many contemporary diseases—obesity, diabetes, cancers, autoimmune disorders, allergies, autism, Alzheimer’s, depression—are now linked to a loss of microbial diversity. Architecture is implicated. These “diseases of the built environment” are inseparable from planetary health and the state of the biosphere. Inequalities must be considered beyond the human, which also means seeing the human differently—as a mobile ecosystem embedded in a microbial world. We the Bacteria operates as both a mirror and a projector. It introduces visitors to their microbial condition, then traces microbes from deep Earth to outer space and from 4.2 billion years ago to today. Recent research by scientists and architects is presented alongside an alternative history of architecture told from the perspective of microbes, culminating in the dysbiosis of the present. The final section looks to the future, presenting working installations by nine international design teams collaborating with microbiologists on new ways of living with microbes.