Human health is fundamentally connected with the ecology of microbial communities living on and in our bodies, according to microbiome studies. This raises problems about the categorical separation of organisms from their environments, which has been important to biomedicine. The field of biomedicine now faces an empirical challenge: determining causal linkages between host health, microbiome, and environment. To think about this topic, we recommend using the concept of environmentality. Environmentality is a fully perspectival notion that describes the state or characteristic of being an environment for something else in a specific context. Its strength stems in part from what Isabelle Stengers refers to as the efficacy of the term itself, in contrast to the prevailing understanding of the word environment as both external and fixed. We suggest that environmentality can assist think about the causality of microbiota on host health in a processual, relational, and situated manner, spanning scales and temporalities, using three case studies. We place this intervention in the context of biomedical thinking history, emphasising on the difficulty that microbiome research provides to an aperspectival body. We believe that tackling entanglements between microbial and human lives necessitates bringing the environment into the clinic, hence reducing the time spent there.