<p>This paper examines the historical split of microbiology into the fields of medicine and ecology from a feminist perspective, using Helen Longino’s contextual empiricism and her onto-epistemic view of interactions. Examining microbial interactions is interesting for two reasons, one is ontological as microbial metabolic interactions constitute the bio-geo-chemical cycles that are the driving force of life on Earth. The second reason is epistemic, involving our conceptual challenges in understanding microbial traits and classification, as their activities and ability to evolve are, for the most part, driven by their interactions. I follow the work and methodology of Sergei Vinogradskii (1856–1953) and Robert Koch (1843–1910), as two main founders each of a different microbiology field. Koch focused on medicine, developing pure mass cultures and the Koch postulates. Vinogradskii focused on soil microbiology and ecosystem ecology, developing the elective culture technique, and is known for the Winogradsky Column. I use contextual empiricism to discuss their methodological differences in classification and cultivation and reflect on their position regarding microbial individuality and interactions. For instance, Vinogradskii’s research focused on metabolic interactions and microbial life cycles, considering individual microbes as part of their environment and never in isolation. This view emphasizes the individual, the interactions, and the environment as equally focal in causal explanations. Thus, in his view, the individual should be studied as part of its milieu and never in isolation. Based on Longino’s ontology of interactions, I elaborate on this view of the microbial individual in a given state of interdependence with changing levels of autonomy. This onto-epistemic understanding of the microbial phenomena is empirically consistent with today’s microbiome studies and discussions on host-holobiont definitions in microbiology, ecology, and medicine.</p>