Experimental evolution in a laboratory helps researchers to understand the genetic and phenotypic background of adaptation under a particular condition. Simultaneously, the simplified environment that represents certain aspects of a complex natural niche permits the dissection of relevant parameters behind the selection, including temperature, oxygen availability, nutrients, and biotic factors. The presence of other microorganisms or a host has a major influence on microbial evolution that often differs from the adaptation paths observed in response to abiotic conditions. In the current issue of the ISME Journal, Cosetta and colleagues reveal how cross-kingdom interaction representing the cheese microbiome succession promotes distinct evolution of the food- and animal-associated bacterium, Staphylococcus xylosus. The authors also identified a global regulator-dependent adaption that leads to evolved derivatives exhibiting reduced pigment production and colony morphologies in addition to altered differentiation phenotypes that potentially contribute to increased fitness.