###### Abstract  
Continuous cultures assure the invariability of environmental conditions and the metabolic state of cultured microorganisms, whereas batch-cultured cells undergo constant changes in nutrients availability. For that reason, continuous culture is sometimes employed in the whole transcriptome, whole proteome, or whole metabolome studies. However, the typical method for establishing uniform growth of a cell population, i.e., by limited chemostat, results in the enrichment of the cell population gene pool with mutations adaptive for starvation conditions. These adaptive changes can skew the results of large-scale studies. It is commonly assumed that these adaptations reflect changes in the genome, and this assumption has been confirmed experimentally in rare cases. Here we show that in a population of budding yeast cells grown for over 200 generations in continuous culture in non-limiting minimal medium and therefore not subject to selection pressure, remodeling of transcriptome occurs, but not as a result of the accumulation of adaptive mutations. The observed changes indicate a shift in the metabolic balance towards catabolism, a decrease in ribosome biogenesis, a decrease in general stress alertness, reorganization of the cell wall, and transactions occurring at the cell periphery. These adaptive changes signify the acquisition of a new lifestyle in a stable nonstressful environment. The absence of underlying adaptive mutations suggests these changes may be regulated by another mechanism. t 1 (2020) 11 (2020) 25 November 2020 (2020) 27 November 2020  
are performed [2], for which it is important to discern the anticipated transcriptome changes from those pertaining to growth conditions and/or other factors escaping experimenter control. In batch culture, cells experience constant changes in nutrient availability as well as the build-up of byproducts and final metabolites. This is also true for the cells of budding yeast _Saccharomyces cerevisiae_, the model organism in the studies described in this paper. When grown in a medium with glucose as a carbon source its predominant way of obtaining energy is fermentation, which leads to the accumulation of ethanol. The regulatory mechanism called glucose repression prevents budding yeast cells from entering into respiratory metabolism despite the availability of oxygen until glucose is exhausted [3]. At this point, budding yeast cells undergo a diauxic shift from fermentation to oxidation of ethanol, which reprograms the whole metabolism and affects the expression of hundreds of genes [4; 5]. This is an extreme example; however, growth phase-specific changes in the transcriptome constitute a common source of artifacts often distorting the resulting data [2] and leading the experimenters astray. Unquestionably, continuous culture also has limitations [6] and cultured cells do not preserve constant features indefinitely. Indeed, prolonged continuous cultures, typically in limited chemostats and exposed to some selection pressure are commonly employed when microevolution experiments are performed. In these approaches, gradual adaptive changes in cell populations in response to that selection are expected and desired [7; 8] and cell cultures are maintained for hundreds or even thousands of generations. On the other hand, in typical transcriptome studies, continuous culture should not be carried out for too long to avoid admixture of adaptive-borne changes. To prevent this, cells should be harvested soon after a culture reaches the steady-state and the number of generations in the continuous culture should not exceed twenty [7]. The phenomenon of adaptation in a prolonged culture is well known. It has been demonstrated in numerous microevolution studies that during the adaptive phase of continuous culture, mutations accumulate in the cell population gene pool, and cells gaining fitness due to these mutations dominate the population [9; 10; 11; 12].