Scaling up microbial fermentation from laboratory to industrial levels presents significant challenges. This study examines the factors affecting strain production stability by using a β-carotene producing Yarrowia lipolytica strain as a model. Through experiments and kinetic modeling, we evaluate the influence of fermentation modes, carbon sources, oxygen levels, and media on production longevity. In shaking flask subcultures, the strain maintains production over 50 growth generations. However, continuous fermentations often drive a subpopulation shift toward low producing but faster-growing cells, leading to production losses within as few as 10 generations. Oxygen limitation in bioreactors further accelerates this shift. Notably, using oil as the carbon source increases population heterogeneity, but enhances carotene titer and prolongs production compared to glucose-based media. Kinetic models reveal that the highest-producing strains in laboratory conditions may lack robustness in industrial settings, where suboptimal producers with faster growth rates are more likely to thrive under stresses and extended cultivation periods.
