Challenges and pitfalls of inferring microbial growth rates from lab cultures

Abstract

Introduction: After more than 100 years of generating monoculture batch culture growth curves, microbial ecologists and evolutionary biologists still lack a reference method for inferring growth rates. Our work highlights the challenges of estimating the growth rate from growth curve data. It shows that inaccurate estimates of growth rates significantly impact the estimated relative fitness, a principal quantity in evolution and ecology. Methods and results: First, we conducted a literature review and found which methods are currently used to estimate growth rates. These methods differ in the meaning of the estimated growth rate parameter. Mechanistic models estimate the intrinsic growth rate µ, whereas phenomenological methods – both model-based and model-free – estimate the maximum per capita growth rate µmax. Using math and simulations, we show the conditions in which µmax is not a good estimator of µ. Then, we demonstrate that inaccurate absolute estimates of µ are not overcome by calculating relative values. Importantly, we find that poor approximations for µ sometimes lead to wrongly classifying a beneficial mutant as deleterious. Finally, we re-analyzed four published data sets, using most of the methods found in our literature review. We detected no single best-fitting model across all experiments within a data set and found that the Gompertz models, which were among the most commonly used, were often among the worst-fitting. Discussion: Our study suggests how experimenters can improve their growth rate and associated relative fitness estimates and highlights a neglected but fundamental problem for nearly everyone who studies microbial populations in the lab.