RT Journal Article
SR Electronic
T1 Challenges and pitfalls of inferring microbial growth rates from lab cultures
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2022.06.24.497412
DO 10.1101/2022.06.24.497412
A1 Ana-Hermina Ghenu
A1 Loïc Marrec
A1 Claudia Bank
YR 2022
UL http://biorxiv.org/content/early/2022/06/25/2022.06.24.497412.abstract
AB 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 and shows that inaccurate estimates of growth rates significantly impact the estimated relative fitness, a principal quantity in evolution and ecology. First, we conducted a literature review and found which different types of methods are currently used to estimate growth rates. These methods differ in the meaning of the estimated growth rate parameter. Kinetic models estimate the intrinsic growth rate µ whereas statistical 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 is 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 by 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. Our study provides suggestions for 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.Competing Interest StatementThe authors have declared no competing interest.