Michael and former lab Ph.D. student and postdoc Justus have recently published their paper "Quantifying microbial fitness in high-throughput experiments" in eLife (PDF and code are available).
Fitness is a fundamental concept in evolutionary biology, but there is no single operational definition, even in the context of laboratory growth of microbes. But new high-throughput experiments, especially using DNA barcodes and growth curves from plate readers, are producing significant new data with insights into microbial fitness, creating an urgent need to determine how different definitions of fitness vary and whether there are any principles that we should use in quantifying fitness from these experiments. In this work, we unify several common definitions into a single framework and investigate how they differ using a few example data sets. We ultimately conclude some best practices for quantifying microbial fitness in these experiments, which we hope will enable better reproducibility and direct comparisons across studies in the future.
