Microbial division rates determine the speed of mutation accumulation and thus the emergence of antimicrobial resistance. Microbial death rates are affected by antibiotic action and the immune system. Therefore, measuring these rates has advanced our understanding of host-pathogen interactions and antibiotic action. Several methods based on marker-loss or few inheritable neutral markers exist that allow estimating microbial division and death rates, each of which has advantages and limitations. Technical bottlenecks, i.e., experimental sampling events, during the experiment can distort the rate estimates and are typically unaccounted for or require additional calibration experiments.

In this work, we introduce RESTAMP (Rate Estimates by Sequence Tag Analysis of Microbial Populations) as a method for determining bacterial division and death rates. This method uses hundreds of fitness neutral sequence barcodes to measure the rates and account for experimental bottlenecks at the same time. We experimentally validate RESTAMP and compare it to established plasmid loss methods.

We find that RESTAMP has a number of advantages over plasmid loss or previous marker based techniques. (i) It enables to correct the distortion of rate estimates by technical bottlenecks. (ii) Rate estimates are independent of the sequence tag distribution in the starting culture allowing the use of an arbitrary number of tags. (iii) It introduces a bottleneck sensitivity measure that can be used to maximize the accuracy of the experiment.

RESTAMP allows studying microbial population dynamics with great resolution over a wide dynamic range and can thus advance our understanding of host-pathogen interactions or the mechanisms of antibiotic action.

微生物分裂率决定了突变积累的速度，从而决定了抗药性的出现。微生物死亡率受抗生素作用和免疫系统影响。因此，测量这些速率已经使我们对宿主-病原体相互作用和抗生素作用有了更深入的了解。存在几种基于标记丢失的方法，或者很少有可遗传的中性标记，这些方法可以估算微生物的分裂和死亡率，每种方法都有其优点和局限性。实验期间的技术瓶颈（例如实验采样事件）可能会使速率估算值失真，并且通常无法解决或需要进行其他校准实验。

在这项工作中，我们介绍了RESTAMP（通过微生物种群的序列标签分析进行费率估算）作为确定细菌分裂和死亡率的方法。此方法使用数百个健身中性序列条形码来测量速率并同时解决实验瓶颈。我们通过实验验证RESTAMP，并将其与已建立的质粒缺失方法进行比较。

我们发现，RESTAMP相对于质粒丢失或以前的基于标记的技术具有许多优势。（i）它可以纠正由于技术瓶颈造成的费率估计失真。（ii）速率估计与起始培养物中序列标签的分布无关，从而允许使用任意数量的标签。（iii）引入了瓶颈敏感度度量，可以用来最大化实验的准确性。

RESTAMP可以在较宽的动态范围内高分辨率地研究微生物种群动态，因此可以增进我们对宿主-病原体相互作用或抗生素作用机制的了解。