School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Ibaraki, 305-8572, Japan.
Institute of Biology and Information Science, East China Normal University, 3663 Zhongshan Road (N), Shanghai, 200062, China.
BMC Microbiol. 2018 Sep 3;18(1):101. doi: 10.1186/s12866-018-1242-4.
Bacterial growth is an important topic in microbiology and of crucial importance to better understand living cells. Bacterial growth dynamics are quantitatively examined using various methods to determine the physical, chemical or biological features of growing populations. Due to methodological differences, the exponential growth rate, which is a parameter that is representative of growth dynamics, should be differentiated. Ignoring such differentiation in the growth analysis might overlook somehow slight but significant changes in cellular features of the growing population. Both experimental and theoretical investigations are required to address these issues.
This study experimentally verified the differentiation in growth rates attributed to different methodologies, and demonstrated that the most popular method, optical turbidity, led to the determination of a lower growth rate in comparison to the methods based on colony formation and cellular adenosine triphosphate, due to a decay effect of reading OD during a population increase. Accordingly, the logistic model, which is commonly applied to the high-throughput growth data reading the OD, was revised by introducing a new parameter: the decay rate, to compensate for the lowered estimation in growth rates. An improved goodness of fit in comparison to the original model was acquired due to this revision. Applying the modified logistic model to hundreds of growth data acquired from an assortment of Escherichia coli strains carrying the reduced genomes led to an intriguing finding of a correlation between the decay rate and the genome size. The decay effect seemed to be partially attributed to the decrease in cell size accompanied by a population increase and was medium dependent.
The present study provides not only an improved theoretical tool for the high-throughput studies on bacterial growth dynamics linking with optical turbidity to biological meaning, but also a novel insight of the genome reduction correlated decay effect, which potentially reflects the changing cellular features during population increase. It is valuable for understanding the genome evolution and the fitness increase in microbial life.
细菌生长是微生物学中的一个重要课题，对于更好地理解活细胞至关重要。使用各种方法定量研究细菌生长动力学，以确定生长群体的物理、化学或生物学特征。由于方法学上的差异，应区分代表生长动力学的参数——指数生长率。在生长分析中忽略这种差异，可能会忽略细胞特征在生长群体中发生的一些细微但显著的变化。需要进行实验和理论研究来解决这些问题。
本研究通过实验验证了不同方法学导致的生长率差异，并证明了最常用的方法——光密度法，与基于菌落形成和细胞三磷酸腺苷的方法相比，由于在种群增加过程中读取 OD 时会出现衰减效应，导致生长率的测定值较低。因此，对常用的用于高吞吐量生长数据读取 OD 的 logistic 模型进行了修订，引入了一个新参数：衰减率，以补偿生长率的低估。由于这种修正，改进了拟合优度。将改进的 logistic 模型应用于从携带缩小基因组的大肠杆菌菌株中获取的数百个生长数据，发现了一个有趣的结果，即衰减率与基因组大小之间存在相关性。衰减效应似乎部分归因于伴随种群增加的细胞大小减小，并且与介质有关。
本研究不仅为将光密度与生物学意义相关联的细菌生长动力学的高通量研究提供了一个改进的理论工具，还为与基因组缩小相关的衰减效应提供了一个新的见解，这可能反映了细胞特征在种群增加过程中的变化。对于理解微生物生命的基因组进化和适应性增加具有重要价值。
