Biosciences and Living Systems Institute, University of Exeter, Exeter, United Kingdom.
PLoS Comput Biol. 2021 Mar 18;17(3):e1008817. doi: 10.1371/journal.pcbi.1008817. eCollection 2021 Mar.
Developing mathematical models to accurately predict microbial growth dynamics remains a key challenge in ecology, evolution, biotechnology, and public health. To reproduce and grow, microbes need to take up essential nutrients from the environment, and mathematical models classically assume that the nutrient uptake rate is a saturating function of the nutrient concentration. In nature, microbes experience different levels of nutrient availability at all environmental scales, yet parameters shaping the nutrient uptake function are commonly estimated for a single initial nutrient concentration. This hampers the models from accurately capturing microbial dynamics when the environmental conditions change. To address this problem, we conduct growth experiments for a range of micro-organisms, including human fungal pathogens, baker's yeast, and common coliform bacteria, and uncover the following patterns. We observed that the maximal nutrient uptake rate and biomass yield were both decreasing functions of initial nutrient concentration. While a functional form for the relationship between biomass yield and initial nutrient concentration has been previously derived from first metabolic principles, here we also derive the form of the relationship between maximal nutrient uptake rate and initial nutrient concentration. Incorporating these two functions into a model of microbial growth allows for variable growth parameters and enables us to substantially improve predictions for microbial dynamics in a range of initial nutrient concentrations, compared to keeping growth parameters fixed.
开发能够准确预测微生物生长动态的数学模型仍然是生态学、进化生物学、生物技术和公共卫生领域的一个关键挑战。为了繁殖和生长，微生物需要从环境中摄取必需的营养物质，而经典的数学模型假设营养物质摄取率是营养物质浓度的饱和函数。在自然界中，微生物在所有环境尺度上都经历着不同水平的营养可用性，然而，营养物质摄取函数的参数通常是在单一初始营养浓度下估计的。这使得模型在环境条件发生变化时无法准确捕捉微生物的动态。为了解决这个问题，我们对一系列微生物进行了生长实验，包括人类真菌病原体、面包酵母和常见的大肠菌群，并揭示了以下模式。我们观察到最大营养物质摄取率和生物量产量都是初始营养浓度的递减函数。虽然之前已经从第一代谢原理推导出了生物量产量与初始营养浓度之间关系的函数形式，但在这里我们也推导出了最大营养物质摄取率与初始营养浓度之间关系的函数形式。将这两个函数纳入微生物生长模型中，可以使生长参数具有可变性，并使我们能够在一系列初始营养浓度下大大提高对微生物动态的预测，而不是将生长参数固定不变。
