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bioRxiv · 10.1101/2022.07.29.501982

A ready-to-use logistic Verhulst model implemented in R shiny to estimate growth parameters of microorganisms

Garel, M.·Izard, L.·Vienne, M.·Nerini, D.·Tamburini, C.·Martini, S.
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Abstract

In microbiology, the estimation of the growth rate of microorganisms is a critical parameter to describe a new strain or characterize optimal growth conditions. Traditionally, this parameter is estimated by selecting subjectively the exponential phase of the growth, and then determining the slope of this curve section, by linear regression. However, for some experiments, the number of points to describe the growth can be very limited, and consequently such linear model will not fit, or the parameters estimation can much lower and strongly variable. In this paper, we propose a tools to estimate growth parameters using a logistic Verhulst model that take into account the entire growth curve for the estimation of the growth rate. The efficiency of such model is compared to the linear model. Finally, the novelty of our work is to propose a "Shiny-web application", online, without any programming or modelling skills, to allow estimating growth parameters including growth rate, maximum population, and beginning of the exponential phase, as well as an estimation of their variability. The final results can be displayed in the form of a scatter plot representing the model, its efficiency and the estimated parameters are downloadable.

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Garel, M., Izard, L., Vienne, M., Nerini, D., Tamburini, C., Martini, S.. 2022-07-29. A ready-to-use logistic Verhulst model implemented in R shiny to estimate growth parameters of microorganisms. https://doi.org/10.1101/2022.07.29.501982

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