MiniRead: a simple and inexpensive do-it-yourself device for multiple analyses of micro-organism growth kinetics

Abstract

Fitness in micro-organisms can be proxied by growth parameters on different media and/or temperatures. This is achieved done by measuring optical density at 600 nm using a spectrophotometer, which measures the effect of absorbance and side scattering due to turbidity of cells suspensions. However, when growth kinetics must be monitored in many 96-well plates at the same time, buying several 96-channels spectrophotometers is often beyond budgets. The MiniRead device presented here is a simple and inexpensive do-it-yourself 96-well temperature-controlled turbidimeter designed to measure the interception of white light via absorption or side scattering through liquid culture medium. Turbidity is automatically recorded in each well at regular time intervals for up to several days or weeks. Output tabulated text files are recorded into a micro-SD memory card to be easily transferred to a computer. We propose also an R package which allows (1) to compute the non-linear calibration curves required to convert raw readings into cell concentration values, and (2) to analyze growth kinetics output files to automatically estimate growth parameters such as lag time, maximum growth rate, or cell concentration at the plateau. The MiniRead project is freely available under GPL license from https://forgemia.inra.fr/gqe-base/MiniRead. The project includes (1): user manual (Supplementary Material 1), firmware, list of electronic components and printed circuit board manufacturing files for the MiniRead device, and (2) a release containing the MiniRead R package for calibration and data analysis (Supplementary Material 2) with its tutorial (Supplementary Material 3). Detailed device building instructions are available at https://moulon.inrae.fr/materiel_labo/miniread/.