Emerging Clostridioides difficile ribotypes have divergent metabolic phenotypes

Dataset of multi-well plate reader files related to the analysis of the growth of C. difficile isolates on differnet carbon substrates. 

Data Collection. This dataset accompanies an mSystems article which is available at https://doi.org/10.1128/msystems.01075-24. The "Materials and Methods" section in this article fully describes the biological nature of these samples and how the samples were processed and analyzed.  

Repository Content. The amiga folders contains both the raw data (see data and mapping sub-folders), intermediate outpus (see dervied sub-folders), and final outputs (see figures and summary sub-folders). Each amiga folder corresponds to a single working directory analyzed by the AMiGA software. For the amiga-biolog directory, the notes sub-folder also includes text files related to flagging plates and wells for quality issues.

Data Organization. Growth plate data are organized by the following experiments. 

biolog

validation

ribotype-255

clade-5

yeast-extract-biolog

yeast-extract-validation

Data Analysis. Code used for manipulating and analyzing these samples is also publicly available on GitHub (https://github.com/firasmidani/cdiff-biolog-growth) under the GNU GPL-3.0 license. The scripts in "analyze-code" can be used to analyze all data and the scripts in the "generate-figures" folder can be used to reproduce all figures included in the manuscript. See the GitHub repository for instructions on how to do so.