Code repository for the analysis of experimental evolution of Bacteroides thetaiotaomicron during adaptation to the mouse gut under different dietary regimes.
Link: https://www.sciencedirect.com/science/article/abs/pii/S1931312822000385
The .Rmd files contain all of the analysis, except those that were carried with Graphpad Prism. Bash or R scripts are called from the .Rmd files.
Intermediate files are in the data and analysis folders.
Cloning/downloading this repository, and oppening BthetaDietEvolution.Rproj (RStudio) will allow rendering each of the .Rmd files into html files with statistical output and figures.
NOTE: The ancestral strain, identified here as TDA1000 is a direct descendent of B. thetaiotaomicron DSMZ 2079, which was ordered from the DSMZ collection and stored unmodified at -80ºC at IGC. An assembly of B. thetaiotaomicron DSMZ 2079 was deposited the Helmholtz Centre for Environmental Research - UFZ at NCBI, having the following GenBank assembly accession: GCA_014131755.1 (https://www.ncbi.nlm.nih.gov/assembly/GCF_014131755.1/).