You can generate the main analysis from the manuscript installing this repository into R using this command (this required devtools package):
library(devtools)
install_github("tapj/AlimIntest")
browseVignettes("AlimIntest")
If you use dataset and/or source code from this AlimIntest repository please cite this article published in Environmental Microbiology :
Tap J, Furet JP, Bensaada M, Philippe C, Roth H, Rabot S, Lakhdari O, Lombard V, Henrissat B, Corthier G, Fontaine E, Doré J, Leclerc M. Gut microbiota richness promotes its stability upon increased dietary fiber intake in healthy adults. Environ Microbiol. 2015 Jul 31. doi: 10.1111/1462-2920.13006.