In this repository are code and data for analysis and plots in the paper "Bacteroidetes to Firmicutes - captivity changes the gut microbiota composition and diversity in a social subterranean rodent" (https://doi.org/10.1186/s42523-023-00231-1). 16S Amplicon data from 109 fecal samples from Damaraland mole-rats used in this analysis, ASV table, taxonomy table and metadata can be found in "data" - folder.
Please note that all animals origin from the same source population (the captive animals origin from the wild) and "Population" in metadata is equal to "group" in manuscript.
Scripts:
- Alphadiv.Rmd - Alpha diversity
- Ancom.Rmd - difference abundance
- Betadiv.Rmd - beta diversity
- Relab.Rmd - Relative abundances & prop. unassigned taxa