Fecal microbiota degradation over time in ex situ Namibian Cheetahs (Part 1 of 2)

The relationships between gut microbiota and animal health are an important consideration that are increasingly influential in the management of wild and ex situ endangered species, such as the cheetah (Acinonyx jubatus). To better understand these relationships, fresh fecal samples are currently required as a non-invasive alternative for the gut microbiome. Unfortunately, fresh samples are challenging to collect, especially in the wild. This study had two main aims: 1) to determine the optimal collection time point for cheetah feces after deposit in their native environment of Namibia as a guide for wild cheetah fecal microbiome studies; and 2) to characterize the cheetah fecal microbiota between two ex situ cheetah populations from two locations (Front Royal, VA, USA and Otjiwarongo, Namibia), which also consume different diets (commercial diet + carcass supplements and carcass only, respectively). Fresh fecal samples were collected from 16 cheetahs (Virginia, n = 8; Namibia n = 8) an..., , , # Fecal microbiota degradation over time in ex situ Namibian Cheetahs (Part 1 of 2)

## Description of the data and file structure

Code and files for preprocessing and analyses of 16S fecal microbiota data from cheetahs. Fecal samples were collected fresh and analyzed for an additional 4 days to observe microbial changes in fecals exposed to the environment.

This data is for Objective 1 in the article: \"Fecal Microbiota is More Stable During Degradation and More Diverse for *Ex Situ* Cheetahs in Namibia Compared to the USA\"

Data from the same article for Objective 2 can be found: DOI: 10.5061/dryad.jm63xsjm5

### R Markdown Files

1. NAM_Degradation_Preprocessing.Rmd - code for preprocessing unpaired FASTQ files (dada2, decontam, rarefactin curve, alpha calculations, create phyloseq object files)
2. NAM_Degradation_Analyses.Rmd - code for statistical tests and visualizations for relative abundance, alpha and beta diversity
3. NAM_Degradation_MaAslin2_Code.Rmd - code for runni...