Comparison of fresh fecal samples from two populations (NAM and USA) (Part 2 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..., , , # Comparison of fresh fecal samples from two populations (NAM and USA) (Part 2 of 2)

Code for preprocessing FASTQ files and analysis to produce figures for Objective 2: fresh fecal comparison objective of \"Fecal Microbiota is More Stable During Degradation and More Diverse for Ex Situ Cheetahs in Namibia Compared to the USA\"

## Description of the data and files

### Coding files

1. Two.Pop.Comparisons_Preprocessing.Rmd - code for preprocessing unpaired FASTQ files for fresh samples from NAM and USA (dada2, decontam, build phylogenetic tree, create phyloseq files, calculate alpha diversity metrics)
2.Two.Pop.Comparisons_Analyses.Rmd - code for statistical tests and visualizations of relative abundance and alpha and beta diversity
2. CPTf23_Picrust2.ipynb - Jupyter Notebook file for running PICRUSt2
3. CPTf23_Picrust2_categorize_by_function.Rmd - code for merging and categorizing Picrust output into level 1, 2, and 3 categories
4. CPTf23_ALDEx2_PICRUST.Rmd - code for statistical ana...