Endangered deep-snow mountain caribou have a distinct winter diet and gut microbiome that may be altered by maternal penning

This repository contains supporting material for the manuscript entitled "Endangered deep-snow mountain caribou have a distinct gut microbiome that may be altered by maternal penning," which is published in Molecular Ecology (https://doi.org/10.1111/mec.17783). The R code and terminal scripts required to reproduce all analyses and figures are currently available: 01-otu-seq-processing brings the raw sequencing files into phyloseq objects and performs initial quality filtering and OTU clustering. 02-analyze-controls evaluates the mock community and negative control samples. 03-statistical-analysis includes code for all statistical analysis described in the manuscript and supplementary material. 04-figures reproduces all the figures and tables in the manuscript. terminal_scripts includes examples of any code that could not be run in R (e.g., cutadapt, CAZyme annotation). The original sequencing files have been deposited in the NCBI Short Read Archive (SRA) under BioProject PRJNA1067083. Please contact the corresponding author ([e-mail]) if you have any questions.