DOI: 10.5061/dryad.2bvq83bvw
title: Data from: Stability of fecal microbiota during degradation in ex situ Cheetahs in the US

description: Objective: Gut health and its relationship to gut microbiota is an
 important consideration in the care and well-being of managed endangered
 species, such as the cheetah (Acinonyx jubatus). Non-invasive fecal
 sampling as a proxy for gut microbiota is preferred and collecting fresh
 fecals is the current gold standard. Unfortunately, even in
 managed facilities, collecting fresh samples from difficult to
 observe or dangerous animals is challenging. Therefore, we conducted a
 study to determine the terminal collection timepoint for fecal microbial
 studies in the cheetah. Methods: We longitudinally sampled eight freshly
 deposited fecals every 24 h for 5 days and assessed bacterial
 relative abundance, diversity, and composition changes over time.
 Results: Our data indicated that fecal samples up to 24 h post defecation
 provided accurate representations of the fresh fecal microbiome.
 After 24 h, major changes in community composition began to occur. By 72
 h, individual cheetah fecal microbiota signatures were lost.
 Conclusion: Our findings suggest that cheetah fecal samples should be
 collected within 24 h of defecation in humid environments,
 especially if precipitation occurs, in order to provide a more
 biologically accurate representation of the gut microbiome, and
 we provide visual characteristics that can aid researchers in
 approximating time since defecation. Significance: These data
 provide guidelines for researchers investigating cheetah and other large
 felids and carnivores where the ability to collect fresh fecal
 deposits is limited.
description: # Data from: Stability of fecal microbiota during degradation in ex situ
 Cheetahs in the US ## Description of the data and file structure Files and
 code for preprocessing and analyses of 16S rRNA fecal microbiota data from
 cheetahs associated with the article "Comparing Stability of Fecal
 Microbiota by Time and Weather Conditions in a Carnivore, the Cheetah
 (Acinonyx jubatus)". Fecal samples were collected fresh and analyzed
 for an additional 5 days to observe microbial changes in fecals exposed to
 the environment. ## Data files included (needed to run analyses without
 running all preprocessing code) 1. Feature file - Aju_featuretable.csv
 (ASV counts for each sample, first column are row names and there is no
 header for column 1 as is expected format for phyloseq processing) 2.
 Taxonomy file - Aju_taxonomy.csv (taxonomy file for mapping ASV numbers to
 taxonomy classifications, first column has no header as expected format
 for phyloseq processing) 1. NAs: when NAs are present it indicates the
 corresponding column name/level could not be identified 3. Metadata file -
 Aju_Metadata.csv (metadata for samples, first column has no header these
 are the row names for the data frame) Column descriptions are below: |
 LifeStage | Life stage of the cheetah from which the fecal sample was
 collected from | | :--------------------------- |
 :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | | **FecalSeries** | Which fecal series the subsample came from | | **SampleDay** | Which day fresh or post fresh the subsample was collected in the series | | **Max.Humidity** | Maximum humidity reading for day leading up to collection. | | **SampleDate** | Calendar date the subsample was collected | | **quant\_reading** | DNA concentration of extracted DNA from fecal sample measured by qubit fluorometer | | **sample.type** | TRUE or FALSE. TRUE for all fecal subsamples (used to filter out negative controls) | | **Sample\_or\_Control** | True Sample for all fecal subsamples (used to filter out negative controls) | | **is.neg** | FALSE for all fecal subsamples (used to filter out negative controls) | | **PD** | Faith's phylogenetic diversity index. | | **SR** | species richness (ASV count) | | **sample\_sums.clean1PTr2.** | total sequence sums for subsample after filtering and processing | | **FecalConsistency** | Consistency of fecal subsample. Normal = healthy looking normal fecal sample, Loose = runny/diarrhea like fecal sample | | **MaxDailyCR** | Max Daily cumulatuve rainfall. This is all the previous max daily rainfall amounts added together for each previous day in the fecal series. So a sample from Day 3 includes the max daily rainfall amounts from Day 0, 1, and 2 to indicate how much total rain the Day 3 sample was exposed to. | | **MaxDailyR** | Max daily rainfall for one specific sample day | | **MaxCelsius** | max daily temperature for one specific sample day | 4. DNA sequences file - Aju_DNAsequences_2runs.fasta (Sequences of ASVs) 5. Phylogenetic tree file - Aju_tree.nwk (phylogenetic tree of DNA sequences from ASVs) ## Code files 1. Maly_2024_Processing_dada2_decontam.Rmd: for running dada2, decontam, calculating alpha diversity metrics, and making phylogenetic tree in QIIME2 2. Maly_2024_DAtesting_ASVandPhylum_Code.Rmd: Code for running DAtest and calculating differential abundance at the ASV and Phylum level 3. Maly_et_al2024_Final_Manuscript_Analyses_and_Figures.Rmd: Code for analyses and figures 4. Convert_values_to_metric.R: Code to convert rainfall and temperature measures into metric values