Data from: Stability of fecal microbiota during degradation in ex situ Cheetahs in the US
Data files
Jan 13, 2025 version files 330.02 KB
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Aju_DNAsequences_2runs.fasta
230.39 KB
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Aju_featuretable.csv
29.45 KB
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Aju_meta_noAlpha.csv
2.72 KB
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Aju_Metadata_old.csv
4.49 KB
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Aju_metadata.csv
5.67 KB
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Aju_taxonomy.csv
28.41 KB
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Aju_tree.nwk
19.99 KB
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README.md
7.46 KB
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S8_DA_ASVtable_Apr2022.csv
1.44 KB
Abstract
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.
README: 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)
- 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)
- 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)
- NAs: when NAs are present it indicates the corresponding column name/level could not be identified
- 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 |
- DNA sequences file - Aju_DNAsequences_2runs.fasta (Sequences of ASVs)
- Phylogenetic tree file - Aju_tree.nwk (phylogenetic tree of DNA sequences from ASVs)
Code files
- Maly_2024_Processing_dada2_decontam.Rmd: for running dada2, decontam, calculating alpha diversity metrics, and making phylogenetic tree in QIIME2
- Maly_2024_DAtesting_ASVandPhylum_Code.Rmd: Code for running DAtest and calculating differential abundance at the ASV and Phylum level
- Maly_et_al2024_Final_Manuscript_Analyses_and_Figures.Rmd: Code for analyses and figures
- Convert_values_to_metric.R: Code to convert rainfall and temperature measures into metric values