Comparison of fresh fecal samples from two populations (NAM and USA) (Part 2 of 2)
Data files
Jan 09, 2025 version files 349.90 KB
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CPT23_featuretable_Nov23.csv
10.05 KB
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CPT23_taxonomy_Nov23.csv
23.37 KB
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CPTf_2023_DNAsequences.csv
302.62 KB
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CPTf23_cleanseqs_tree.nwk
7.65 KB
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Metadata_CPT23_final.csv
1.58 KB
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README.md
4.62 KB
Abstract
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) and analyzed for bacterial community diversity and composition using 16S rRNA gene amplicon sequencing. First, we found no difference in bacterial richness, diversity, or community composition from fresh fecal material compared to subsequent samples of decomposing fecals over a four-day sampling period in Namibia. Second, fresh cheetah samples in semi-wild conditions in Namibia had higher number of bacterial taxa, more phylogenetically diverse bacteria and contained compositionally distinct microbiomes (Bray-Curtis dissimilarity, Jaccard, and unweighted UniFrac measures) from cheetahs in zoo-managed conditions in the USA. We also found few differences in predictive functions of the fecal microbiota between the populations, where only one disease-related pathway was higher in the USA samples. Overall, our findings suggest that in dry season conditions (no recorded rainfall) in Namibia, fecals may be usable for up to three days after defecation for microbial ecology studies. We provide observational data on how to identify fecals within four days of being voided (see supplemental photos). There are major demographic and dietary differences between ex situ Namibian and USA populations, and we suggest further investigation into the influence of diet and population on the gut microbiota and health of cheetahs.
README: 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
- 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
- CPTf23_Picrust2.ipynb - Jupyter Notebook file for running PICRUSt2
- CPTf23_Picrust2_categorize_by_function.Rmd - code for merging and categorizing Picrust output into level 1, 2, and 3 categories
- CPTf23_ALDEx2_PICRUST.Rmd - code for statistical analyses and visualizations of picrust data at levels 1, 2, and 3
Files for phyloseq object (needed for Analyses code if not building from scratch)
- CPTf23_featuretable_Nov23.csv - table of ASV counts by samples (first column has no header as is expected format for phyloseq)
- CPTf23_taxonomy_Nov23.csv - mapping file for ASV numbers to taxonomic classifications (first column has no header as is expected format for phyloseq)
NAs in taxonomy file indicate corresponding taxonomy level was not identified for that ASV.
- Metadata_CPT23_final.csv - metadata for samples, see below table for explanation of columns
| Row.names | Row names for importing data set |
| :----------------------- | :----------------------------------------------------------------------------------- |
| SampleID.x | Sample ID names that match FASTQ sequences |
| FecalID | Fecal Series sample belongs to |
| SampleDay | Which day of the series it was collected |
| SampleDate | Calendar day the fecal subsample was collected |
| quant_reading | DNA concentration of extraced DNA from fecal (before PCRs) as measured by flurometer |
| sample.type | TRUE for fecal samples (FALSE for negative controls before filtering) |
| is.neg | FALSE for fecal samples (TRUE for negative controls before filtering) |
| Sample_or_Control | True Sample for fecal samples (Control for negative controls before filtering) |
| Population | Which population the fecal sample came from (USA or NAM for Namibia) |
| PD | Faith's Phylogenetic Diversity |
| SR | Species Richness (ASV count) |
| SampleID.y | Copy of rownames for metadata/sequencing matching |
| sample_sums(CPTf23) | sequence count per sample after decontam and filtering |
- CPTf_2023_DNAsequences.csv - DNA sequences for all ASVs
- CPTf23_cleanseqs_tree.nwk - phylogenetic tree of ASV sequences
Sharing/Access information
Raw FASTQ sequences used to generate these summary data files (and code) can be found: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1160820
Other related datasets include:
- Objective 1 (Part 1 of 2): DOI: 10.5061/dryad.sn02v6xdq
- Separate manuscript where USA samples were originally published: (manuscript: https://mah.bioscientifica.com/view/journals/mah/2/1/MAH-23-0022.xml
The code and data can also be found on GitHub:
Objective 1: https://github.com/Malytherin/CheetahFecalStability_Namibia
Objective 2 (this data set): https://github.com/Malytherin/Comparing.Fresh.Fecals_NAMvUSA
USA manuscript data: https://github.com/Malytherin/CheetahFecalStability_USA