Data and code for: Diurnal oscillations in gut bacterial load and composition eclipse seasonal and lifetime dynamics in wild meerkats, Suricata suricatta

Data and code to go with our publication "Diurnal oscillations in gut bacterial load and composition eclipse seasonal and lifetime dynamics in wild meerkats, Suricata suricatta", Nature Communications (2021).

FILE DESCRIPTIONS

****** DATA ******

meerkat_16S_data.tar.gz    # 16S V4 amplicon sequences  sequenced on an Illumina MiSeq platform using primer pair 515F and 806R, including all faecal samples, controls, and sand samples. Sequence identifiers and basic metadata are in sequence_identifiers.csv.

sequence_identifiers.csv    # Simple metadata and identifiers for all sequences/samples (what type of sample/sequencing run, etc), required for QIIME2 processing of the raw fasta.gz files contained in meerkat_16S_data.tar.gz. It contains a column for whether the sample was included in the final analysis. Does not include sample biological metadata as generating this data requires access to Kalahari Meerkat Project database. Biological metadata for samples included in the final analysis are instead provided in processed_data_phyloseq.RDS and can be accessed via phyloseq::sample_data(processed_data_phyloseq).

processed_data_phyloseq.RDS # Phyloseq object containing the processed data used in the presented analysis. Contains data for 1109 samples, and includes the ASV table, the taxonomic classification, the phylogenetic tree, and the sample metadata used in the analysis.

technical_replicate_data_phyloseq.RDS # Phyloseq object containing data from the 16 technical replicates.

pilot_study_data_phyloseq.RDS # Phyloseq object containing data from the pilot study on captive meerkats.

****** CODE ******

CODE1_QIIME_script.R   # QIIME2 script to generate ASV table, taxonomy, and phylo tree from meerkat_16S_data.tar.gz. Requires a reference taxonomy (SILVA) and a reference phylogeny (SEPP) for taxonomic and phylogenetic placements.

CODE2_processing_QIIME_output.Rmd  # R markdown script that processes the QIIME2 output generated by CODE1_QIIME_script.R. Does not generate meerkat metadata as this requires access to the Kalahari Meerkat Project database. This metadata is provided in processed_data_phyloseq.RDS.

CODE3_data_analysis_script.Rmd # R markdown script that generates data and figures presented in paper, using data from processed_data_phyloseq.RDS, technical_replicate_data_phyloseq.RDS, and pilot_study_data_phyloseq.RDS.

****** R MARKDOWN REPORTS ******

The following reports are html files that show the code output for the two RMD files above.

RMARKDOWN_data_processing.html # R markdown report for CODE2_processing_QIIME_output.Rmd

RMARKDOWN_data_analysis.html # R markdown report for CODE3_data_analysis_script.Rmd

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For general queries, unexpected errors and/or inconsistencies, please contact riselya@gmail.com.