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Description of the data and file structure The data here consists of bacterial 16S rDNA metabarcoding results from Bryde's whale and southern right whale faecal samples. Files and variables File: whale-microbiome.R -> available from https://github.com/aashiparikh/Baleen-whale-gut-microbiomes Description: R code for statistical analyses including alpha and beta diversity, core microbiome and functional analyses performed on 16S metabarcoding results to examine baleen whale gut microbiomes. File: metadata.csv Description: Metadata associated with whale faecal samples. Input file for whale-microbiome.R. Variables Sample_ID: Sample ID including sample name and replicate number Control_Type: Whether a true sample, positive control, extraction negative, or PCR negative Sample_Control: Whether a true sample or a control Species: Whale species Location: Country of sample collection Site: Specific location of sample collection Year: Year (if known) of sample collection Sample_name: Biological sample name Replicate: Technical replicate number Sample_no: Sample number based on sample name Migratory_status: Migratory status of whale File: metadata-noreps.csv Description: Metadata associated with whale faecal samples, same file as above except technical replicates of samples have been combined for some analyses. Input file for whale-microbiome.R. File: 16S-OTU.csv Description: OTU table of 16S metabarcoding results. Input file for whale-microbiome.R. File: 16S-OTU-noreps.csv Description: OTU table of 16S metabarcoding results as above, however, technical replicates of biological samples have been combined by averaging their reads. Input file for whale-microbiome.R. File: 16S-tree-NJ.newick Description: Neighbour-Joining phylogenetic tree constructed to examine phylogenetic distances between microbial communities of different whales. Input file for whale-microbiome.R. File: EC.tsv Description: PICRUSt2 output file with Enzyme Commission numbers mapped to 16S rRNA sequences to predict functionality. Input file for whale-microbiome.R. File: ec-table.csv Description: Mapping file to match EC numbers to their names. Input file for whale-microbiome.R. File: Supplementary_Information.docx Description: Supplementary figures and tables associated with main research article. Code/software All statistical analyses were performed in the open source stastistical software R (R version 4.3.1, The R Foundation for Statistical Computing, 2023), and the included code is designed to be run in R. The code itself may also be opened in a standard text editor to view. All R packages required to run the code are included in the script file.