Microbial artists: testing the role of the microbiome in parasite manipulation and colour polymorphisms among amphipods
Creators: name: Salloum, Priscila
Publisher: name: figshare
Year: 2024
Subjects: classificationCode: 310405
subject: Evolutionary ecology
classificationCode: 310499
subject: Evolutionary biology not elsewhere classified
classificationCode: 310407
subject: Host-parasite interactions
classificationCode: 310599
subject: Genetics not elsewhere classified
classificationCode: 310799
subject: Microbiology not elsewhere classified
classificationCode: 310301
subject: Behavioural ecology

description: Information about the files and folders of this repository are detailed below (same as in the README.txt and README.docx files).· masked.zip – zip compressed folder containing all normalised and masked images used for colour quantification analyses (black background RGB 0,0,0)· raw_images.zip – zip compressed folder containing all unprocessed images corresponding to the masked images on the masked.zip folder, as well as the grey card used for normalising images.· normalised.zip – zip compressed folder containing all normalised images (unmasked).· masked_matchMicrobiome_singleInf – masked images only of amphipods with single infections and microbiome data available.· masked_singleInf – masked images only of amphipods with single infections.· metadata_8254.csv – metadata file for each sample (amphipods, parasites, and controls).· Metadata_8254.tsv – metadata file for each sample (amphipods, parasites and controls), including Qubit concentration values (used to detect contamination with the R script decontam.R), in tsv format.· colourData.zip: zip compressed folder with the output files of the RGB and CIELab values for each image, as well as the output of the colour distance estimates.- amphipods_rgb_masked_8bins_matchMicrobiomeSamples.csv: RGB values based on eight bins only for amphipods with microbiome data available.- amphipods_rgb_masked_eigth_bin.csv: RGB values based on eight bins, 93 amphipods (single infections and uninfected).- amphipods_rgb_masked_one_bin.csv: RGB values based on a single bin, 93 amphipods (single infections and uninfected).- colour_distance_8binsEMD_amphipods.csv: colour distances for 93 amphipods (single infections and uninfected), eight-binned dataset.- colour_distance_8binsEMD_tree_amphipods.newick: tree of colour distances in newick format, 93 amphipods (single infections and uninfected), eight-binned dataset.- colour_distance_EMD_amphipods.csv: colour distances for 93 amphipods (single infections and uninfected), single-binned dataset.- colour_distance_EMD_amphipods8bins_matchMicrobiomeSamples.csv: colour distances for 71 amphipods (all with microbiome data available), eight-binned dataset.- colour_distance_EMD_tree_amphipods.newick: tree of colour distances in newick format, 93 amphipods (single infections and uninfected), single-binned dataset.- eight_bin_rgb_AND_metadata.csv: metadata and RGB values (eight-binned dataset)- one_bin_rgb_AND_metadata.csv: metadata and RGB values (single-binned dataset)· OG8254_2023_Qiime2.html and OG8254_2023_Qiime2.ipynb – All the scripts used to run the bioinformatics analyses on Qiime2, in html format and in ipynb format. Scripts were run on the New Zealand eScience Infrastructure (NeSI) cluster.· qza_with_blanks_Silva.zip – zip compressed folder with Qiime2 qza files prior to decontamination (with negative controls), used to generate qzv files in Qiime2 and make a data frame to be used for decontamination (with the R script decontam.R)- hits-08-no-mtchlor-withP-noEuk-silva.csv: csv file used in decontam, with frequency per sample.- hits-08-no-mtchlor-withP-noEuk-silva.qza: feature table in qza format, with negative controls, noe Eukaryotes, no features without phylum assignment and no mitochondria/chloroplast sequences.- hits-08-no-mtchlor-withP-noEuk-silva-rep-seqs.qza: representative sequences of the features included in the table above (hits-08-no-mtchlor-withP-noEuk-silva.qza), in qza format.- hits-08-observed-taxonomy-silva.qza: taxonomy table of the features included in the table above hits-08-no-mtchlor-withP-noEuk-silva.qza), in qza format.· Dataset3_SingleInfections.zip – zip compressed folder with filtered qza and qzv files resulting from the bioinformatics steps in Qiime2 (using the script OG8254_2023_Qiime2 above).- D3_clean-filtered-table-2-500-silva_singleInfs.qza: feature table in qza format- D3_clean-filtered-2-500-unrooted-tree_singleInfs.qza: unrooted tree in qza format- D3_clean-filtered-2-500-taxonomy-silva_singleInfs.qza.qzv: taxonomy table in qzv format- D3_clean-filtered-2-500-taxonomy-silva_singleInfs.qza: taxonomy table in qza format- D3_clean-filtered-2-500-rooted-tree_singleInfs.qza: rooted tree in qza format- D3_clean-filtered-2-500-rep-seqs-silva_singleInfs.qzv: representative sequences (ASV sequences table) in qzv format- D3_clean-filtered-2-500-rep-seqs-silva_singleInfs.qza: representative sequences (ASV sequences table) in qza format- D3_clean-filtered-2-500-masked-aligned_singleInfs.qza: masked alignment in qza format- D3_clean-filtered-2-500-alpha-rarefaction-singleInfs.qzv: alpha rarefaction curve in qzv format- D3_clean-filtered-2-500-aligneds_singleInfs.qza: alignment in qza formt· reports.zip – zip compressed folder containing FastQC and MultiQC reports.· Rscipts.zip – zip compressed folder containing all R scripts used for analyses, detailed below:- various_colour_analyses.R: Extract RGB and CIELab values from masked images, PCA, statistical analyses (ANOVA, Kruskal-Wallis, multinomial logistic regression).- colourdistance_EMD_trees.R: bin the images using a single bin and eight bins, estimate colour distances using the Earth Mover’s Distance method (EMD) and output a tree file in newick format. Note that these analyses required memory and processing power, so they were run on a computer cluster (New Zealand eScience Infrastructure – NeSI)- colordistanceOUT_plotsANDanalyses.R: heatmaps and nmds, using the output from the colordistance R package (generated with the script colourdistance_EMD_trees.R.- decontam.R: script for the decontam package, used to remove contaminating features.- beta_diversity_rarefied_hosts.R: split amphipod hosts into colour groups and calculate beta diversity (only for amphipod hosts, not for parasites), as well as microbiome distances (based on beta diversity).- beta_diversity_rarefied_parasites.R: split amphipod hosts into colour groups and calculate microbiome distances among parasites (not among amphipod hosts).- correlation_colour-microbiome_distances.R: Mantel tests of colour distance-beta diversity distances; Shapiro test of normality on distance matrices, effect sizes (for microbiomes of hosts and parasites separately)- RDA_microbiome-colour.R: RDA between microbiome and amphipod colour (microbiome of hosts and of parasites done separately).- alpha_diversity_rarefied.R: split amphipod hosts into colour groups and calculate alpha diversity (only for amphipod hosts, not for parasites).- differential_abundance_tests.R: tests of differential abundance among colour groups (using three methods: Aldex2_kw, corncob and LinDA).- barPlots_UpsetPlot.R: bar plots of relative abundance for hosts microbiome data and upset plot of shared/unique taxa (based on amphipod colour groups).- beta_diversity_barPlots_Amphipods-Parasites.R: analyses comparing the bacteriota of all amphipods with that of acanthocephalan and cestode parasites (rarefied beta diversity and non-rarefied bar plots of relative abundance).