Gut Microbiome Shifts During Frog Development

Overview This dataset accompanies the manuscript "Gut Microbiome Shifts During Frog Development Parallel Host-Association Patterns Across Vertebrate Lineages" and provides the processed data, analysis scripts, and figure-generation code used for the microbiome analyses. The files summarize bacterial community patterns associated with frog developmental stages, including eggs, tadpoles, froglets, and adult frogs, together with environmental and comparative vertebrate microbiome reference data used in downstream analyses. data: Processed data files used for microbiome analyses and figure generation. alpha_md.tsv: Alpha diversity metrics and sample metadata across frog developmental stages. bugbase.tsv: BugBase phenotype prediction results for frog samples. indval_for_plot.tsv: Processed indicator value analysis results used for plotting stage- or environment-associated taxa. metadata.tsv: Sample metadata containing sample identifiers and developmental-stage group information. mixing-proportions-family-vertbrates.tsv: source contribution estimates at the family level using vertebrate and environmental reference sources using SourceTracker2. prokatlas_result_frog.tsv: ProkAtlas habitat preference score results for samples across frog's development. prokatlas_result_vertebrates.tsv: ProkAtlas habitat preference score results for comparative vertebrate microbiome data. ps_frog.rds: Processed phyloseq object for frog microbiome samples. ps_frog_env.rds: Processed phyloseq object including frog and environmental samples. ps_vert.rds: Processed phyloseq object for comparative vertebrate microbiome samples. analysis: Files related to the ProkAtlas habitat preference analysis. prokatlas_standalone_200905.zip: Original standalone ProkAtlas script used for habitat preference analysis. prokatlas.py: Author-prepared wrapper script used to run the ProkAtlas workflow in a single execution step for the datasets in this study. script: R scripts used to reproduce the main analyses and manuscript figures. Figure1_alpha_diversity.R: Calculates alpha diversity metrics and generates the alpha diversity plot. Figure1_beta_diversity.R: Calculates beta diversity metrics and generates ordination and group-dissimilarity plots. Figure2.R: Generates visualization for Bugbase and PICRUSt2 results. Figure3_indicator_value_analysis.R: Performs indicator value analysis for taxa associated with frog developmental stages and environmental sources. Figure3_indicator_value_plot.R: Generates Figure 3 plots from the processed indicator value analysis results. Figure4.R: Visualizes SourceTracker-style source contribution estimates and ProkAtlas habitat preference results. Figure5.R: Generates Figure 5 using processed comparative microbiome analysis results.