MS-Hymenolepis-diet_data.zip

All datasets used for the transcriptomics, metabolomics, differential gene expression analysis, bacteriome studies, annotations, and enrichment analysis.

The Bacteriome directory Figures5-7 contains:
This dataset contains a checklist of bacteriome sequencing samples deposited in the European Nucleotide Archive (ENA), including sample identifiers, accession numbers, and associated metadata. The table documents the mapping between individual rat samples and their corresponding ENA accessions and supports the bacteriome analyses and visualizations presented in Figures 5–7.
The Bacteriome metadata directory:
This dataset contains a metadata sheet associated with bacteriome sequencing samples used in this study. The table includes sample identifiers and corresponding DNA-related information, such as extraction details and sample characteristics required for sequencing, data submission, and traceability. These metadata support the bacteriome analyses presented in Figures 5-7 and complement the sequencing data deposited in the European Nucleotide Archive (ENA).
The cytokines directory contains:
Relative expression levels (%) of cytokine genes (Ifng, Il1b, Il4, Il13) measured by qPCR in individual rats across experimental groups (W-HD, W-NC, A-HD, A-NC) at day 60 of the experiment. Values were normalized to the housekeeping gene B2M and are shown relative to the maximum expression level for each gene. These data were used for visualization and statistical analyses shown in Figure 9. Raw Cp values for all cytokines measured by qPCR in individual rat samples at day 60 of the experiment are also provided. Each value represents a technical replicate, with each sample measured in duplicate.
The DE directory contains:
AHD replicates from the Accessible Fiber diet
WHD replicates from the Western diet.
count matrix computed using featureCounts of the Subread R package (featureCounts_Westen_diet_Accessible_Fiber_diet.txt) and used for the differential expression analysiscomplete table with the differential expression results (Diff_expression_all_comparisons.csv)eggnog annotations used for the enrichment analysis (MM_s0ho_r8j.emapper.annotations.csv)summary of the enrichment analysis using clusterProfiler and top30 hits from topGO for the clusters recovered using k-means clustering (k-menasclustering_enrichment_all.xlsx)summary of the enrichment analysis using clusterProfiler and top30 hits from topGO for the differentially expressed genes (enrichment.xlsx)differentially expressed genes with annotations (DEGs_annotations.xlsx)The directory of Figure 2A–F contains:
Additional representative microphotographs and two video recordings documenting Hymenolepis diminuta morphology under Ancestral Fiber diet and Western diet conditions. Microphotographs illustrate morphological features corresponding to panels shown in Figure 2A–E. Videos provide complementary dynamic visualization of parasites collected from hosts maintained on Ancestral fiber diet or Western diet.
The Figure_2F directory contains:
Raw worm length data (in cm) for Hymenolepis collected from rats fed Western (W-HD) or Accessible fiber (A-HD) diets. Each value corresponds to an individual tapeworm recovered from a single rat and was used for data visualization and statistical analyses shown in Figure 2F and the Results section.
The Figure_3 directory contains:
Raw egg counts per gram of feces measured longitudinally in individual rats during Experiment 2. Data are shown for rats maintained on an Accessible fiber diet (AD), Western diet (AD-WD), or subjected to dietary switches (AD-WD-AD), as indicated. Rows correspond to days of the experiment and columns to individual rats. Values represent raw counts without transformation or normalization. Statistical analyses are shown in Figure 3 and the Results section.
The directory to the Metabolite annotation summary and Figure 8:
This dataset contains a summary table of metabolite annotations derived from the metabolomics analyses performed in this study. The table includes metabolite names, annotation confidence levels, mass-to-charge ratios (m/z), retention times, and information on analytical standards where available. These data document the metabolite identification framework underlying the metabolomics results and support the analyses presented in Figure 8.
The Metabolome directory contains:
raw data from LC/MSThe directory of the Supplementary figure 5 contains:
This dataset contains raw body weight measurements and calculated weight change (%) of individual rats monitored longitudinally during the experiment. Raw body weights were recorded at defined time points across the experimental period for rats maintained on Western diet or Accessible fiber diet under different nutritional conditions (W-HD, W-NC, A-HD, A-NC), as indicated. Weight change (%) was calculated for each individual rat relative to its baseline body weight at day 0 and used for data visualization and statistical analyses shown in Supplementary Figure 5. Each data point represents an individual animal; values are shown as raw measurements without transformation or normalization.