Dataset DOI: 10.5061/dryad.fn2z34v78

Description of the data and file structure

This data set contains the data and codes needed to replicate analyses for the testing of the hypothesis of mixed microplastic particles differentially regulating the murine gut microbiome and the serum metabolome. To investigate the impact of ingested MPs on the gut microbiome and the metabolome, 8 weeks-old male and female C57/BL6 mice were orally gavaged mixed plastic (5 um) exposure consisting of polystyrene, polyethylene, and the biodegradable/biocompatible plastic, poly- (lactic-co-glycolic acid) twice a week for 4 weeks at 0, 2, or 4 mg/week (n = 8/group).  Fecal pellets were collected for bacterial DNA extraction and metagenomic shotgun sequencing, and serum was subjected to targeted and untargeted metabolomics. Data set includes both raw and filtered count of bacterial taxa and associated predictive functional analysis from the metagenomic shotgun sequencing as well as raw values from both targeted (SCFA) and untargeted metabolomics from serum. MPs exposure resulted in significant sex-specific and dose-dependent changes to the gut microbiome composition along with substantial regulation of the predicted metabolic pathways. Untargeted metabolomics in serum showed that a low MPs dose displayed a more prominent effect on key metabolic pathways such as amino acid metabolism, mitochondrial function, and inflammation. Additionally, SCFA-targeted metabolomics showed significant changes in neuroprotective SCFAs levels in both sexes by MPs exposure.

Files and variables

Bioinformatics R-script (.R files)

Code(bonferroni).R, Code(FDR).R, Kyle_normalize_untargeted_data.R, Kyle_untargeted_ANOVA_DUNCAN.R, Kyle_untargeted_ANOVA_FDR.R, One_way_ANOVA.R, PCA___elipses.R, PCA_plotting.R, Targeted_metabolite_ANOVA_boxplot.R, Untargeted_boxplot.R, up_down_barplot.R

These .R files were all utilized throughout this project to generate the bioinformatics and associated visualization plots.

Raw sequencing files (.zip and .tar)

Sample columns are labeled with sample number followed by time course duration (ex. 1.4wk is sample 1 for 4 weeks time point group where wk signifies week)

Archive.zip, fasta.tar, fastq.tar

Fasta.tar contains three folders that contain the .log files of the initial screening and trimming (sequence data preparation) logs that were done by Diversigen Inc during the initial steps of the metagenomic shotgun sequencing (Step0, Step1, and Step2). The three .fn files contained within this .tar file are the raw output files of each trimming and preparation steps from Step_0, Step1, and Step_2.

Fastq.tar contains .fq files which are the raw nucleotide sequences from the metagenomic shotgun sequencing after the original files were trimmed and prepared.

.fq files are designated in a similar manner to the sample ID in the various raw counts files (ex. 1.4wk_1.fq is sample 1 for 4 weeks time point group where wk signifies week and 1 for forward read vs 2 for reverse read).

Raw targeted SCFA metabolomics dataset

These files contain the raw targeted SCFA metabolomics data set from this project.

SCFA_raw_data_MPS_Calibration_curve.csv, SCFA_raw_data_MPS_Raw_Data.csv, SCFA_raw_data_MPS_Results.csv, SCFA_raw_data_MPS_Serum.csv

Raw count and relative abundance files (.txt files)

Sample columns are labeled with sample number followed by time course duration (ex. 1.4wk is sample 1 for 4 weeks time point group where wk signifies week)

All_Levels_Filtered_Table_(relative_abundance).txt, All_levels_taxa_data_(count_data).txt, Alpha_Diversity_Table.txt, Kegg_Enzyme_(count_data).txt, Kegg_Enzyme_(relative_abundance).txt, Kegg_Enzyme_Bray-Curtis_distance_matrix.txt, Kegg_Enzymes_(count_data).txt, Kegg_Enzymes_(relative_abundance).txt, Kegg_level-2_pathways_(count_data).txt, Kegg_level-2_pathways_(relative_abundance).txt, Kegg_level-3_pathways_(count_data).txt, Kegg_level-3_pathways_(relative_abundance).txt, Kegg_modules_(count_data).txt, Kegg_modules_(relative_abundance).txt, Kegg_Modules_distance_matrix.txt, Kegg_Orthology_(count_data).txt, Kegg_Orthology_Groups_(count_data).txt, Species_Bray-Curtis_Distance_matrix.txt

These .txt files contain either the raw or relative abundance values associated with the microbiome (and predictive) data sets from the metagenomic shotgun sequencing output. All data sets are formatted as sample groups in the columns and experimental parameters of interest in rows.

Microbiome associated stratified raw files (.tsv)

Sample columns are labeled with sample number followed by time course duration (ex. 1.4wk is sample 1 for 4 weeks time point group where wk signifies week)

taxatable-class-absolute.tsv, taxatable-class-relative.tsv, taxatable-class-short-absolute.tsv, taxatable-class-short-relative.tsv, taxatable-family-absolute.tsv, taxatable-family-relative.tsv, taxatable-family-short-absolute.tsv, taxatable-family-short-relative.tsv, taxatable-genus-absolute.tsv, taxatable-genus-relative.tsv, taxatable-genus-short-absolute.tsv, taxatable-genus-short-relative.tsv, taxatable-kingdom-absolute.tsv, taxatable-kingdom-relative.tsv, taxatable-kingdom-short-absolute.tsv, taxatable-kingdom-short-relative.tsv, taxatable-order-absolute.tsv, taxatable-order-relative.tsv, taxatable-order-short-absolute.tsv, taxatable-order-short-relative.tsv, taxatable-phylum-absolute.tsv, taxatable-phylum-relative.tsv, taxatable-phylum-short-absolute.tsv, taxatable-phylum-short-relative.tsv, taxatable-species-absolute.tsv, taxatable-species-relative.tsv, taxatable-species-short-absolute.tsv, taxatable-species-short-relative.tsv, taxatable-strain-absolute.tsv, taxatable-strain-relative.tsv, taxatable-strain-short-absolute.tsv, taxatable-strain-short-relative.tsv

These data sets contain microbiome associated datasets stratified by various parameters of interest (species specification and sample depth). All data sets are formatted as sample groups in the columns and experimental parameters of interest in rows.

Alternative sources to access data

Metabolomics Workbench data repository (metabolomics data set): 

Project ID ST004200 (untargeted metabolomics) and ST004201 (targeted SCFA metabolomics)

Data set source

Diversigen Inc. (sequencing company)