Summary of Study ST004200

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR002649. The data can be accessed directly via it's Project DOI: 10.21228/M87P0Z This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

Study ID	ST004200
Study Title	untargeted metabolomics in serum of microplastics exposed mice - Untargeted LC/MS
Study Type	in vivo
Study Summary	To investigate the impact of ingested MPs on the gut microbiome and the metabolome, 8-week-old male and female C57/BL6 mice were orally gavaged mixed plastic (5 µm) 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. A total of 1162 bacterial species and 1205 metabolites were evaluated for downstream analysis.
Institute	University of Washington
Department	Environmental and Occupational Health Science
Laboratory	Cui Lab
Last Name	Kim
First Name	Kyle
Address	3150 Stephanie Loop Northeast
Email	kk1109@uw.edu
Phone	3606883268
Submit Date	2025-09-08
Num Groups	6
Total Subjects	24
Num Males	12
Num Females	12
Raw Data Available	Yes
Raw Data File Type(s)	mzML, raw(Thermo)
Analysis Type Detail	LC-MS
Release Date	2025-10-10
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR002649
Project DOI:	doi: 10.21228/M87P0Z
Project Title:	In vivo exposure of mixed microplastic particles in mice and its impacts on the murine gut microbiome and metabolome
Project Type:	MS quantitative analysis
Project Summary:	Microplastics (MPs) are emerging environmental contaminants due to increasing global plastic production and waste. Microplastics, defined as plastic particles less than 5 mm in diameter, are formed through degradation of larger plastics via sunlight, weathering, and microbes. These plastic compounds are widely detected in water, soil, food, as well as human stool and blood. The gut microbiome, often referred to as our second genome, is important in human health and is the primary point of contact for orally ingested microplastics. To investigate the impact of ingested MPs on the gut microbiome and the metabolome, 8-week-old male and female C57/BL6 mice were orally gavaged mixed plastic (5 µm) 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. A total of 1162 bacterial species and 1205 metabolites were evaluated for downstream analysis. MPs exposure resulted in significant sex-specific and dose-dependent changes to the gut microbiome composition along with substantial regulation of 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. Our study demonstrates that microplastics dysregulate the gut microbiome and serum metabolome, highlighting potential human disease risks.
Institute:	University of Washington
Department:	Environmental and Occupational Health Science
Laboratory:	Cui Lab
Last Name:	Kim
First Name:	Kyle
Address:	3150 Stephanie Loop Northeast, Lacey, Washington, 98516, USA
Email:	kk1109@uw.edu
Phone:	3606883268
Funding Source:	National Institute of Health (NIH), National Institute of Environmental Health Sciences (NIEHS)

Subject:

Subject ID:	SU004352
Subject Type:	Mammal
Subject Species:	Mus musculus
Taxonomy ID:	10090
Age Or Age Range:	8-12 weeks
Gender:	Male and female
Animal Animal Supplier:	Taconic Biosciences
Animal Housing:	Temperature (20–24°C) and humidity (30%–60%)
Animal Light Cycle:	12-h light/dark cycle
Animal Feed:	ad libitum
Animal Water:	ad libitum
Species Group:	C57BL/6

Factors:

Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id	local_sample_id	Sample source	Sex	Treatment
SA484354	FCTRL4	Serum	Female	Control
SA484355	FCTRL3	Serum	Female	Control
SA484356	FCTRL2	Serum	Female	Control
SA484357	FCTRL1	Serum	Female	Control
SA484358	FHIGH3	Serum	Female	High_MPs
SA484359	FHIGH4	Serum	Female	High_MPs
SA484360	FHIGH1	Serum	Female	High_MPs
SA484361	FHIGH2	Serum	Female	High_MPs
SA484362	FLOW2	Serum	Female	Low_MPs
SA484363	FLOW1	Serum	Female	Low_MPs
SA484364	FLOW3	Serum	Female	Low_MPs
SA484365	FLOW4	Serum	Female	Low_MPs
SA484366	MCTRL2	Serum	Male	Control
SA484367	MCTRL4	Serum	Male	Control
SA484368	MCTRL3	Serum	Male	Control
SA484369	MCTRL1	Serum	Male	Control
SA484370	MHIGH1	Serum	Male	High_MPs
SA484371	MHIGH4	Serum	Male	High_MPs
SA484372	MHIGH3	Serum	Male	High_MPs
SA484373	MHIGH2	Serum	Male	High_MPs
SA484374	MLOW1	Serum	Male	Low_MPs
SA484375	MLOW2	Serum	Male	Low_MPs
SA484376	MLOW3	Serum	Male	Low_MPs
SA484377	MLOW4	Serum	Male	Low_MPs
SA484378	blank_1	Serum	NA	Blank
SA484379	blank_2	Serum	NA	Blank
SA484380	Serum_QC_1	Serum	NA	QC
SA484381	Serum_QC_2	Serum	NA	QC
SA484382	Serum_QC_3	Serum	NA	QC
SA484383	Serum_QC_4	Serum	NA	QC

Showing results 1 to 30 of 30

Showing results 1 to 30 of 30

Collection:

Collection ID:	CO004345
Collection Summary:	Blood was collected via cardiac puncture and samples were spun and separated for serum. Frozen serum samples were first thawed overnight under 4oC, and 50 μL of each sample was placed in a 2 mL Eppendorf vial prior to metabolomic analysis
Sample Type:	Blood (serum)

Treatment:

Treatment ID:	TR004361
Treatment Summary:	8-week-old male and female C57/BL6 mice were orally gavaged mixed plastic (5 µm) 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).
Treatment:	in vivo oral ingestion
Treatment Compound:	mixed microplastics (polystyrene, polyethylene, poly lactic-co glycolic acid)
Treatment Route:	gastric oral gavage
Treatment Dose:	0mg/wk, 2mg/wk, 4mg/wk
Treatment Dosevolume:	100 ul of 10mg/ml twice a week for 2mg/wk and 200ul of 10mg/ml twice a week for 4mg/wk
Treatment Doseduration:	4 weeks
Treatment Vehicle:	water

Sample Preparation:

Sampleprep ID:	SP004358
Sampleprep Summary:	Frozen serum samples were first thawed overnight under 4oC, and 50 μL of each sample was placed in a 2 mL Eppendorf vial. The initial step for protein precipitation and metabolite extraction was performed by adding 500 μL MeOH and 50 μL internal standard solution (containing 1,810.5 μM 13C3-lactate and 142 μM 13C5-glutamic acid). The mixture was then vortexed for 10 s and stored at -20oC for 30 min, followed by centrifugation at 14,000 RPM for 10 min at 4° C. The supernatants (450 μL) were collected into a new Eppendorf vial and dried using a CentriVap Concentrator (Labconco, Fort Scott, KS). The dried samples were reconstituted in 150 μL of 40% PBS/60% ACN. A pooled sample, which was a mixture of all plasma samples was used as the quality-control (QC) sample. Briefly, all LC-MS experiments were performed on a Thermo Vanquish UPLC-Exploris 240 Orbitrap MS instrument (Waltham, MA). Each sample was injected twice, 10 µL for analysis using negative ionization mode and 4 µL for analysis using positive ionization mode. Both chromatographic separations were performed in hydrophilic interaction chromatography (HILIC) mode on a Waters XBridge BEH Amide column (150 x 2.1 mm, 2.5 µm particle size, Waters Corporation, Milford, MA). The flow rate was 0.3 mL/min, the auto-sampler temperature was kept at 4 ̊C, and the column compartment was set at 40 ̊C. The mobile phase was composed of Solvents A (10 mM ammonium acetate, 10 mM ammonium hydroxide in 95% H2O/5% ACN) and B (10 mM ammonium acetate, 10 mM ammonium hydroxide in 95% ACN/5% H2O). After the initial 1 min isocratic elution of 90% B, the percentage of Solvent B decreased to 40% at t=11 min. The composition of Solvent B maintained at 40% for 4 min (t=15 min), and then the percentage of B gradually went back to 90%, to prepare for the next injection. Using a mass spectrometer equipped with an electrospray ionization (ESI) source, we will collect untargeted data from 70 to 1050 m/z.

Sampleprep ID:

SP004358

Sampleprep Summary:

Frozen serum samples were first thawed overnight under 4oC, and 50 μL of each sample was placed in a 2 mL Eppendorf vial. The initial step for protein precipitation and metabolite extraction was performed by adding 500 μL MeOH and 50 μL internal standard solution (containing 1,810.5 μM 13C3-lactate and 142 μM 13C5-glutamic acid). The mixture was then vortexed for 10 s and stored at -20oC for 30 min, followed by centrifugation at 14,000 RPM for 10 min at 4° C. The supernatants (450 μL) were collected into a new Eppendorf vial and dried using a CentriVap Concentrator (Labconco, Fort Scott, KS). The dried samples were reconstituted in 150 μL of 40% PBS/60% ACN. A pooled sample, which was a mixture of all plasma samples was used as the quality-control (QC) sample. Briefly, all LC-MS experiments were performed on a Thermo Vanquish UPLC-Exploris 240 Orbitrap MS instrument (Waltham, MA). Each sample was injected twice, 10 µL for analysis using negative ionization mode and 4 µL for analysis using positive ionization mode. Both chromatographic separations were performed in hydrophilic interaction chromatography (HILIC) mode on a Waters XBridge BEH Amide column (150 x 2.1 mm, 2.5 µm particle size, Waters Corporation, Milford, MA). The flow rate was 0.3 mL/min, the auto-sampler temperature was kept at 4 ̊C, and the column compartment was set at 40 ̊C. The mobile phase was composed of Solvents A (10 mM ammonium acetate, 10 mM ammonium hydroxide in 95% H2O/5% ACN) and B (10 mM ammonium acetate, 10 mM ammonium hydroxide in 95% ACN/5% H2O). After the initial 1 min isocratic elution of 90% B, the percentage of Solvent B decreased to 40% at t=11 min. The composition of Solvent B maintained at 40% for 4 min (t=15 min), and then the percentage of B gradually went back to 90%, to prepare for the next injection. Using a mass spectrometer equipped with an electrospray ionization (ESI) source, we will collect untargeted data from 70 to 1050 m/z.

Chromatography:

Chromatography ID:	CH005303
Chromatography Summary:	The untargeted LC-MS metabolomics method used here was modeled after that developed and used in a growing number of studies (Gu et al. 2015; Wei et al. 2021; Jin et al. 2023; Mohr et al. 2024; Scieszka et al. 2023; Kim et al. 2023; Garcia et al. 2024). Briefly, all LC-MS experiments were performed on a Thermo Vanquish UPLC-Exploris 240 Orbitrap MS instrument (Waltham, MA). Each sample was injected twice, 10 µL for analysis using negative ionization mode and 4 µL for analysis using positive ionization mode. Both chromatographic separations were performed in hydrophilic interaction chromatography (HILIC) mode on a Waters XBridge BEH Amide column (150 x 2.1 mm, 2.5 µm particle size, Waters Corporation, Milford, MA). The flow rate was 0.3 mL/min, the auto-sampler temperature was kept at 4 ̊C, and the column compartment was set at 40 ̊C. The mobile phase was composed of Solvents A (10 mM ammonium acetate, 10 mM ammonium hydroxide in 95% H2O/5% ACN) and B (10 mM ammonium acetate, 10 mM ammonium hydroxide in 95% ACN/5% H2O). After the initial 1 min isocratic elution of 90% B, the percentage of Solvent B decreased to 40% at t=11 min. The composition of Solvent B maintained at 40% for 4 min (t=15 min), and then the percentage of B gradually went back to 90%, to prepare for the next injection. Using a mass spectrometer equipped with an electrospray ionization (ESI) source, we will collect untargeted data from 70 to 1050 m/z.
Instrument Name:	Thermo Vanquish
Column Name:	XBridge BEH Amide (150 x 2.1 mm, 2.5 um)
Column Temperature:	40 ̊C
Flow Gradient:	After the initial 1 min isocratic elution of 90% B, the percentage of Solvent B decreased to 40% at t=11 min. The composition of Solvent B maintained at 40% for 4 min (t=15 min), and then the percentage of B gradually went back to 90%, to prepare for the next injection
Flow Rate:	0.3 mL/min
Solvent A:	95% water/5% acetonitrile; 10 mM ammonium acetate; 10 mM ammonium hydroxide
Solvent B:	95% acetonitrile/5% water; 10 mM ammonium acetate; 10 mM ammonium hydroxide
Chromatography Type:	HILIC

Analysis:

Analysis ID:	AN006985
Analysis Type:	MS
Chromatography ID:	CH005303
Num Factors:	8
Num Metabolites:	1437
Units:	Relative abundance

Analysis ID:	AN006986
Analysis Type:	MS
Chromatography ID:	CH005303
Num Factors:	8
Num Metabolites:	1437
Units:	Relative abundance