Summary of Study ST004259

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 PR002687. The data can be accessed directly via it's Project DOI: 10.21228/M8B85N This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php

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Study ID	ST004259
Study Title	Phytate enhances gut Parasutterella colonization to alleviate radiation injury via anti-inflammatory and antioxidant effects
Study Summary	Food as medicine shows promise for disease intervention or treatment. Here, we found phytate, an active ingredient of plant-based diets, exhibits properties in mitigating radiotherapy-related complications. Oral gavage of phytate restored hematogenic organ atrophy, elevated peripheral blood neutrophils and white blood cells, reduced inflammation, and improved gastrointestinal (GI) integrity in irradiated mice. Phytate intake modulated the gut microbiota, facilitating the colonization of symbiotic Parasutterella in GI tract, thus combating intestinal radiation toxicity. In vitro assays and untargeted metabolomics identified 3-Phenyllactic acid (PLA) and N-Acetyl-L-leucine (NL) as functional metabolites produced by Parasutterella. In vitro, ex vivo, and in vivo models showed that PLA induces M2-like polarization in macrophages, while NL reduced oxidative stress, both counteracting radiation toxicity and working synergistically. Our findings offer mechanistic insights into phytate for alleviating radiation-associated complications and suggest that Parasutterella and its metabolites might be employed as promising probiotics or postbiotics for cancer patients with radiotherapy.
Institute	Chinese Academy of Medical Sciences
Last Name	Li
First Name	Yuan
Address	Baidi Road, Tianjin, Tianjin, 300192, China
Email	liyuan@irm-cams.ac.cn
Phone	+8615900383739
Submit Date	2025-09-29
Raw Data Available	Yes
Raw Data File Type(s)	raw(Thermo)
Analysis Type Detail	LC-MS
Release Date	2025-10-28
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR002687
Project DOI:	doi: 10.21228/M8B85N
Project Title:	Phytate enhances gut Parasutterella colonization to alleviate radiation injury via anti-inflammatory and antioxidant effects
Project Summary:	Food as medicine shows promise for disease intervention or treatment. Here, we found phytate, an active ingredient of plant-based diets, exhibits properties in mitigating radiotherapy-related complications. Oral gavage of phytate restored hematogenic organ atrophy, elevated peripheral blood neutrophils and white blood cells, reduced inflammation, and improved gastrointestinal (GI) integrity in irradiated mice. Phytate intake modulated the gut microbiota, facilitating the colonization of symbiotic Parasutterella in GI tract, thus combating intestinal radiation toxicity. In vitro assays and untargeted metabolomics identified 3-Phenyllactic acid (PLA) and N-Acetyl-L-leucine (NL) as functional metabolites produced by Parasutterella. In vitro, ex vivo, and in vivo models showed that PLA induces M2-like polarization in macrophages, while NL reduced oxidative stress, both counteracting radiation toxicity and working synergistically. Our findings offer mechanistic insights into phytate for alleviating radiation-associated complications and suggest that Parasutterella and its metabolites might be employed as promising probiotics or postbiotics for cancer patients with radiotherapy.
Institute:	Chinese Academy of Medical Sciences
Last Name:	Li
First Name:	Yuan
Address:	Baidi Road, Tianjin, Tianjin, 300192, China
Email:	liyuan@irm-cams.ac.cn
Phone:	+8615900383739

Subject:

Subject ID:	SU004412
Subject Type:	Bacteria
Subject Species:	Homo sapiens
Taxonomy ID:	9606

Factors:

Subject type: Bacteria; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id	local_sample_id	Treatment	Sample source
SA496928	PE0h-6	Sample collection after 0h of cultivation	Culture supernatant
SA496929	PE0h-2	Sample collection after 0h of cultivation	Culture supernatant
SA496930	PE0h-1	Sample collection after 0h of cultivation	Culture supernatant
SA496931	PE0h-5	Sample collection after 0h of cultivation	Culture supernatant
SA496932	PE0h-4	Sample collection after 0h of cultivation	Culture supernatant
SA496933	PE0h-3	Sample collection after 0h of cultivation	Culture supernatant
SA496934	PE24h-1	Sample collection after 24h of cultivation	Culture supernatant
SA496935	PE24h-2	Sample collection after 24h of cultivation	Culture supernatant
SA496936	PE24h-3	Sample collection after 24h of cultivation	Culture supernatant
SA496937	PE24h-4	Sample collection after 24h of cultivation	Culture supernatant
SA496938	PE24h-5	Sample collection after 24h of cultivation	Culture supernatant
SA496939	PE24h-6	Sample collection after 24h of cultivation	Culture supernatant
SA496940	PE6h-1	Sample collection after 6h of cultivation	Culture supernatant
SA496941	PE6h-2	Sample collection after 6h of cultivation	Culture supernatant
SA496942	PE6h-3	Sample collection after 6h of cultivation	Culture supernatant
SA496943	PE6h-5	Sample collection after 6h of cultivation	Culture supernatant
SA496944	PE6h-6	Sample collection after 6h of cultivation	Culture supernatant
SA496945	PE6h-4	Sample collection after 6h of cultivation	Culture supernatant

Showing results 1 to 18 of 18

Showing results 1 to 18 of 18

Collection:

Collection ID:	CO004405
Collection Summary:	Culture supernatants of Parasutterella excrementihominis (DSM 21040) were collected at 0, 6, and 24 hours, followed by centrifugation at 3000 rpm for 10 minutes at 4ºC. The samples were then rapidly frozen in liquid nitrogen for 15 minutes and stored at -80ºC until further use.
Sample Type:	Media

Treatment:

Treatment ID:	TR004421
Treatment Summary:	Not applicable

Sample Preparation:

Sampleprep ID:	SP004418
Sampleprep Summary:	The samples (1 mL) were freeze-dried and resuspended with prechilled 80% methanol by well vortex. Then the samples were incubated on ice for 5 min and centrifuged at 15,000 g, 4°C for 15 min. Some of supernatant was diluted to final concentration containing 53% methanol by LC-MS grade water. The samples were subsequently transferred to a fresh Eppendorf tube and were centrifuged at 15000 g, 4°C for 15 min. Finally, the supernatant was injected into the LC-MS/MS system analysis.

Sampleprep ID:

SP004418

Sampleprep Summary:

The samples (1 mL) were freeze-dried and resuspended with prechilled 80% methanol by well vortex. Then the samples were incubated on ice for 5 min and centrifuged at 15,000 g, 4°C for 15 min. Some of supernatant was diluted to final concentration containing 53% methanol by LC-MS grade water. The samples were subsequently transferred to a fresh Eppendorf tube and were centrifuged at 15000 g, 4°C for 15 min. Finally, the supernatant was injected into the LC-MS/MS system analysis.

Combined analysis:

Analysis ID	AN007087	AN007088
Chromatography ID	CH005384	CH005385
MS ID	MS006784	MS006785
Analysis type	MS	MS
Chromatography type	Reversed phase	Reversed phase
Chromatography system	Thermo Vanquish	Thermo Vanquish
Column	Thermo Hypersil GOLD aQ (100 x 2.1 mm, 1.9 μm)	Thermo Hypersil GOLD aQ (100 x 2.1 mm,1.9 μm)
MS Type	ESI	ESI
MS instrument type	Orbitrap	Orbitrap
MS instrument name	Thermo Q Exactive HF hybrid Orbitrap	Thermo Q Exactive HF hybrid Orbitrap
Ion Mode	POSITIVE	NEGATIVE
Units	Peak area	Peak area

Chromatography:

Chromatography ID:	CH005384
Instrument Name:	Thermo Vanquish
Column Name:	Thermo Hypersil GOLD aQ (100 x 2.1 mm, 1.9 μm)
Column Temperature:	40°C
Flow Gradient:	2%B, 1.5 min;2-85% B, 3 min; 85-100% B, 10 min；100-2% B, 10.1 min；2%B, 12 min.
Flow Rate:	0.2 mL/min
Solvent A:	100% Water; 0.1% Formic acid
Solvent B:	100% Methanol
Chromatography Type:	Reversed phase

Chromatography ID:	CH005385
Instrument Name:	Thermo Vanquish
Column Name:	Thermo Hypersil GOLD aQ (100 x 2.1 mm,1.9 μm)
Column Temperature:	40°C
Flow Gradient:	2%B, 1.5 min;2-85% B, 3 min; 85-100% B, 10 min；100-2% B, 10.1 min；2%B, 12 min.
Flow Rate:	0.2 mL/min
Solvent A:	100% Water; 5 mM Ammonium acetate, pH9.0
Solvent B:	100% Methanol
Chromatography Type:	Reversed phase

MS:

MS ID:	MS006784
Analysis ID:	AN007087
Instrument Name:	Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	The raw data files generated by UHPLC-MS/MS were processed using the Compound Discoverer 3.1 (CD3.1, ThermoFisher) to perform peak alignment, peak picking, and quantitation for each metabolite. The main parameters were set as follows: retention time tolerance, 0.2 minutes; actual mass tolerance, 5ppm; signal intensity tolerance, 30%; signal/noise ratio, 3; and minimum intensity, et al. After that, peak intensities were normalized to the total spectral intensity. The normalized data was used to predict the molecular formula based on additive ions, molecular ion peaks and fragment ions. And then peaks were matched with the mzCloud(https://www.mzcloud.org/)，mzVault and Mass List database to obtain the accurate qualitative and relative quantitative results. Statistical analyses were performed using the statistical software R (R version R-3.4.3), Python (Python 2.7.6 version) and CentOS (CentOS release 6.6), When data were not normally distributed, standardize according to the formula: sample raw quantitation value / (The sum of sample metabolite quantitation value / The sum of QC1 sample metabolite quantitation value)to obtain relative peak areas; And compounds whose CVs of relative peak areas in QC samples were greater than 30% were removed, and finally the metabolites' identification and relative quantification results were obtained.
Ion Mode:	POSITIVE

MS ID:	MS006785
Analysis ID:	AN007088
Instrument Name:	Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	The raw data files generated by UHPLC-MS/MS were processed using the Compound Discoverer 3.1 (CD3.1, ThermoFisher) to perform peak alignment, peak picking, and quantitation for each metabolite. The main parameters were set as follows: retention time tolerance, 0.2 minutes; actual mass tolerance, 5ppm; signal intensity tolerance, 30%; signal/noise ratio, 3; and minimum intensity, et al. After that, peak intensities were normalized to the total spectral intensity. The normalized data was used to predict the molecular formula based on additive ions, molecular ion peaks and fragment ions. And then peaks were matched with the mzCloud(https://www.mzcloud.org/)，mzVault and Mass List database to obtain the accurate qualitative and relative quantitative results. Statistical analyses were performed using the statistical software R (R version R-3.4.3), Python (Python 2.7.6 version) and CentOS (CentOS release 6.6), When data were not normally distributed, standardize according to the formula: sample raw quantitation value / (The sum of sample metabolite quantitation value / The sum of QC1 sample metabolite quantitation value)to obtain relative peak areas; And compounds whose CVs of relative peak areas in QC samples were greater than 30% were removed, and finally the metabolites' identification and relative quantification results were obtained.
Ion Mode:	NEGATIVE