Summary of Study ST004173

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 PR002633. The data can be accessed directly via it's Project DOI: 10.21228/M89K0J This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php

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Study IDST004173
Study TitleStudy on the metabolic pathways of evolutionary Lacticaseibacillus casei and wild-type Lacticaseibacillus casei under oxidative stress
Study SummaryThis study took evolutionary Lacticaseibacillus casei and wild-type Lacticaseibacillus casei as research objects, focusing on analyzing the differences in metabolic pathways between the two strains under oxidative stress. First, sample processing and stress induction were conducted: 1.5 mM hydrogen peroxide was used as the oxidative stressor, and the two strains were subjected to stress treatment for 2 hours respectively. After the stress treatment, the bacterial cells were collected by low-temperature centrifugation.Subsequently, ultra-high performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) technology was employed for metabolite detection. Primary and secondary mass spectrometry data of metabolites were collected in positive and negative ion modes respectively, and the types of metabolites were initially identified by matching with metabolomics databases such as HMDB and METLIN.Finally, data analysis was carried out: first, partial least squares discriminant analysis (PLS-DA) was used for pattern recognition of the metabolomic data of the two strains. Metabolites with significant differences between groups were screened based on the criteria of VIP>1 and P<0.05. Then, the differential metabolites were mapped to the KEGG database, and metabolic pathway enrichment analysis was performed via Fisher’s Exact Test. Focus was placed on antioxidant, energy, and amino acid-related metabolic pathways to clarify the differences in metabolic pathway regulation between the two strains under oxidative stress, providing methodological support for analyzing the stress resistance mechanism of the evolutionary strain.
Institute
Kunming university of science and technology
Last NameSu
First Namelei
AddressWujiaying Street, Chenggong District, Kunming City, Yunnan Province, Kunming, Yunnan, 650599, China
Emailsuleilei21@163.com
Phone17775175972
Submit Date2025-09-03
Raw Data AvailableYes
Raw Data File Type(s)mzML, raw(Thermo)
Analysis Type DetailLC-MS
Release Date2025-09-30
Release Version1
lei Su lei Su
https://dx.doi.org/10.21228/M89K0J
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR002633
Project DOI:doi: 10.21228/M89K0J
Project Title:Metabolomics of Evolutionary Lacticaseibacillus casei (SEvo) and Wild-Type Lacticaseibacillus casei (SAnc)
Project Summary:To compare the higher survival ability of evolutionary Lacticaseibacillus casei(SEvo) than wild-type Lacticaseibacillus casei(SAnc) under hydrogen peroxide (a strong oxidative stressor), we used 1.5 mM hydrogen peroxide for a 2-hour stress treatment and conducted metabolomic studies based on mass spectrometry technology. we analyzed the differences in metabolites among them, and performed KEGG pathway enrichment analysis by investigating the abundance of metabolites and the classification of metabolites, so as to explore the metabolic pathways that contribute to the superiority of evolutionary strains over wild-type strains under oxidative stress.
Institute:Kunming university of science and technology
Last Name:Su
First Name:lei
Address:Wujiaying Street, Chenggong District, Kunming City, Yunnan Province, Kunming, Yunnan, 650599, China
Email:suleilei21@163.com
Phone:17775175972

Subject:

Subject ID:SU004324
Subject Type:Bacteria
Subject Species:Lacticaseibacillus casei
Taxonomy ID:1582

Factors:

Subject type: Bacteria; Subject species: Lacticaseibacillus casei (Factor headings shown in green)

mb_sample_id local_sample_id Sample source Bacterial strain
SA482088SEvo_1bacterial cells Evo
SA482089SEvo_2bacterial cells Evo
SA482090SEvo_3bacterial cells Evo
SA482091SEvo_4bacterial cells Evo
SA482092SEvo_5bacterial cells Evo
SA482093SEvo_6bacterial cells Evo
SA482094SAnc_1bacterial cells WT
SA482095SAnc_2bacterial cells WT
SA482096SAnc_3bacterial cells WT
SA482097SAnc_4bacterial cells WT
SA482098SAnc_5bacterial cells WT
SA482099SAnc_6bacterial cells WT
Showing results 1 to 12 of 12

Collection:

Collection ID:CO004317
Collection Summary:We obtained an evolved strain of Lacticaseibacillus casei (formerly Lactobacillus casei) from the wild-type Lacticaseibacillus casei via aerobic stress. Both the wild-type and evolved Lacticaseibacillus casei strains were cultured overnight in MRS medium for approximately 16 hours. Subsequently, hydrogen peroxide was added to adjust its concentration to 1.5 mM, and the mixture was incubated in a constant-temperature incubator at 37°C for 2 hours. After that, the bacterial cells were collected by centrifugation at 4°C (3,000 rpm for 8 minutes). The collected cells were washed three times with distilled water, followed by another centrifugation step at 4°C (3,000 rpm for 8 minutes). The final bacterial cells were placed in 1.5 mL centrifuge tubes, with the weight of each sample required to be at least 80 mg. These samples were then transported at 4°C for subsequent testing.
Sample Type:Bacterial cells

Treatment:

Treatment ID:TR004333
Treatment Summary:Sample type: bacterial cells; Collection time: 2 hours post-treatment; Collection tools and conditions: sterile centrifuge tubes were used, and samples were transported under refrigeration at 4°C; Collection volume: 80 mg.Intervention subjects: two bacterial strains, namely evolved bacteria and wild-type bacteria. The overnight cultures of evolved bacteria and wild-type bacteria were centrifuged, then resuspended in 1.5 mM hydrogen peroxide, and incubated for 2 hours.After being treated with 1.5 mM hydrogen peroxide for 2 hours, the evolved bacteria and wild-type bacteria were washed three times with distilled water. Subsequently, bacterial cells were collected via centrifugation at 4°C (3,000 rpm for 8 minutes), and finally placed in 1.5 mL centrifuge tubes for subsequent detection.

Sample Preparation:

Sampleprep ID:SP004330
Sampleprep Summary:After being treated with 1.5 mM hydrogen peroxide for 2 hours, the evolved bacteria and wild-type bacteria were washed three times with distilled water. Subsequently, bacterial cells were collected via centrifugation at 4°C (3,000 rpm for 8 minutes), and finally placed in 1.5 mL centrifuge tubes for subsequent detection.

Combined analysis:

Analysis ID AN006927 AN006928
Chromatography ID CH005260 CH005260
MS ID MS006624 MS006625
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Thermo Vanquish Thermo Vanquish
Column Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um) Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Orbitrap Exploris 120 Thermo Orbitrap Exploris 120
Ion Mode POSITIVE NEGATIVE
Units intensity intensity

Chromatography:

Chromatography ID:CH005260
Chromatography Summary:Ultra-High Performance Liquid Chromatography (UPLC) with Reverse Phase (RP) chromatography (based on the use of ACQUITY UPLC HSS T3 column, a typical reverse-phase chromatographic column, and mobile phases with water and acetonitrile, consistent with RP separation principles)
Instrument Name:Thermo Vanquish
Column Name:Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um)
Column Temperature:40
Flow Gradient:0.0 min 5% B; 1.0 min 5% B; 4.7 min 95% B; 6 min 95% B; 6.1 min 5% B; 8.5 min 5% B
Flow Rate:0.4mL/min
Solvent A:100% water; 0.1% formic acid
Solvent B:99.9% acetonitrile/0.1% formic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS006624
Analysis ID:AN006927
Instrument Name:Thermo Orbitrap Exploris 120
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Spray voltage +3.5 kV; sheath gas 40 arb; auxiliary gas 10 arb (N₂); capillary temp 320 ℃; auxiliary gas temp 300 ℃; MS1 full scan, m/z 70–1000, resolution 60,000 FWHM, AGC target standard, Max IT 100 ms; MS2 top-4 DDA, HCD CE 30%, dynamic exclusion 4 s, resolution 15,000 FWHM, AGC target standard, Max IT Auto. Raw data (*.raw) directly imported into MS-DIAL; peaks absent in >50% QC samples filtered; missing values imputed (gap filling); normalization applied. Suitable for protonated metabolites. Thermo Xcalibur (v4.7) for DDA acquisition. MS-DIAL (v4.9.221218) for feature extraction and annotation; databases: PSNGM, mzCloud, LIPID MAPS, HMDB, MoNA, NIST_2020_MSMS, AI-predicted MS/MS. Matching tolerance: MS1 ±0.01 m/z, MS2 ±0.05 m/z; features with score ≥70 accepted.
Ion Mode:POSITIVE
  
MS ID:MS006625
Analysis ID:AN006928
Instrument Name:Thermo Orbitrap Exploris 120
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Spray voltage –3.0 kV; other parameters (sheath/auxiliary gas, temps, scan range, resolution, AGC, Max IT, collision energy, dynamic exclusion) are the same as positive mode. Raw data (*.raw) directly imported into MS-DIAL; peaks absent in >50% QC samples filtered; missing values imputed (gap filling); normalization applied. Suitable for deprotonated metabolites. Thermo Xcalibur (v4.7) for DDA acquisition. MS-DIAL (v4.9.221218) for feature extraction and annotation; databases: PSNGM, mzCloud, LIPID MAPS, HMDB, MoNA, NIST_2020_MSMS, AI-predicted MS/MS. Matching tolerance: MS1 ±0.01 m/z, MS2 ±0.05 m/z; features with score ≥70 accepted.
Ion Mode:NEGATIVE
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