Summary of Study ST004294

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 PR002711. The data can be accessed directly via it's Project DOI: 10.21228/M87C30 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	ST004294
Study Title	Investigation on the spaceflight-induced phenotypic changes and potential mechanisms of Bacillus Licheniformis
Study Summary	Bacillus licheniformis (BL) is a common probiotic clinically used to treat acute and chronic enteritis and diarrhea. The present study aimed to investigate the phenotypic changes and potential mechanisms of BL after a 6-month spaceflight aboard the China Space Station based on characterization test, morphological observation and multi-omics analysis. 6-month spaceflight delayed BL growth curve, reduced its cell wall thickness, and impaired BL biofilm formation ability and adhesion capacity to Caco-2 cells. BL viability at pH 9.0 was decreased by 9.42%. In the 6-month spaceflight BL, proteomics revealed 164 of differentially expressed proteins mainly involved on DNA damage, ATP binding, helicase activity. Metabolomics identified 55 of significantly altered metabolites, and whole-genome sequencing detected five mutated genes. After 6-month spaceflight, physiological characteristics of BL were significantly changed. Various proteins, metabolites and genes were dramatically altered as well. These novel findings may provide new insights into adaptive evolution of BL under long-term space environment, which is expected to benefit for further clinical application of BL.
Institute	Beijing Institute of Technology
Last Name	shen
First Name	shuyan
Address	Beijing Institute of Technology, Zhongguancun Campus, beijing, China, 100081, China
Email	1819599261@qq.com
Phone	18526251633
Submit Date	2025-09-18
Raw Data Available	Yes
Raw Data File Type(s)	mzML, raw
Analysis Type Detail	LC-MS
Release Date	2025-11-06
Release Version	1

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Project:

Project ID:	PR002711
Project DOI:	doi: 10.21228/M87C30
Project Title:	Investigation on the spaceflight-induced phenotypic changes and potential mechanisms of Bacillus Licheniformis
Project Summary:	Bacillus licheniformis (BL) is a common probiotic clinically used to treat acute and chronic enteritis and diarrhea. The present study aimed to investigate the phenotypic changes and potential mechanisms of BL after a 6-month spaceflight aboard the China Space Station based on characterization test, morphological observation and multi-omics analysis. 6-month spaceflight delayed BL growth curve, reduced its cell wall thickness, and impaired BL biofilm formation ability and adhesion capacity to Caco-2 cells. BL viability at pH 9.0 was decreased by 9.42%. In the 6-month spaceflight BL, proteomics revealed 164 of differentially expressed proteins mainly involved on DNA damage, ATP binding, helicase activity. Metabolomics identified 55 of significantly altered metabolites, and whole-genome sequencing detected five mutated genes. After 6-month spaceflight, physiological characteristics of BL were significantly changed. Various proteins, metabolites and genes were dramatically altered as well. These novel findings may provide new insights into adaptive evolution of BL under long-term space environment, which is expected to benefit for further clinical application of BL.
Institute:	Beijing Institute of Technology
Last Name:	shen
First Name:	shuyan
Address:	Beijing Institute of Technology, Zhongguancun Campus, beijing, China, 100081, China
Email:	1819599261@qq.com
Phone:	18526251633

Subject:

Subject ID:	SU004447
Subject Type:	Bacteria
Subject Species:	Bacillus licheniformis
Taxonomy ID:	1402

Factors:

Subject type: Bacteria; Subject species: Bacillus licheniformis (Factor headings shown in green)

mb_sample_id	local_sample_id	Sample source	factor
SA504634	NEG-G2	Bacillus licheniformis	ground
SA504635	POS-G6	Bacillus licheniformis	ground
SA504636	POS-G5	Bacillus licheniformis	ground
SA504637	POS-G4	Bacillus licheniformis	ground
SA504638	POS-G3	Bacillus licheniformis	ground
SA504639	POS-G2	Bacillus licheniformis	ground
SA504640	NEG-G1	Bacillus licheniformis	ground
SA504641	POS-G1	Bacillus licheniformis	ground
SA504642	NEG-G6	Bacillus licheniformis	ground
SA504643	NEG-G3	Bacillus licheniformis	ground
SA504644	NEG-G5	Bacillus licheniformis	ground
SA504645	NEG-G4	Bacillus licheniformis	ground
SA504646	NEG-F1	Bacillus licheniformis	space
SA504647	NEG-F2	Bacillus licheniformis	space
SA504648	NEG-F6	Bacillus licheniformis	space
SA504649	NEG-F4	Bacillus licheniformis	space
SA504650	NEG-F5	Bacillus licheniformis	space
SA504651	POS-F1	Bacillus licheniformis	space
SA504652	POS-F2	Bacillus licheniformis	space
SA504653	POS-F3	Bacillus licheniformis	space
SA504654	POS-F4	Bacillus licheniformis	space
SA504655	POS-F5	Bacillus licheniformis	space
SA504656	POS-F6	Bacillus licheniformis	space
SA504657	NEG-F3	Bacillus licheniformis	space

Showing results 1 to 24 of 24

Showing results 1 to 24 of 24

Collection:

Collection ID:	CO004440
Collection Summary:	The spaceflight strain (SS) and ground strain (GS) were inoculated into 30 mL of LB liquid medium and cultured until the mid-exponential growth phase (OD₆₀₀=0.6). 300 µL of methanol was added in SS and GS suspension for protein precipitation. The supernatant was collected after centrifugation at 12000 rpm for 10 min at 4 °C. The supernatant of SS and GS was freeze-dried under vacuum. The powder was redissolved with 200 µL of acetonitrile: water (1:1, v/v), then centrifuged at 12,000 rpm for 5 min.
Sample Type:	Bacterial cells

Treatment:

Treatment ID:	TR004456
Treatment Summary:	Bacillus licheniformis from the ground group and the flight group flown in space for 6 months, respectively.

Sample Preparation:

Sampleprep ID:	SP004453
Sampleprep Summary:	300 µL of methanol was added in spaceflight strain (SS) and ground strain (GS) suspension for protein precipitation. The supernatant was collected after centrifugation at 12000 rpm for 10 min at 4 °C. The supernatant of SS and GS was freeze-dried under vacuum. The powder was redissolved with 200 µL of acetonitrile: water (1:1, v/v), then centrifuged at 12,000 rpm for 5 min. The ultra-high performance liquid chromatography (UHPLC) analysis (Thermo Fisher Scientific, Q Exactive HF-X, China) was used for metabolites detection, and the experimental quality was evaluated by quality control (QC) samples. Chromatographic separation was carried out on an ACQUITY UPLC BEH C18 column (2.1×100 mm, 1.7 µm, Thermo Fisher Scientific, America). The mobile phase flow rate was set at 0.3 mL/min with the injection volume of 2 µL and the column temperature was maintained at 45 ℃. The mobile phase consisted of 0.1% formic acid in water (A) and acetonitrile (B). The linear elution program was set at 0-0.5 min, 1% B; 0.5-2 min, 1%-50% B; 2-9 min, 50%-99% B; 9-10 min, 99% B; 10-10.5 min, 99%-1% B and 10.5-13 min, 1% B. MS analysis was performed in positive ion equipped with an electrospray spray ionization (ESI) source. MS tuning parameters were set as follows: Spray voltage 3.9 kV, the capillary temperature 320 ℃, the sampling cone 40 V, the source offset 80 V, the desolvation temperature 450 ℃, the cone gas flow 50 L/h, the desolvation gas flow 800 L/h. The data were imported into Masslynx V4.1 data analysis software (Nonlinear Dynamics, Newcastle, UK) for peak alignment, picking, and normalization, resulting in peak intensities for retention time (TR) and m/z value. The obtained data were imported into SIMCA-P14.0 statistical software (UMETRICS, Sweden) for statistical analysis. The criteria of P value was less than 0.05 in One-way analysis of variance (ANOVA). S plots and VIP values were used to assess the importance of each variable in class separation. The unsupervised principal component analysis (PCA) and supervised orthogonal partial least squares discriminant analysis (OPLS-DA) models were established. To prevent overfitting, a 200 permutations test was conducted on the OPLS-DA model. Different metabolites were screened out according to the variable importance in the projection (VIP) > 1.5 in the OPLS-DA analysis, and the criteria of P value < 0.05 in One-way ANOVA. Finally, those features were further annotated by KEGG database to explore the most relevant the metabolic pathways.

Sampleprep ID:

SP004453

Sampleprep Summary:

300 µL of methanol was added in spaceflight strain (SS) and ground strain (GS) suspension for protein precipitation. The supernatant was collected after centrifugation at 12000 rpm for 10 min at 4 °C. The supernatant of SS and GS was freeze-dried under vacuum. The powder was redissolved with 200 µL of acetonitrile: water (1:1, v/v), then centrifuged at 12,000 rpm for 5 min. The ultra-high performance liquid chromatography (UHPLC) analysis (Thermo Fisher Scientific, Q Exactive HF-X, China) was used for metabolites detection, and the experimental quality was evaluated by quality control (QC) samples. Chromatographic separation was carried out on an ACQUITY UPLC BEH C18 column (2.1×100 mm, 1.7 µm, Thermo Fisher Scientific, America). The mobile phase flow rate was set at 0.3 mL/min with the injection volume of 2 µL and the column temperature was maintained at 45 ℃. The mobile phase consisted of 0.1% formic acid in water (A) and acetonitrile (B). The linear elution program was set at 0-0.5 min, 1% B; 0.5-2 min, 1%-50% B; 2-9 min, 50%-99% B; 9-10 min, 99% B; 10-10.5 min, 99%-1% B and 10.5-13 min, 1% B. MS analysis was performed in positive ion equipped with an electrospray spray ionization (ESI) source. MS tuning parameters were set as follows: Spray voltage 3.9 kV, the capillary temperature 320 ℃, the sampling cone 40 V, the source offset 80 V, the desolvation temperature 450 ℃, the cone gas flow 50 L/h, the desolvation gas flow 800 L/h. The data were imported into Masslynx V4.1 data analysis software (Nonlinear Dynamics, Newcastle, UK) for peak alignment, picking, and normalization, resulting in peak intensities for retention time (TR) and m/z value. The obtained data were imported into SIMCA-P14.0 statistical software (UMETRICS, Sweden) for statistical analysis. The criteria of P value was less than 0.05 in One-way analysis of variance (ANOVA). S plots and VIP values were used to assess the importance of each variable in class separation. The unsupervised principal component analysis (PCA) and supervised orthogonal partial least squares discriminant analysis (OPLS-DA) models were established. To prevent overfitting, a 200 permutations test was conducted on the OPLS-DA model. Different metabolites were screened out according to the variable importance in the projection (VIP) > 1.5 in the OPLS-DA analysis, and the criteria of P value < 0.05 in One-way ANOVA. Finally, those features were further annotated by KEGG database to explore the most relevant the metabolic pathways.

Chromatography:

Chromatography ID:	CH005424
Instrument Name:	Thermo Fisher Scientific, Q Exactive HF-X,
Column Name:	Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um)
Column Temperature:	60°C
Flow Gradient:	The linear elution program was set at 0-0.5 min, 1% B; 0.5-2 min, 1%-50% B; 2-9 min, 50%-99% B; 9-10 min, 99% B; 10-10.5 min, 99%-1% B and 10.5-13 min, 1% B.
Flow Rate:	0.3 mL/min
Solvent A:	100% water; 0.1% formic acid
Solvent B:	100% acetonitrile
Chromatography Type:	Ion pair

Analysis:

Analysis ID:	AN007139
Analysis Type:	MS
Chromatography ID:	CH005424
Num Factors:	2
Num Metabolites:	235
Units:	Peak area

Analysis ID:	AN007140
Analysis Type:	MS
Chromatography ID:	CH005424
Num Factors:	2
Num Metabolites:	138
Units:	Peak area