Summary of Study ST003301

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 PR002051. The data can be accessed directly via it's Project DOI: 10.21228/M8H521 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	ST003301
Study Title	Short chain fatty acid (SCFA) analysis of human stool samples under different sample logistics
Study Summary	We sought to understand how sample logistics, i.e. sample storage directly upon sampling and during transportation to the processing laboratory, impacts on the microbiota in terms of the SCFA concentration in 6 different donors.Effects of oxygen exposure were negligible. At ambient temperature, SCFA were stable for 24 h and 48 h, respectively, while at 4°C, SCFA profiles were maintained for 48 h.
Institute	Helmholtz Centre for Environmental Research
Department	Molecular Systems Biology
Last Name	Engelmann
First Name	Beatrice
Address	Permoserstraße 15, Leipzipg, Saxony, 03418, Germany
Email	beatrice.engelmann@ufz.de
Phone	004934160251099
Submit Date	2024-01-05
Raw Data Available	Yes
Raw Data File Type(s)	wiff
Analysis Type Detail	LC-MS
Release Date	2024-07-20
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR002051
Project DOI:	doi: 10.21228/M8H521
Project Title:	Integrated multi-omics analysis unravels the impact of stool sample logistics on metabolites and microbial composition
Project Summary:	Using four different ‘Omics layers, we determined structural (16S rRNA sequencing, cytometric microbiota profiling) and functional integrity (SCFAs, global metabolome) of the microbiota in relation to different real-world conditions.
Institute:	Helmholtz Centre for Environmental Research
Department:	Molecular Systems Biology
Last Name:	Engelmann
First Name:	Beatrice
Address:	Permoserstraße 15, Leipzipg, Saxony, 03418, Germany
Email:	beatrice.engelmann@ufz.de
Phone:	004934160251099

Subject:

Subject ID:	SU003422
Subject Type:	Human
Subject Species:	Homo sapiens
Taxonomy ID:	9606
Species Group:	Mammals

Factors:

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

mb_sample_id	local_sample_id	donor	timepoint	oxyesgeno
SA358132	H1_0_no_fresh_verd	D1	0h	fresh
SA358133	H1_0_no_fresh	D1	0h	fresh
SA358134	H1_168_n_-20°C_verd	D1	168h	no
SA358135	H1_168_n_-20°C	D1	168h	no
SA358136	H1_168_n_-20°C_glycerol	D1	168h	no
SA358137	H1_168_n_RT_verd	D1	168h	no
SA358138	H1_168_n_4°C_verd	D1	168h	no
SA358139	H1_168_n_-20°C_glycerol_verd	D1	168h	no
SA358140	H1_168_n_4°C	D1	168h	no
SA358141	H1_168_n_RT	D1	168h	no
SA358142	H1_168_y_4°C	D1	168h	yes
SA358143	H1_168_y_-20°C_glycerol	D1	168h	yes
SA358144	H1_168_y_RT_verd	D1	168h	yes
SA358145	H1_168_y_4°C_verd	D1	168h	yes
SA358146	H1_168_y_-20°C_glycerol_verd	D1	168h	yes
SA358147	H1_168_y_-20°C_verd	D1	168h	yes
SA358148	H1_168_y_-20°C	D1	168h	yes
SA358149	H1_168_y_RT	D1	168h	yes
SA358150	H1_24_n_-20°C	D1	24h	no
SA358151	H1_24_n_4°C	D1	24h	no
SA358152	H1_24_n_RT	D1	24h	no
SA358153	H1_24_n_RT_verd	D1	24h	no
SA358154	H1_24_n_4°C_verd	D1	24h	no
SA358155	H1_24_n_-20°C_glycerol_verd	D1	24h	no
SA358156	H1_24_n_-20°C_verd	D1	24h	no
SA358157	H1_24_n_-20°C_glycerol	D1	24h	no
SA358158	H1_24_y_RT	D1	24h	yes
SA358159	H1_24_y_4°C	D1	24h	yes
SA358160	H1_24_y_-20°C_glycerol	D1	24h	yes
SA358161	H1_24_y_-20°C	D1	24h	yes
SA358162	H1_24_y_4°C_verd	D1	24h	yes
SA358163	H1_24_y_-20°C_glycerol_verd	D1	24h	yes
SA358164	H1_24_y_RT_verd	D1	24h	yes
SA358165	H1_24_y_-20°C_verd	D1	24h	yes
SA358166	H1_48_n_4°C_verd	D1	48h	no
SA358167	H1_48_n_-20°C_glycerol_verd	D1	48h	no
SA358168	H1_48_n_RT_verd	D1	48h	no
SA358169	H1_48_n_RT	D1	48h	no
SA358170	H1_48_n_4°C	D1	48h	no
SA358171	H1_48_n_-20°C_glycerol	D1	48h	no
SA358172	H1_48_n_-20°C	D1	48h	no
SA358173	H1_48_n_-20°C_verd	D1	48h	no
SA358174	H1_48_y_-20°C_verd	D1	48h	yes
SA358175	H1_48_y_-20°C_glycerol_verd	D1	48h	yes
SA358176	H1_48_y_4°C_verd	D1	48h	yes
SA358177	H1_48_y_RT_verd	D1	48h	yes
SA358178	H1_48_y_-20°C_glycerol	D1	48h	yes
SA358179	H1_48_y_-20°C	D1	48h	yes
SA358180	H1_48_y_4°C	D1	48h	yes
SA358181	H1_48_y_RT	D1	48h	yes
SA358182	H1_4_n_-20°C_verd	D1	4h	no
SA358183	H1_4_n_RT_verd	D1	4h	no
SA358184	H1_4_n_4°C_verd	D1	4h	no
SA358185	H1_4_n_-20°C_glycerol_verd	D1	4h	no
SA358186	H1_4_n_RT	D1	4h	no
SA358187	H1_4_n_4°C	D1	4h	no
SA358188	H1_4_n_-20°C_glycerol	D1	4h	no
SA358189	H1_4_n_-20°C	D1	4h	no
SA358190	H1_4_y_-20°C_glycerol	D1	4h	yes
SA358191	H1_4_y_-20°C_verd	D1	4h	yes
SA358192	H1_4_y_4°C	D1	4h	yes
SA358193	H1_4_y_RT	D1	4h	yes
SA358194	H1_4_y_4°C_verd	D1	4h	yes
SA358195	H1_4_y_-20°C_glycerol_verd	D1	4h	yes
SA358196	H1_4_y_-20°C	D1	4h	yes
SA358197	H1_4_y_RT_verd	D1	4h	yes
SA358198	H2_0_no_fresh_verd	D2	0h	fresh
SA358199	H2_0_no_fresh	D2	0h	fresh
SA358200	H2_168_n_RT_verd	D2	168h	no
SA358201	H2_168_n_-20°C	D2	168h	no
SA358202	H2_168_n_-20°C_verd	D2	168h	no
SA358203	H2_168_n_4°C_verd	D2	168h	no
SA358204	H2_168_n_-20°C_glycerol_verd	D2	168h	no
SA358205	H2_168_n_-20°C_glycerol	D2	168h	no
SA358206	H2_168_n_4°C	D2	168h	no
SA358207	H2_168_n_RT	D2	168h	no
SA358208	H2_168_y_-20°C_glycerol	D2	168h	yes
SA358209	H2_168_y_4°C	D2	168h	yes
SA358210	H2_168_y_-20°C_verd	D2	168h	yes
SA358211	H2_168_y_-20°C_glycerol_verd	D2	168h	yes
SA358212	H2_168_y_RT	D2	168h	yes
SA358213	H2_168_y_4°C_verd	D2	168h	yes
SA358214	H2_168_y_-20°C	D2	168h	yes
SA358215	H2_168_y_RT_verd	D2	168h	yes
SA358216	H2_24_n_RT_verd	D2	24h	no
SA358217	H2_24_n_RT	D2	24h	no
SA358218	H2_24_n_4°C	D2	24h	no
SA358219	H2_24_n_-20°C_glycerol	D2	24h	no
SA358220	H2_24_n_-20°C	D2	24h	no
SA358221	H2_24_n_-20°C_verd	D2	24h	no
SA358222	H2_24_n_-20°C_glycerol_verd	D2	24h	no
SA358223	H2_24_n_4°C_verd	D2	24h	no
SA358224	H2_24_y_-20°C_glycerol_verd	D2	24h	yes
SA358225	H2_24_y_4°C_verd	D2	24h	yes
SA358226	H2_24_y_RT_verd	D2	24h	yes
SA358227	H2_24_y_-20°C	D2	24h	yes
SA358228	H2_24_y_-20°C_verd	D2	24h	yes
SA358229	H2_24_y_-20°C_glycerol	D2	24h	yes
SA358230	H2_24_y_4°C	D2	24h	yes
SA358231	H2_24_y_RT	D2	24h	yes

Showing page 1 of 4 Results: 1 2 3 4 Next Showing results 1 to 100 of 396

Collection:

Collection ID:	CO003415
Collection Summary:	Stool of six healthy donors (2 female, 4 male donors, aged between 24 and 44) was collected. The stool samples were put under anaerobic conditions, directly after defecation and transported to the laboratory within one hour. There, the stool samples were transferred into an anaerobic chamber for homogenization. As fresh reference sample, 100 mg homogenized stool was directly processed anaerobically and snap frozen in liquid nitrogen for subsequent storage at 80 °C.
Sample Type:	Faecal samples

Treatment:

Treatment ID:	TR003431
Treatment Summary:	The homogenized stool was split in two equal parts for (i) anaerobic processing and (ii) aerobic sample processing and was again homogenized. Each sample was split in four parts to simulate the respective storage conditions, i.e. 1. native at 20°C, 2. 1:10 diluted 20°C in 12.5% glycerol in PBS, 3. native at 4°C and 4. native at room temperature (RT). The selected conditions mirror frozen in the absence (1.) or presence (2.) of glycerol under faecal microbiota transplantation conditions, chilled (3.) and unchilled (4.) storage and subsequent transportation to the laboratory. All anaerobic stool samples were kept under anaerobic atmosphere and were stored like their aerobic counterparts.

Treatment ID:

TR003431

Treatment Summary:

The homogenized stool was split in two equal parts for (i) anaerobic processing and (ii) aerobic sample processing and was again homogenized. Each sample was split in four parts to simulate the respective storage conditions, i.e. 1. native at 20°C, 2. 1:10 diluted 20°C in 12.5% glycerol in PBS, 3. native at 4°C and 4. native at room temperature (RT). The selected conditions mirror frozen in the absence (1.) or presence (2.) of glycerol under faecal microbiota transplantation conditions, chilled (3.) and unchilled (4.) storage and subsequent transportation to the laboratory. All anaerobic stool samples were kept under anaerobic atmosphere and were stored like their aerobic counterparts.

Sample Preparation:

Sampleprep ID:	SP003429
Sampleprep Summary:	In brief, 100 mg of each faecal sample was mixed with 500 µl acetonitrile (ACN):Water (1:1, v/v) and homogenized using a TissueLyser II (30 Hz, 10 min; Retsch Qiagen). After centrifugation (2 min, 14000 rpm) 38 µl were used for further derivatization of short chain fatty acids. Each sample was mixed with ACN to a final concentration of 50%. SCFAs were derivatized with 200 mM 3-nitrophenylhydrazine and 120 mM N-(3-dimethylaminopropyl)-N-ethylcarbodiimide hydrochloride in pyridine and then diluted in 10% ACN.

Sampleprep ID:

SP003429

Sampleprep Summary:

In brief, 100 mg of each faecal sample was mixed with 500 µl acetonitrile (ACN):Water (1:1, v/v) and homogenized using a TissueLyser II (30 Hz, 10 min; Retsch Qiagen). After centrifugation (2 min, 14000 rpm) 38 µl were used for further derivatization of short chain fatty acids. Each sample was mixed with ACN to a final concentration of 50%. SCFAs were derivatized with 200 mM 3-nitrophenylhydrazine and 120 mM N-(3-dimethylaminopropyl)-N-ethylcarbodiimide hydrochloride in pyridine and then diluted in 10% ACN.

Combined analysis:

Analysis ID	AN005408
Chromatography ID	CH004101
MS ID	MS005135
Analysis type	MS
Chromatography type	Reversed phase
Chromatography system	Thermo Dionex Ultimate 3000 RS
Column	Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um)
MS Type	ESI
MS instrument type	Triple quadrupole
MS instrument name	ABI Sciex 5500 QTrap
Ion Mode	NEGATIVE
Units	µmol

Chromatography:

Chromatography ID:	CH004101
Instrument Name:	Thermo Dionex Ultimate 3000 RS
Column Name:	Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um)
Column Temperature:	40°C
Flow Gradient:	0-2 min: 15% B, 2-17 min: 15-50% B, 17-17.1 min: 50-100%, 17.1-18 min: 100% B, 18-18.1 min: 100-15% B, 18.1-21 min: 15% B
Flow Rate:	0.35 mL/min
Solvent A:	100% Water; 0.01% Formic acid
Solvent B:	100% Acetonitrile; 0.01% Formic acid
Chromatography Type:	Reversed phase

MS:

MS ID:	MS005135
Analysis ID:	AN005408
Instrument Name:	ABI Sciex 5500 QTrap
Instrument Type:	Triple quadrupole
MS Type:	ESI
MS Comments:	For identification and quantitation, a scheduled MRM method was used, with specific transitions for every SCFA. Data acquisition and peak integration were performed in Analyst® software (Version 1.7.0). Calculation of concentration was done using external calibration curves and statistics were performed using the R software programme.
Ion Mode:	NEGATIVE