Summary of Study ST001852

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 PR001168. The data can be accessed directly via it's Project DOI: 10.21228/M8QT2F 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	ST001852
Study Title	Screening of unique bile acid metabolizing bacteria
Study Summary	We incubated individual bacterial strains at pH 7 or pH 9 with either CDCA, LCA, or 3-oxo-Δ4-LCA as starting substrates. Culture supernatants were collected after 48 hours and 14 bile acids were measured by targeted metabolomics.
Institute	Keio University School of Medicine
Department	Dept of Microbiology and Immunology
Last Name	Koji
First Name	Atarashi
Address	35 Shinanomachi, Shinjuku-ku, Tokyo, JAPAN
Email	kojiatarashi@keio.jp
Phone	0353633769
Submit Date	2021-06-24
Raw Data Available	Yes
Raw Data File Type(s)	lcd
Analysis Type Detail	LC-MS
Release Date	2021-07-07
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001168
Project DOI:	doi: 10.21228/M8QT2F
Project Title:	Bile acid composition in Human fecal samples
Project Summary:	Centenarians, or individuals who have lived more than a century, represent the ultimate model of successful longevity associated with decreased susceptibility to ageing-associated illness and chronic inflammation. The gut microbiota is considered to be a critical determinant of human health and longevity. Here we show that centenarians (average 107 yo) have a distinct gut microbiome enriched in microbes capable of generating unique secondary bile acids, including iso-, 3-oxo-, allo-, 3-oxoallo-, and isoallo-lithocholic acid (LCA), as compared to elderly (85-89 yo) and young (21-55 yo) controls.
Institute:	Keio University
Department:	School of Medicine
Laboratory:	Dept of Microbiology and Immunology
Last Name:	Atarashi
First Name:	Koji
Address:	35 Shinanomachi, Shinjuku-ku, Tokyo, JAPAN
Email:	kojiatarashi@keio.jp
Phone:	0353633769

Subject:

Subject ID:	SU001929
Subject Type:	Bacteria
Subject Species:	Bacteria

Factors:

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

mb_sample_id	local_sample_id	Strain	Incubation	pH
SA173109	A_C. scindens VE202-1 (50uM_3-oxo-Δ4-LCA_pH7)	A_C. scindens VE202	3-oxo-delta4-LCA	7
SA173110	A_C. scindens VE202-2 (50uM_3-oxo-Δ4-LCA_pH7)	A_C. scindens VE202	3-oxo-delta4-LCA	7
SA173111	A_C. scindens VE202-2 (50uM_3-oxo-Δ4-LCA_pH9)	A_C. scindens VE202	3-oxo-delta4-LCA	9
SA173112	A_C. scindens VE202-1 (50uM_3-oxo-Δ4-LCA_pH9)	A_C. scindens VE202	3-oxo-delta4-LCA	9
SA173113	A_C. scindens VE202-1 (50uM_CDCA_pH7)	A_C. scindens VE202	CDCA	7
SA173114	A_C. scindens VE202-2 (50uM_CDCA_pH7)	A_C. scindens VE202	CDCA	7
SA173115	A_C. scindens VE202-1 (50uM_CDCA_pH9)	A_C. scindens VE202	CDCA	9
SA173116	A_C. scindens VE202-2 (50uM_CDCA_pH9)	A_C. scindens VE202	CDCA	9
SA173117	A_C. scindens VE202-2 (50uM_LCA_pH7)	A_C. scindens VE202	LCA	7
SA173118	A_C. scindens VE202-1 (50uM_LCA_pH7)	A_C. scindens VE202	LCA	7
SA173119	A_C. scindens VE202-1 (50uM_LCA_pH9)	A_C. scindens VE202	LCA	9
SA173120	A_C. scindens VE202-2 (50uM_LCA_pH9)	A_C. scindens VE202	LCA	9
SA173121	Akkermansia muciniphila St.26-2 (50uM_3-oxo-Δ4-LCA_pH7)	Akkermansia muciniphila St.26	3-oxo-delta4-LCA	7
SA173122	Akkermansia muciniphila St.26-1 (50uM_3-oxo-Δ4-LCA_pH7)	Akkermansia muciniphila St.26	3-oxo-delta4-LCA	7
SA173123	Akkermansia muciniphila St.26-2 (50uM_3-oxo-Δ4-LCA_pH9)	Akkermansia muciniphila St.26	3-oxo-delta4-LCA	9
SA173124	Akkermansia muciniphila St.26-1 (50uM_3-oxo-Δ4-LCA_pH9)	Akkermansia muciniphila St.26	3-oxo-delta4-LCA	9
SA173125	Akkermansia muciniphila St.26-2 (50uM_CDCA_pH7)	Akkermansia muciniphila St.26	CDCA	7
SA173126	Akkermansia muciniphila St.26-1 (50uM_CDCA_pH7)	Akkermansia muciniphila St.26	CDCA	7
SA173127	Akkermansia muciniphila St.26-1 (50uM_CDCA_pH9)	Akkermansia muciniphila St.26	CDCA	9
SA173128	Akkermansia muciniphila St.26-2 (50uM_CDCA_pH9)	Akkermansia muciniphila St.26	CDCA	9
SA173129	Akkermansia muciniphila St.26-2 (50uM_LCA_pH7)	Akkermansia muciniphila St.26	LCA	7
SA173130	Akkermansia muciniphila St.26-1 (50uM_LCA_pH7)	Akkermansia muciniphila St.26	LCA	7
SA173131	Akkermansia muciniphila St.26-1 (50uM_LCA_pH9)	Akkermansia muciniphila St.26	LCA	9
SA173132	Akkermansia muciniphila St.26-2 (50uM_LCA_pH9)	Akkermansia muciniphila St.26	LCA	9
SA173133	Akkermansia muciniphila St.27-1 (50uM_3-oxo-Δ4-LCA_pH7)	Akkermansia muciniphila St.27	3-oxo-delta4-LCA	7
SA173134	Akkermansia muciniphila St.27-2 (50uM_3-oxo-Δ4-LCA_pH7)	Akkermansia muciniphila St.27	3-oxo-delta4-LCA	7
SA173135	Akkermansia muciniphila St.27-1 (50uM_3-oxo-Δ4-LCA_pH9)	Akkermansia muciniphila St.27	3-oxo-delta4-LCA	9
SA173136	Akkermansia muciniphila St.27-2 (50uM_3-oxo-Δ4-LCA_pH9)	Akkermansia muciniphila St.27	3-oxo-delta4-LCA	9
SA173137	Akkermansia muciniphila St.27-2 (50uM_CDCA_pH7)	Akkermansia muciniphila St.27	CDCA	7
SA173138	Akkermansia muciniphila St.27-1 (50uM_CDCA_pH7)	Akkermansia muciniphila St.27	CDCA	7
SA173139	Akkermansia muciniphila St.27-1 (50uM_CDCA_pH9)	Akkermansia muciniphila St.27	CDCA	9
SA173140	Akkermansia muciniphila St.27-2 (50uM_CDCA_pH9)	Akkermansia muciniphila St.27	CDCA	9
SA173141	Akkermansia muciniphila St.27-1 (50uM_LCA_pH7)	Akkermansia muciniphila St.27	LCA	7
SA173142	Akkermansia muciniphila St.27-2 (50uM_LCA_pH7)	Akkermansia muciniphila St.27	LCA	7
SA173143	Akkermansia muciniphila St.27-2 (50uM_LCA_pH9)	Akkermansia muciniphila St.27	LCA	9
SA173144	Akkermansia muciniphila St.27-1 (50uM_LCA_pH9)	Akkermansia muciniphila St.27	LCA	9
SA173145	Alistipes finegoldii St.15-1 (50uM_3-oxo-Δ4-LCA_pH7)	Alistipes finegoldii St.15	3-oxo-delta4-LCA	7
SA173146	Alistipes finegoldii St.15-2 (50uM_3-oxo-Δ4-LCA_pH7)	Alistipes finegoldii St.15	3-oxo-delta4-LCA	7
SA173147	Alistipes finegoldii St.15-2 (50uM_3-oxo-Δ4-LCA_pH9)	Alistipes finegoldii St.15	3-oxo-delta4-LCA	9
SA173148	Alistipes finegoldii St.15-1 (50uM_3-oxo-Δ4-LCA_pH9)	Alistipes finegoldii St.15	3-oxo-delta4-LCA	9
SA173149	Alistipes finegoldii St.15-1 (50uM_CDCA_pH7)	Alistipes finegoldii St.15	CDCA	7
SA173150	Alistipes finegoldii St.15-2 (50uM_CDCA_pH7)	Alistipes finegoldii St.15	CDCA	7
SA173151	Alistipes finegoldii St.15-1 (50uM_CDCA_pH9)	Alistipes finegoldii St.15	CDCA	9
SA173152	Alistipes finegoldii St.15-2 (50uM_CDCA_pH9)	Alistipes finegoldii St.15	CDCA	9
SA173153	Alistipes finegoldii St.15-2 (50uM_LCA_pH7)	Alistipes finegoldii St.15	LCA	7
SA173154	Alistipes finegoldii St.15-1 (50uM_LCA_pH7)	Alistipes finegoldii St.15	LCA	7
SA173155	Alistipes finegoldii St.15-1 (50uM_LCA_pH9)	Alistipes finegoldii St.15	LCA	9
SA173156	Alistipes finegoldii St.15-2 (50uM_LCA_pH9)	Alistipes finegoldii St.15	LCA	9
SA173157	Alistipes finegoldii St.16-1 (50uM_3-oxo-Δ4-LCA_pH7)	Alistipes finegoldii St.16	3-oxo-delta4-LCA	7
SA173158	Alistipes finegoldii St.16-2 (50uM_3-oxo-Δ4-LCA_pH7)	Alistipes finegoldii St.16	3-oxo-delta4-LCA	7
SA173159	Alistipes finegoldii St.16-1 (50uM_3-oxo-Δ4-LCA_pH9)	Alistipes finegoldii St.16	3-oxo-delta4-LCA	9
SA173160	Alistipes finegoldii St.16-2 (50uM_3-oxo-Δ4-LCA_pH9)	Alistipes finegoldii St.16	3-oxo-delta4-LCA	9
SA173161	Alistipes finegoldii St.16-2 (50uM_CDCA_pH7)	Alistipes finegoldii St.16	CDCA	7
SA173162	Alistipes finegoldii St.16-1 (50uM_CDCA_pH7)	Alistipes finegoldii St.16	CDCA	7
SA173163	Alistipes finegoldii St.16-2 (50uM_CDCA_pH9)	Alistipes finegoldii St.16	CDCA	9
SA173164	Alistipes finegoldii St.16-1 (50uM_CDCA_pH9)	Alistipes finegoldii St.16	CDCA	9
SA173165	Alistipes finegoldii St.16-2 (50uM_LCA_pH7)	Alistipes finegoldii St.16	LCA	7
SA173166	Alistipes finegoldii St.16-1 (50uM_LCA_pH7)	Alistipes finegoldii St.16	LCA	7
SA173167	Alistipes finegoldii St.16-1 (50uM_LCA_pH9)	Alistipes finegoldii St.16	LCA	9
SA173168	Alistipes finegoldii St.16-2 (50uM_LCA_pH9)	Alistipes finegoldii St.16	LCA	9
SA173169	Alistipes onderdonkii St.17-1 (50uM_3-oxo-Δ4-LCA_pH7)	Alistipes onderdonkii St.17	3-oxo-delta4-LCA	7
SA173170	Alistipes onderdonkii St.17-2 (50uM_3-oxo-Δ4-LCA_pH7)	Alistipes onderdonkii St.17	3-oxo-delta4-LCA	7
SA173171	Alistipes onderdonkii St.17-2 (50uM_3-oxo-Δ4-LCA_pH9)	Alistipes onderdonkii St.17	3-oxo-delta4-LCA	9
SA173172	Alistipes onderdonkii St.17-1 (50uM_3-oxo-Δ4-LCA_pH9)	Alistipes onderdonkii St.17	3-oxo-delta4-LCA	9
SA173173	Alistipes onderdonkii St.17-2 (50uM_CDCA_pH7)	Alistipes onderdonkii St.17	CDCA	7
SA173174	Alistipes onderdonkii St.17-1 (50uM_CDCA_pH7)	Alistipes onderdonkii St.17	CDCA	7
SA173175	Alistipes onderdonkii St.17-2 (50uM_CDCA_pH9)	Alistipes onderdonkii St.17	CDCA	9
SA173176	Alistipes onderdonkii St.17-1 (50uM_CDCA_pH9)	Alistipes onderdonkii St.17	CDCA	9
SA173177	Alistipes onderdonkii St.17-1 (50uM_LCA_pH7)	Alistipes onderdonkii St.17	LCA	7
SA173178	Alistipes onderdonkii St.17-2 (50uM_LCA_pH7)	Alistipes onderdonkii St.17	LCA	7
SA173179	Alistipes onderdonkii St.17-2 (50uM_LCA_pH9)	Alistipes onderdonkii St.17	LCA	9
SA173180	Alistipes onderdonkii St.17-1 (50uM_LCA_pH9)	Alistipes onderdonkii St.17	LCA	9
SA173181	Alistipes onderdonkii St.18-1 (50uM_3-oxo-Δ4-LCA_pH7)	Alistipes onderdonkii St.18	3-oxo-delta4-LCA	7
SA173182	Alistipes onderdonkii St.18-2 (50uM_3-oxo-Δ4-LCA_pH7)	Alistipes onderdonkii St.18	3-oxo-delta4-LCA	7
SA173183	Alistipes onderdonkii St.18-1 (50uM_3-oxo-Δ4-LCA_pH9)	Alistipes onderdonkii St.18	3-oxo-delta4-LCA	9
SA173184	Alistipes onderdonkii St.18-2 (50uM_3-oxo-Δ4-LCA_pH9)	Alistipes onderdonkii St.18	3-oxo-delta4-LCA	9
SA173185	Alistipes onderdonkii St.18-2 (50uM_CDCA_pH7)	Alistipes onderdonkii St.18	CDCA	7
SA173186	Alistipes onderdonkii St.18-1 (50uM_CDCA_pH7)	Alistipes onderdonkii St.18	CDCA	7
SA173187	Alistipes onderdonkii St.18-1 (50uM_CDCA_pH9)	Alistipes onderdonkii St.18	CDCA	9
SA173188	Alistipes onderdonkii St.18-2 (50uM_CDCA_pH9)	Alistipes onderdonkii St.18	CDCA	9
SA173189	Alistipes onderdonkii St.18-2 (50uM_LCA_pH7)	Alistipes onderdonkii St.18	LCA	7
SA173190	Alistipes onderdonkii St.18-1 (50uM_LCA_pH7)	Alistipes onderdonkii St.18	LCA	7
SA173191	Alistipes onderdonkii St.18-2 (50uM_LCA_pH9)	Alistipes onderdonkii St.18	LCA	9
SA173192	Alistipes onderdonkii St.18-1 (50uM_LCA_pH9)	Alistipes onderdonkii St.18	LCA	9
SA173205	Bacteroides dorei St.6-1 (50uM_3-oxo-Δ4-LCA_pH7)	Bacteroides dorei St.6	3-oxo-delta4-LCA	7
SA173206	Bacteroides dorei St.6-2 (50uM_3-oxo-Δ4-LCA_pH7)	Bacteroides dorei St.6	3-oxo-delta4-LCA	7
SA173207	Bacteroides dorei St.6-2 (50uM_3-oxo-Δ4-LCA_pH9)	Bacteroides dorei St.6	3-oxo-delta4-LCA	9
SA173208	Bacteroides dorei St.6-1 (50uM_3-oxo-Δ4-LCA_pH9)	Bacteroides dorei St.6	3-oxo-delta4-LCA	9
SA173209	Bacteroides dorei St.6-1 (50uM_CDCA_pH7)	Bacteroides dorei St.6	CDCA	7
SA173210	Bacteroides dorei St.6-2 (50uM_CDCA_pH7)	Bacteroides dorei St.6	CDCA	7
SA173211	Bacteroides dorei St.6-1 (50uM_CDCA_pH9)	Bacteroides dorei St.6	CDCA	9
SA173212	Bacteroides dorei St.6-2 (50uM_CDCA_pH9)	Bacteroides dorei St.6	CDCA	9
SA173213	Bacteroides dorei St.6-1 (50uM_LCA_pH7)	Bacteroides dorei St.6	LCA	7
SA173214	Bacteroides dorei St.6-2 (50uM_LCA_pH7)	Bacteroides dorei St.6	LCA	7
SA173215	Bacteroides dorei St.6-2 (50uM_LCA_pH9)	Bacteroides dorei St.6	LCA	9
SA173216	Bacteroides dorei St.6-1 (50uM_LCA_pH9)	Bacteroides dorei St.6	LCA	9
SA173217	Bacteroides dorei St.7-2 (50uM_3-oxo-Δ4-LCA_pH7)	Bacteroides dorei St.7	3-oxo-delta4-LCA	7
SA173218	Bacteroides dorei St.7-1 (50uM_3-oxo-Δ4-LCA_pH7)	Bacteroides dorei St.7	3-oxo-delta4-LCA	7
SA173219	Bacteroides dorei St.7-2 (50uM_3-oxo-Δ4-LCA_pH9)	Bacteroides dorei St.7	3-oxo-delta4-LCA	9
SA173220	Bacteroides dorei St.7-1 (50uM_3-oxo-Δ4-LCA_pH9)	Bacteroides dorei St.7	3-oxo-delta4-LCA	9

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Collection:

Collection ID:	CO001922
Collection Summary:	After 48 hr of anaerobic incubation at 37 °C, culture supernatants were collected and stored at -80 °C until sample preparation for the analysis.
Sample Type:	Bacterial cells
Storage Conditions:	-80℃

Treatment:

Treatment ID:	TR001941
Treatment Summary:	Under anaerobic conditions, isolated bacteria strains were cultured together with 50 μM of CDCA, 3-oxo-Δ4-LCA, or LCA to screen for their bile acid metabolism in a 96-deep well plate covered with a gas-permeable membrane. 20 μL of bacterial culture in exponential to stationary phase was inoculated into 1 mL of Wilkins-Chalgren Anaerobe (WCA) media adjusted to pH 7 (using MOPS buffer solution) or pH 9 (TAPS buffer solution).

Treatment ID:

TR001941

Treatment Summary:

Under anaerobic conditions, isolated bacteria strains were cultured together with 50 μM of CDCA, 3-oxo-Δ4-LCA, or LCA to screen for their bile acid metabolism in a 96-deep well plate covered with a gas-permeable membrane. 20 μL of bacterial culture in exponential to stationary phase was inoculated into 1 mL of Wilkins-Chalgren Anaerobe (WCA) media adjusted to pH 7 (using MOPS buffer solution) or pH 9 (TAPS buffer solution).

Sample Preparation:

Sampleprep ID:	SP001935
Sampleprep Summary:	100 μL of culture supernatant was transferred into a screw-cap glass vial containing 10 μL of deuterium-labelled internal standards (d4-CA, d4-CDCA, and d4-LCA, 1 nmol/mL each). 400 μL of water was added and sonicated for 10 min, then applied onto the solid-phase extraction cartridge (Agilent Bond Elut C18, 100 mg/1 mL, preconditioned with 1 mL of methanol and 3 mL of water). The cartridge was washed with 1 mL of water and captured bile acids were eluted with 1 mL of 90% ethanol. After solvent evaporation, the remaining residue was dissolved in 100 μL of 50% ethanol

Sampleprep ID:

SP001935

Sampleprep Summary:

100 μL of culture supernatant was transferred into a screw-cap glass vial containing 10 μL of deuterium-labelled internal standards (d4-CA, d4-CDCA, and d4-LCA, 1 nmol/mL each). 400 μL of water was added and sonicated for 10 min, then applied onto the solid-phase extraction cartridge (Agilent Bond Elut C18, 100 mg/1 mL, preconditioned with 1 mL of methanol and 3 mL of water). The cartridge was washed with 1 mL of water and captured bile acids were eluted with 1 mL of 90% ethanol. After solvent evaporation, the remaining residue was dissolved in 100 μL of 50% ethanol

Combined analysis:

Analysis ID	AN003000
Analysis type	MS
Chromatography type	Reversed phase
Chromatography system	Shimadzu CBM20A
Column	InertSustain C18
MS Type	ESI
MS instrument type	Triple quadrupole
MS instrument name	Shimadzu LCMS-8040
Ion Mode	UNSPECIFIED
Units	uM

Chromatography:

Chromatography ID:	CH002225
Chromatography Summary:	2 μL of the solution was injected to LC/ESI-MS/MS (LC-MS8040 tandem mass spectrometer, equipped with an ESI probe and Nexera X2 ultra-high-pressure liquid chromatography system; Shimadzu). A separation column, InertSustain C18 (150 mm × 2.1 mm ID, 2 μm particle size; GL Sciences Inc.), was utilized at 40 °C. Mixture A (10 mM ammonium acetate, 0.01% formic acid, and 20% acetonitrile) and mixture B (30% acetonitrile and 70% methanol) were used as the eluent, and the separation was carried out by linear gradient elution at a flow rate of 0.2 mL/min. The mobile phase composition was gradually changed as follows: Mixture A:B (80:20, v/v) for 0.1 min, (48:52, v/v) for 0.1-1 min, (30:70, v/v) for 1-27 min, (0:100, v/v) for 27-27.1 min, (0:100, v/v) for 27.1-33 min, (80:20, v/v) for 33-33.1 min, and (80:20 v/v) for 33.1-83 min. The total run time was 38 min.
Instrument Name:	Shimadzu CBM20A
Column Name:	InertSustain C18
Column Temperature:	40
Flow Gradient:	The mobile phase composition was gradually changed as follows: Mixture A:B (80:20, v/v) for 0.1 min, (48:52, v/v) for 0.1-1 min, (30:70, v/v) for 1-27 min, (0:100, v/v) for 27-27.1 min, (0:100, v/v) for 27.1-33 min, (80:20, v/v) for 33-33.1 min, and (80:20 v/v) for 33.1-83 min. The total run time was 38 min.
Flow Rate:	0.2ml/min
Solvent A:	20% acetonitrile/80% water; 0.01% formic acid; 10mM ammonium acetate
Solvent B:	30% acetonitrile/70% methanol
Chromatography Type:	Reversed phase

MS:

MS ID:	MS002789
Analysis ID:	AN003000
Instrument Name:	Shimadzu LCMS-8040
Instrument Type:	Triple quadrupole
MS Type:	ESI
MS Comments:	The following MS parameters were used: spray voltage; 3,000V, heating block temperature; 400°C, nebulizing gas flow; 3 L/min, drying gas flow; 15 L/min, interface temperature 300°C, collision gas (argon) pressure; 230 kPa, collision energy; negative (11 to -35 eV); and positive (-16 to -19 eV) ion modes. Samples were analysed and quantified using LabSolutions Insight LC-MS software (Shimadzu).
Ion Mode:	UNSPECIFIED