Summary of Study ST002117

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 PR001342. The data can be accessed directly via it's Project DOI: 10.21228/M87X3H 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	ST002117
Study Title	Microbial Toll/interleukin-1 domain NADase activities
Study Summary	Recent work indicates that Toll/Interleukin-1 receptor (TIR) domain-containing proteins degrade NAD. Given increasing attention to how the gut microbiome contributes to NAD metabolism and healthy growth, we examined the representation and expressed NADase activities of its TIR domains. The NADase activities of 151 bacterial TIRs were characterized in vitro. Gut bacterial strains representing the diversity of TIRs observed in the microbiome, and activities observed in vitro, were introduced into germ-free mice fed defined diets. Mass spectrometry of cecal metabolites disclosed that a product of TIR NADase activity, variant cyclic-ADPR-x, distinguished colonized from germ-free animals. Mass spectrometry and microbial RNA-Seq of gnotobiotic mice colonized with one, two and all members of this bacterial consortium, identified Bacteroides xylanisolvens as the principal in vivo source of v-cADPR-x. Guided by bioinformatic analyses of biochemically validated TIR domains, we determined that compared to age-matched healthy Bangladeshi children, those with acute malnutrition had significantly lower fecal levels of TIRs known or predicted to generate v-cADPR-x, and of this metabolite. These results indicate that v-cADPR-x may be an informative biomarker of healthy gut microbiome development.
Institute	Washington University in St. Louis
Last Name	Sasaki
First Name	Yo
Address	4515 McKinley Ave St.Louis MO
Email	sasaki@wustl.edu
Phone	314-362-4653
Submit Date	2022-03-22
Raw Data Available	Yes
Raw Data File Type(s)	d
Analysis Type Detail	LC-MS
Release Date	2022-03-30
Release Version	1

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Project:

Project ID:	PR001342
Project DOI:	doi: 10.21228/M87X3H
Project Title:	Microbial Toll/interleukin-1 domain metabolite study.
Project Summary:	The Characterization of NADase activities of 151 bacterial TIRs.
Institute:	Washington University in St. Louis
Last Name:	Yo
First Name:	Sasaki
Address:	4515 McKinley Ave St.Louis MO
Email:	sasaki@wustl.edu
Phone:	314-362-4653

Subject:

Subject ID:	SU002202
Subject Type:	Bacteria
Subject Species:	Bacteroides xylanisolvens

Factors:

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

mb_sample_id	local_sample_id	Cage
SA203044	m06c	1 \| Microbiota:26-member \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203045	m02d	1 \| Microbiota:26-member \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203046	m18b	1 \| Microbiota:26-member \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203047	m15a-S5A	1 \| Microbiota:26-member \| Diet:NAD-precursor sufficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203048	m13a-S5A	1 \| Microbiota:26-member \| Diet:NAD-precursor sufficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203049	m07a-S5A	1 \| Microbiota:26-member \| Diet:NAD-precursor sufficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203050	m11a-S5A	1 \| Microbiota:26-member \| Diet:NAD-precursor sufficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203051	m11a	1 \| Microbiota:BthetaBxylan \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203052	m17b	1 \| Microbiota:BthetaBxylan \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203053	m14b	1 \| Microbiota:BthetaBxylan \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203054	m14a	1 \| Microbiota:Btheta \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203055	m05b	1 \| Microbiota:Btheta \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203056	m13a	1 \| Microbiota:Btheta \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203057	m01c	1 \| Microbiota:Bxylan \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203058	m03c	1 \| Microbiota:Bxylan \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203059	m07a	1 \| Microbiota:Bxylan \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203060	m02a	1 \| Microbiota:Germfree \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203061	m08a	1 \| Microbiota:Germfree \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203062	m01a	1 \| Microbiota:Germfree \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203063	m01b-S5A	1 \| Microbiota:Germfree \| Diet:NAD-precursor sufficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203064	m07b-S5A	1 \| Microbiota:Germfree \| Diet:NAD-precursor sufficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203065	m09a-S5A	1 \| Microbiota:Germfree \| Diet:NAD-precursor sufficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203066	m08a-S5A	1 \| Microbiota:Germfree \| Diet:NAD-precursor sufficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203067	m07c	2 \| Microbiota:26-member \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203068	m01d	2 \| Microbiota:26-member \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203069	m11b	2 \| Microbiota:26-member \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203070	m01a-S5A	2 \| Microbiota:26-member \| Diet:NAD-precursor sufficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203071	m06b-S5A	2 \| Microbiota:26-member \| Diet:NAD-precursor sufficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203072	m18a-S5A	2 \| Microbiota:26-member \| Diet:NAD-precursor sufficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203073	m10b-S5A	2 \| Microbiota:26-member \| Diet:NAD-precursor sufficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203074	m15b	2 \| Microbiota:BthetaBxylan \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203075	m16b	2 \| Microbiota:BthetaBxylan \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203076	m03d	2 \| Microbiota:BthetaBxylan \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203077	m12a	2 \| Microbiota:Btheta \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203078	m04c	2 \| Microbiota:Btheta \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203079	m15a	2 \| Microbiota:Btheta \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203080	m08c	2 \| Microbiota:Bxylan \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203081	m04d	2 \| Microbiota:Bxylan \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203082	m05c	2 \| Microbiota:Bxylan \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203083	m05a	2 \| Microbiota:Germfree \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203084	m04a	2 \| Microbiota:Germfree \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203085	m03a	2 \| Microbiota:Germfree \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203086	m11b-S5A	2 \| Microbiota:Germfree \| Diet:NAD-precursor sufficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203087	m14a-S5A	2 \| Microbiota:Germfree \| Diet:NAD-precursor sufficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203088	m13b-S5A	2 \| Microbiota:Germfree \| Diet:NAD-precursor sufficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203089	m17a-S5A	2 \| Microbiota:Germfree \| Diet:NAD-precursor sufficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203090	m04b-S5A	3 \| Microbiota:26-member \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203091	m06a-S5A	3 \| Microbiota:26-member \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203092	m12b-S5A	3 \| Microbiota:26-member \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203093	m10a-S5A	3 \| Microbiota:26-member \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203094	m10a	3 \| Microbiota:Btheta \| Diet:NA-supplementeded \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203095	m02c	3 \| Microbiota:Btheta \| Diet:NA-supplementeded \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203096	m03b	3 \| Microbiota:Btheta \| Diet:NA-supplementeded \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203097	m13b	3 \| Microbiota:Bxylan \| Diet:NA-supplementeded \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203098	m09b	3 \| Microbiota:Bxylan \| Diet:NA-supplementeded \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203099	m10b	3 \| Microbiota:Bxylan \| Diet:NA-supplementeded \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203103	m16a-S5A	3 \| Microbiota:Germfree \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203104	m05b-S5A	3 \| Microbiota:Germfree \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203105	m02a-S5A	3 \| Microbiota:Germfree \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203106	m14b-S5A	3 \| Microbiota:Germfree \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203100	m06a	3 \| Microbiota:Germfree \| Diet:NA-supplementeded \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203101	m09a	3 \| Microbiota:Germfree \| Diet:NA-supplementeded \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203102	m04b	3 \| Microbiota:Germfree \| Diet:NA-supplementeded \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203107	m04a-S5A	4 \| Microbiota:26-member \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203108	m09b-S5A	4 \| Microbiota:26-member \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203109	m12a-S5A	4 \| Microbiota:26-member \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203110	m03a-S5A	4 \| Microbiota:26-member \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203111	m18a	4 \| Microbiota:Btheta \| Diet:NA-supplementeded \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203112	m16a	4 \| Microbiota:Btheta \| Diet:NA-supplementeded \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203113	m17a	4 \| Microbiota:Btheta \| Diet:NA-supplementeded \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203114	m07b	4 \| Microbiota:Bxylan \| Diet:NA-supplementeded \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203115	m12b	4 \| Microbiota:Bxylan \| Diet:NA-supplementeded \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203116	m06b	4 \| Microbiota:Bxylan \| Diet:NA-supplementeded \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203120	m02b-S5A	4 \| Microbiota:Germfree \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203121	m05a-S5A	4 \| Microbiota:Germfree \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203122	m03b-S5A	4 \| Microbiota:Germfree \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203123	m08b-S5A	4 \| Microbiota:Germfree \| Diet:NAD-precursor deficient \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203117	m08b	4 \| Microbiota:Germfree \| Diet:NA-supplementeded \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203118	m02b	4 \| Microbiota:Germfree \| Diet:NA-supplementeded \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203119	m01b	4 \| Microbiota:Germfree \| Diet:NA-supplementeded \| Age (months):NA \| WLZ:NA \| Health phenotype:NA
SA203124	PS.079	NA \| Microbiota:NA \| Diet:NA \| Age (months):10.3 \| WLZ:-2.7 \| Health phenotype:Malnourished
SA203125	PS.057-10.4	NA \| Microbiota:NA \| Diet:NA \| Age (months):10.4 \| WLZ:-3.8 \| Health phenotype:Malnourished
SA203126	PS.057-10.6	NA \| Microbiota:NA \| Diet:NA \| Age (months):10.6 \| WLZ:-2.81 \| Health phenotype:Malnourished
SA203127	BG1C0473-11	NA \| Microbiota:NA \| Diet:NA \| Age (months):11 \| WLZ:-0.82 \| Health phenotype:Healthy
SA203128	PS.158	NA \| Microbiota:NA \| Diet:NA \| Age (months):12.5 \| WLZ:-3.48 \| Health phenotype:Malnourished
SA203129	BG1C0466-12	NA \| Microbiota:NA \| Diet:NA \| Age (months):12 \| WLZ:0.2 \| Health phenotype:Healthy
SA203130	PS.120-13.3	NA \| Microbiota:NA \| Diet:NA \| Age (months):13.3 \| WLZ:-3.16 \| Health phenotype:Malnourished
SA203131	PS.120-13.9	NA \| Microbiota:NA \| Diet:NA \| Age (months):13.9 \| WLZ:-2.17 \| Health phenotype:Malnourished
SA203132	BG1C0466-13	NA \| Microbiota:NA \| Diet:NA \| Age (months):13 \| WLZ:-0.3 \| Health phenotype:Healthy
SA203133	BG1C0473-13	NA \| Microbiota:NA \| Diet:NA \| Age (months):13 \| WLZ:-0.93 \| Health phenotype:Healthy
SA203134	PS.132	NA \| Microbiota:NA \| Diet:NA \| Age (months):14.1 \| WLZ:-3.01 \| Health phenotype:Malnourished
SA203135	Bgsng8064	NA \| Microbiota:NA \| Diet:NA \| Age (months):15 \| WLZ:0.6 \| Health phenotype:Healthy
SA203136	PS.170	NA \| Microbiota:NA \| Diet:NA \| Age (months):16.2 \| WLZ:-3.5 \| Health phenotype:Malnourished
SA203137	PS.004	NA \| Microbiota:NA \| Diet:NA \| Age (months):21.9 \| WLZ:-2.03 \| Health phenotype:Malnourished
SA203138	Bgsng8119	NA \| Microbiota:NA \| Diet:NA \| Age (months):25 \| WLZ:1.7 \| Health phenotype:Healthy
SA203139	Bgsng8169-28	NA \| Microbiota:NA \| Diet:NA \| Age (months):28 \| WLZ:- \| Health phenotype:Healthy
SA203140	Bgsng8169-30	NA \| Microbiota:NA \| Diet:NA \| Age (months):30 \| WLZ:1.77 \| Health phenotype:Healthy
SA203141	Bgsng8153	NA \| Microbiota:NA \| Diet:NA \| Age (months):6 \| WLZ:1.58 \| Health phenotype:Healthy
SA203142	BG1C0462	NA \| Microbiota:NA \| Diet:NA \| Age (months):8 \| WLZ:-0.43 \| Health phenotype:Healthy
SA203143	PS.011	NA \| Microbiota:NA \| Diet:NA \| Age (months):9.9 \| WLZ:-5.54 \| Health phenotype:Malnourished

Showing results 1 to 100 of 100

Showing results 1 to 100 of 100

Collection:

Collection ID:	CO002195
Collection Summary:	Cecal contents were collected on 10 uL plastic inoculation loops at the time of sacrifice, snap frozen in liquid nitrogen, and stored at -80 °C. Aliquots were kept frozen, removed from the loops and weighed.
Sample Type:	Cecum
Storage Conditions:	-80℃

Treatment:

Treatment ID:	TR002214
Treatment Summary:	Germ-free C57BL/6J mice were reared in plastic flexible film gnotobiotic isolators (Class Biologically Clean) at 23 °C under a strict 12-hour light cycle (lights on at 0600h, off at 1800h). Animals were weaned onto an autoclaved, low-fat, plant polysaccharide-rich chow (catalog number 2018S, Envigo) that was administered ad libitum. Five days prior to colonization, 8-week-old male mice were switched to the NAD precursor-sufficient diet; 2 days later, they were either placed on a NAD precursor-deficient diet, or a NA-supplemented diet or were continued on the NAD precursor-sufficient diet.

Treatment ID:

TR002214

Treatment Summary:

Germ-free C57BL/6J mice were reared in plastic flexible film gnotobiotic isolators (Class Biologically Clean) at 23 °C under a strict 12-hour light cycle (lights on at 0600h, off at 1800h). Animals were weaned onto an autoclaved, low-fat, plant polysaccharide-rich chow (catalog number 2018S, Envigo) that was administered ad libitum. Five days prior to colonization, 8-week-old male mice were switched to the NAD precursor-sufficient diet; 2 days later, they were either placed on a NAD precursor-deficient diet, or a NA-supplemented diet or were continued on the NAD precursor-sufficient diet.

Sample Preparation:

Sampleprep ID:	SP002208
Sampleprep Summary:	10 uL of ice-cold methanol was added per mg of sample, which was then thawed on ice. The mixture was subsequently shaken for two minutes in a BioSpec bead beater. Samples were then centrifuged for 10 minutes at 3,000 x g at 4 °C; a 150 uL aliquot of the supernatant was transferred to a new tube containing 150 uL ice-cold chloroform, then mixed by pulse vortexing and centrifuged for 10 minutes at 3,000 x g at 4 °C. 100 uL of the methanol fraction was transferred to a new tube containing 100 uL of ice-cold chloroform, mixed by pulse-vortexing, and centrifuged for 10 minutes at 3,000 x g at 4 °C. 70 uL was transferred to a new tube and lyophilized in a Labconco SpeedVac.

Sampleprep ID:

SP002208

Sampleprep Summary:

10 uL of ice-cold methanol was added per mg of sample, which was then thawed on ice. The mixture was subsequently shaken for two minutes in a BioSpec bead beater. Samples were then centrifuged for 10 minutes at 3,000 x g at 4 °C; a 150 uL aliquot of the supernatant was transferred to a new tube containing 150 uL ice-cold chloroform, then mixed by pulse vortexing and centrifuged for 10 minutes at 3,000 x g at 4 °C. 100 uL of the methanol fraction was transferred to a new tube containing 100 uL of ice-cold chloroform, mixed by pulse-vortexing, and centrifuged for 10 minutes at 3,000 x g at 4 °C. 70 uL was transferred to a new tube and lyophilized in a Labconco SpeedVac.

Combined analysis:

Analysis ID	AN003465
Analysis type	MS
Chromatography type	Reversed phase
Chromatography system	Agilent 1290 Infinity
Column	Waters Atlantis C18
MS Type	ESI
MS instrument type	Triple quadrupole
MS instrument name	Agilent 6490 QQQ
Ion Mode	POSITIVE
Units	pmol/mg

Chromatography:

Chromatography ID:	CH002559
Instrument Name:	Agilent 1290 Infinity
Column Name:	Waters Atlantis C18
Chromatography Type:	Reversed phase

MS:

MS ID:	MS003226
Analysis ID:	AN003465
Instrument Name:	Agilent 6490 QQQ
Instrument Type:	Triple quadrupole
MS Type:	ESI
MS Comments:	Metabolites were quantified by MassHunter quantitative analysis tool (Agilent)
Ion Mode:	POSITIVE