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