Summary of Study ST001219

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 PR000818. The data can be accessed directly via it's Project DOI: 10.21228/M8Z68P This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

Study ID	ST001219
Study Title	Vitamin D regulates the microbiota to induce RORgt/FoxP3+ regulatory T cells
Study Summary	The active form of vitamin D (1,25(OH)2D) suppresses experimental models of inflammatory bowel disease in part by regulating the microbiota. In this study, the role of vitamin D in the regulation of microbe induced RORgt/FoxP3+ T regulatory (reg) cells in the colon was determined. Vitamin D sufficient (D+) mice had significantly higher frequencies of FoxP3+ and RORgt/FoxP3+ T reg cells in the colon compared to vitamin D deficient (D-) mice. The higher frequency of RORgt/FoxP3+ T reg cells in D+ colon correlated with higher numbers of bacteria from the Clostridium XIVa and Bacteroides in D+ compared to D- cecum. D- mice with fewer RORgt/FoxP3+ T reg cells were significantly more susceptible to colitis than D+ mice. Transfer of the cecal bacteria from D+ or D- mice to germfree recipients phenocopied the higher numbers of RORgt/FoxP3+ cells and reduced susceptibility to colitis in D+ versus D- recipient mice. 1,25(OH)2D treatment of the D- mice beginning at 3 weeks of age did not completely recover RORgt/FoxP3+ T reg cells or the Bacteriodes, Bacteriodes thetaiotaomicron, and Clostridium XIVa numbers to D+ values. Early vitamin D status shapes the microbiota to optimize the population of colonic RORgt/FoxP3+ T reg cells important for resistance to colitis.
Institute	Pennsylvania State University
Last Name	Nichols
First Name	Robert
Address	917 Old Boalsburg Road, State College, Pennsylvania, 16801, USA
Email	rgn5011@psu.edu
Phone	7247662694
Submit Date	2019-07-17
Raw Data Available	Yes
Analysis Type Detail	NMR
Release Date	2019-09-23
Release Version	1

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Project:

Project ID:	PR000818
Project DOI:	doi: 10.21228/M8Z68P
Project Title:	Vitamin D regulates the microbiota to induce RORgt/FoxP3+ regulatory T cells
Project Summary:	The active form of vitamin D (1,25(OH)2D) suppresses experimental models of inflammatory bowel disease in part by regulating the microbiota. In this study, the role of vitamin D in the regulation of microbe induced RORgt/FoxP3+ T regulatory (reg) cells in the colon was determined. Vitamin D sufficient (D+) mice had significantly higher frequencies of FoxP3+ and RORgt/FoxP3+ T reg cells in the colon compared to vitamin D deficient (D-) mice. The higher frequency of RORgt/FoxP3+ T reg cells in D+ colon correlated with higher numbers of bacteria from the Clostridium XIVa and Bacteroides in D+ compared to D- cecum. D- mice with fewer RORgt/FoxP3+ T reg cells were significantly more susceptible to colitis than D+ mice. Transfer of the cecal bacteria from D+ or D- mice to germfree recipients phenocopied the higher numbers of RORgt/FoxP3+ cells and reduced susceptibility to colitis in D+ versus D- recipient mice. 1,25(OH)2D treatment of the D- mice beginning at 3 weeks of age did not completely recover RORgt/FoxP3+ T reg cells or the Bacteriodes, Bacteriodes thetaiotaomicron, and Clostridium XIVa numbers to D+ values. Early vitamin D status shapes the microbiota to optimize the population of colonic RORgt/FoxP3+ T reg cells important for resistance to colitis.
Institute:	Pennsylvania State University
Last Name:	Nichols
First Name:	Robert
Address:	650 toftrees Ave apt 108, state college, PA, 16803
Email:	rgn5011@psu.edu
Phone:	7247662694

Subject:

Subject ID:	SU001286
Subject Type:	Mammal
Subject Species:	Mus musculus
Taxonomy ID:	10090
Species Group:	Mammals

Factors:

Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id	local_sample_id	Group
SA086187	Sup_Fig4B-6	Vitamin D -
SA086188	Sup_Fig4B-7	Vitamin D -
SA086189	Sup_Fig4B-11	Vitamin D -
SA086190	Sup_Fig4B-9	Vitamin D -
SA086191	Sup_Fig4B-10	Vitamin D -
SA086192	Sup_Fig4B-8	Vitamin D -
SA086193	Sup_Fig4B-5	Vitamin D+
SA086194	Sup_Fig4B-2	Vitamin D+
SA086195	Sup_Fig4B-3	Vitamin D+
SA086196	Sup_Fig4C-1	Vitamin D+
SA086197	Sup_Fig4C-6	Vitamin D+
SA086198	Sup_Fig4C-7	Vitamin D+
SA086199	Sup_Fig4C-8	Vitamin D+
SA086200	Sup_Fig4C-5	Vitamin D+
SA086201	Sup_Fig4C-4	Vitamin D+
SA086202	Sup_Fig4C-2	Vitamin D+
SA086203	Sup_Fig4C-3	Vitamin D+
SA086204	Sup_Fig4B-1	Vitamin D+
SA086205	Sup_Fig4B-4	Vitamin D+
SA086206	Sup_Fig4A-14	Vitamin D+
SA086207	Sup_Fig4A-15	Vitamin D+
SA086208	Sup_Fig4A-16	Vitamin D+
SA086209	Sup_Fig4A-17	Vitamin D+
SA086210	Sup_Fig4A-13	Vitamin D+
SA086211	Sup_Fig4A-12	Vitamin D+
SA086212	Sup_Fig4A-9	Vitamin D+
SA086213	Sup_Fig4A-10	Vitamin D+
SA086214	Sup_Fig4A-11	Vitamin D+
SA086215	Sup_Fig4A-18	Vitamin D+
SA086216	Sup_Fig4A-8	Vitamin D+
SA086217	Sup_Fig4A-19	Vitamin D+
SA086218	Sup_Fig4A-5	Vitamin D-
SA086219	Sup_Fig4A-6	Vitamin D-
SA086220	Sup_Fig4A-21	Vitamin D-
SA086221	Sup_Fig4A-4	Vitamin D-
SA086222	Sup_Fig4A-3	Vitamin D-
SA086223	Sup_Fig4A-2	Vitamin D-
SA086224	Sup_Fig4A-1	Vitamin D-
SA086225	Sup_Fig4A-22	Vitamin D-
SA086226	Sup_Fig4A-7	Vitamin D-
SA086227	Sup_Fig4A-27	Vitamin D-
SA086228	Sup_Fig4A-23	Vitamin D-
SA086229	Sup_Fig4A-20	Vitamin D-
SA086230	Sup_Fig4A-26	Vitamin D-
SA086231	Sup_Fig4A-28	Vitamin D-
SA086232	Sup_Fig4A-25	Vitamin D-
SA086233	Sup_Fig4A-24	Vitamin D-
SA086234	Sup_Fig4C-20	Vitamin D-, +1,25D
SA086235	Sup_Fig4C-19	Vitamin D-, +1,25D
SA086236	Sup_Fig4C-21	Vitamin D-, +1,25D
SA086237	Sup_Fig4C-23	Vitamin D-, +1,25D
SA086238	Sup_Fig4C-18	Vitamin D-, +1,25D
SA086239	Sup_Fig4C-24	Vitamin D-, +1,25D
SA086240	Sup_Fig4C-22	Vitamin D-, +1,25D
SA086241	Sup_Fig4C-9	Vitamin D-, +1,25D
SA086242	Sup_Fig4C-12	Vitamin D-, +1,25D
SA086243	Sup_Fig4C-11	Vitamin D-, +1,25D
SA086244	Sup_Fig4C-10	Vitamin D-, +1,25D
SA086245	Sup_Fig4C-13	Vitamin D-, +1,25D
SA086246	Sup_Fig4C-14	Vitamin D-, +1,25D
SA086247	Sup_Fig4C-16	Vitamin D-, +1,25D
SA086248	Sup_Fig4C-15	Vitamin D-, +1,25D
SA086249	Sup_Fig4C-17	Vitamin D-, +1,25D

Showing results 1 to 63 of 63

Showing results 1 to 63 of 63

Collection:

Collection ID:	CO001280
Collection Summary:	C57BL/6 mice were originally from Jackson Labs (Bar Harbor, MN) and maintained at the Pennsylvania State University (University Park, PA). All mice used were housed within the same rooms in the animal facility. Mice were fed purified diets made in the lab as described that either contained vitamin D (D+) or did not (D-) 24. GF C57BL/6 mice were bred and maintained at the Pennsylvania State University gnotobiotic animal research facility. For some experiments, 1,25D was started in the diets of 3-5 week old mice (25ng/d until 5 weeks of age) and mice that were >5 weeks old were fed 50ng/d 1,25D exactly as described 24. For microbial transplantation experiments (two independent experiments), the 4 week old GF mice were gavaged with 100 µl/10 µg cecal contents from D+ and D- mice, and used for experiments after 2 weeks 25. All of the experimental procedures were approved by the Institutional Animal Care and Use Committee at the Pennsylvania State University
Sample Type:	Cecum

Treatment:

Treatment ID:	TR001301
Treatment Summary:	C57BL/6 mice were originally from Jackson Labs (Bar Harbor, MN) and maintained at the Pennsylvania State University (University Park, PA). All mice used were housed within the same rooms in the animal facility. Mice were fed purified diets made in the lab as described that either contained vitamin D (D+) or did not (D-) 24. GF C57BL/6 mice were bred and maintained at the Pennsylvania State University gnotobiotic animal research facility. For some experiments, 1,25D was started in the diets of 3-5 week old mice (25ng/d until 5 weeks of age) and mice that were >5 weeks old were fed 50ng/d 1,25D exactly as described 24. For microbial transplantation experiments (two independent experiments), the 4 week old GF mice were gavaged with 100 µl/10 µg cecal contents from D+ and D- mice, and used for experiments after 2 weeks 25. All of the experimental procedures were approved by the Institutional Animal Care and Use Committee at the Pennsylvania State University

Treatment ID:

TR001301

Treatment Summary:

C57BL/6 mice were originally from Jackson Labs (Bar Harbor, MN) and maintained at the Pennsylvania State University (University Park, PA). All mice used were housed within the same rooms in the animal facility. Mice were fed purified diets made in the lab as described that either contained vitamin D (D+) or did not (D-) 24. GF C57BL/6 mice were bred and maintained at the Pennsylvania State University gnotobiotic animal research facility. For some experiments, 1,25D was started in the diets of 3-5 week old mice (25ng/d until 5 weeks of age) and mice that were >5 weeks old were fed 50ng/d 1,25D exactly as described 24. For microbial transplantation experiments (two independent experiments), the 4 week old GF mice were gavaged with 100 µl/10 µg cecal contents from D+ and D- mice, and used for experiments after 2 weeks 25. All of the experimental procedures were approved by the Institutional Animal Care and Use Committee at the Pennsylvania State University

Sample Preparation:

Sampleprep ID:	SP001294
Sampleprep Summary:	Extract metabolites from cecal contents, then run samples. Pleas see the NMR protocol doc attached to this file
Sampleprep Protocol Filename:	NMR_protocol.docx

Analysis:

Analysis ID:	AN002032
Analysis Type:	NMR
Num Factors:	4
Num Metabolites:	6
Units:	umol/mg

NMR:

NMR ID:	NM000151
Analysis ID:	AN002032
Instrument Name:	Bruker Avance II
Instrument Type:	FT-NMR
NMR Experiment Type:	1D-1H
Spectrometer Frequency:	600