Summary of Study ST000190
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 PR000161. The data can be accessed directly via it's Project DOI: 10.21228/M8DS3P This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000190 |
| Study Title | Assessment of dietary zinc on SCFA cecal production |
| Study Type | Short-chain fatty acid analysis |
| Study Summary | Zinc (Zn) deficiency is a prevalent micronutrient insufficiency. Although the gut is a vital organ for Zn utilization, and Zn deficiency is associated with impaired intestinal permeability and a global decrease in gastrointestinal health, alterations in the gut microbial ecology of the host under conditions of Zn deficiency have yet to be studied. Using the broiler chicken (Gallus gallus) model, the aim of this study was to characterize distinct cecal microbiota shifts induced by chronic dietary Zn depletion. We demonstrate that Zn deficiency induces significant taxonomic alterations and decreases overall species richness and diversity, establishing a microbial profile resembling that of various other pathological states. Through metagenomic analysis, we show that predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways responsible for macro- and micronutrient uptake are significantly depleted under Zn deficiency; along with concomitant decreases in beneficial short chain fatty acids, such depletions may further preclude optimal host Zn availability. We also identify several candidate microbes that may play a significant role in modulating the bioavailability and utilization of dietary Zn during prolonged deficiency. Our results are the first to characterize a unique and dysbiotic cecal microbiota during Zn deficiency, and provide evidence for such microbial perturbations as potential effectors of the Zn deficient phenotype. Experiment setup Upon hatching, chicks were randomly allocated into two treatment groups on the basis of body weight and gender (aimed to ensure equal distribution between groups, n = 6): 1. Zn(+): 42 µg/g zinc; 2. Zn(−): 2.5 µg/g zinc. Research is published: http://www.mdpi.com/2072-6643/7/12/5497/htm |
| Institute | University of Michigan |
| Department | Biomedical Research Core Facilities |
| Laboratory | Metabolomics core |
| Last Name | Kachman |
| First Name | Maureen |
| Address | 6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714 |
| mkachman@umich.edu | |
| Submit Date | 2015-06-08 |
| Num Groups | 2 |
| Total Subjects | 12 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Uploaded File Size | 64 M |
| Analysis Type Detail | GC-MS |
| Release Date | 2015-12-28 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000161 |
| Project DOI: | doi: 10.21228/M8DS3P |
| Project Title: | Zinc Studies |
| Project Summary: | Zinc Deficiency and SCFA |
| Institute: | USDA Agricultural Research Service;Cornell University |
| Department: | Trace minerals and Nutrition |
| Laboratory: | Tako Lab |
| Last Name: | Tako |
| First Name: | Elad |
| Address: | Ithaca, New York |
| Email: | et79@cornell.edu |
| Phone: | 607-255-5434 |
Subject:
| Subject ID: | SU000209 |
| Subject Type: | Animal |
| Subject Species: | Gallus gallus |
| Taxonomy ID: | 9031 |
| Species Group: | Birds |
Factors:
Subject type: Animal; Subject species: Gallus gallus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Zinc |
|---|---|---|
| SA009649 | S00016512 | MINUS |
| SA009650 | S00016508 | MINUS |
| SA009651 | S00016511 | MINUS |
| SA009652 | S00016513 | MINUS |
| SA009653 | S00016510 | MINUS |
| SA009654 | S00016509 | MINUS |
| SA009655 | S00016518 | PLUS |
| SA009656 | S00016519 | PLUS |
| SA009657 | S00016517 | PLUS |
| SA009658 | S00016515 | PLUS |
| SA009659 | S00016514 | PLUS |
| SA009660 | S00016516 | PLUS |
| Showing results 1 to 12 of 12 |
Collection:
| Collection ID: | CO000197 |
| Collection Summary: | - |
| Sample Type: | Intestinal Secretions |
Treatment:
| Treatment ID: | TR000217 |
Sample Preparation:
| Sampleprep ID: | SP000211 |
| Sampleprep Summary: | - |
| Sampleprep Protocol Filename: | SCFA_analysis_protocol-2015-03-10.docx |
Combined analysis:
| Analysis ID | AN000291 |
|---|---|
| Analysis type | MS |
| Chromatography type | GC |
| Chromatography system | |
| Column | Phenomenex Zebron ZB-WAXplus (30m x 0.25mm,0.25um) |
| MS Type | EI |
| MS instrument type | Single quadrupole |
| MS instrument name | Agilent 5975C |
| Ion Mode | POSITIVE |
| Units | pmol/mg dry weight |
Chromatography:
| Chromatography ID: | CH000213 |
| Methods ID: | AQM030 |
| Methods Filename: | WAXPLUS_100-200C_2_SIM.txt |
| Column Name: | Phenomenex Zebron ZB-WAXplus (30m x 0.25mm,0.25um) |
| Chromatography Type: | GC |
MS:
| MS ID: | MS000240 |
| Analysis ID: | AN000291 |
| Instrument Name: | Agilent 5975C |
| Instrument Type: | Single quadrupole |
| MS Type: | EI |
| Ion Mode: | POSITIVE |
| Acquisition Parameters File: | WAXPLUS_100-200C_2_SIM.txt |
| Processing Parameters File: | EX00360-SCFA-Quant-methods.m.zip |
