Summary of Study ST003546
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 PR002182. The data can be accessed directly via it's Project DOI: 10.21228/M8KC1B This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST003546 |
| Study Title | Improved Soil Health and Pasture Phytochemical Richness Underlies Improved Beef Nutrient Density in Southern US Grass-Finished Beef Systems |
| Study Summary | With growing concerns about beef production's impact on health and environment, there is increasing interest in practices that may improve the soil-plant-animal-human health continuum. We compared three Southern US grass-fed beef systems to grain-fed control, examining effects on soil health in terms of physicochemical properties whereas feed and beef samples were tested for metabolomic profile using orbitrap mass spectrometer. Pasturelands displayed healthier soils compared to paired feedcrop lands, showing 1.4-fold more organic matter and 1.7 to 3.0-fold higher potassium, phosphorus, calcium, and zinc levels (all, p<0.05). Of 784 compounds analyzed, 165 differed between grass-fed and grain-fed beef (all, p<0.05). Grass-fed beef had 3.1-fold higher phytochemical antioxidants, tied to 118.2-fold higher precursor levels in pasture samples compared to total mixed rations (p<0.05). This resulted in reduced oxidative stress in grass-fed animals, with 0.35- and 0.37-fold lower levels of homocysteine and 4-hydroxynonenal glutathione, respectively (both, p<0.05). Findings highlight potential linked benefits across the soil-plant-animal-human nutrition continuum in beef production. |
| Institute | Utah State University |
| Department | Department of Nutrition, Dietetics and Food Sciences |
| Laboratory | Center for Human Nutrition Studies |
| Last Name | Van Vliet |
| First Name | Stephan |
| Address | 8700, Old Main Hill Logan, Utah 84322 |
| stephan.vanvliet@usu.edu | |
| Phone | 435-797-5369 |
| Submit Date | 2024-10-09 |
| Num Groups | 2 |
| Total Subjects | 16 |
| Analysis Type Detail | Other |
| Release Date | 2024-11-22 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002182 |
| Project DOI: | doi: 10.21228/M8KC1B |
| Project Title: | Linking Beef Nutrient Density to Feed Type and Soil Health in Grass-Fed vs. Grain-Fed Systems |
| Project Summary: | This study analyzed the metabolomic profiles of Black Angus beef (longissimus dorsi) derived from two U.S. finishing systems: pasture-finished cattle from three Southern U.S. farms and grain-finished cattle from a single Midwest feedlot, with eight samples collected per finishing group (n=16). Pasture samples (n=13) were obtained from the three grass-fed farms, while total mixed ration (TMR) samples (n=4) were collected from the grain-fed feedlot. Four beef samples were collected from each of the three grass-fed farms and from the grain-fed feedlot, providing a comprehensive comparison of metabolomic differences influenced by distinct feed types and finishing systems. |
| Institute: | Utah State University |
| Department: | Department of Nutrition, Dietetics and Food Sciences |
| Laboratory: | Center for Human Nutrition Studies |
| Last Name: | Van Vliet |
| First Name: | Stephan |
| Address: | 8700, Old Main Hill Logan, Utah 84322 |
| Email: | stephan.vanvliet@usu.edu |
| Phone: | 435-797-5369 |
| Funding Source: | U.S. Department of Agriculture, under award number 2020-38640-31521 and USDA-NIFA-AFRI Post-Doctoral Fellowship (2021-67034-35118) |
Subject:
| Subject ID: | SU003675 |
| Subject Type: | Mammal |
| Subject Species: | Bos taurus |
| Taxonomy ID: | 9913 |
Factors:
Subject type: Mammal; Subject species: Bos taurus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Feed |
|---|---|---|---|
| SA387745 | Midwest TMR #4 | Beef Feed | Grain |
| SA387746 | Midwest TMR #3 | Beef Feed | Grain |
| SA387747 | Midwest TMR #2 | Beef Feed | Grain |
| SA387748 | Midwest TMR #1 | Beef Feed | Grain |
| SA387749 | SPH #3 | Beef Feed | Grass |
| SA387750 | BLP #2 | Beef Feed | Grass |
| SA387751 | SPH #5 | Beef Feed | Grass |
| SA387752 | SPH #4 | Beef Feed | Grass |
| SA387753 | BLP #1 | Beef Feed | Grass |
| SA387754 | SPH #2 | Beef Feed | Grass |
| SA387755 | SBR #5 | Beef Feed | Grass |
| SA387756 | SBR #4 | Beef Feed | Grass |
| SA387757 | SBR #3 | Beef Feed | Grass |
| SA387758 | SBR #2 | Beef Feed | Grass |
| SA387759 | SBR #1 | Beef Feed | Grass |
| SA387760 | BLP #3 | Beef Feed | Grass |
| SA387761 | SPH #1 | Beef Feed | Grass |
| SA387762 | MWF Ribeye #2 | Bovine Meat | Grain |
| SA387763 | MWF Ribeye #8 | Bovine Meat | Grain |
| SA387764 | MWF Ribeye #7 | Bovine Meat | Grain |
| SA387765 | MWF Ribeye #6 | Bovine Meat | Grain |
| SA387766 | MWF Ribeye #5 | Bovine Meat | Grain |
| SA387767 | MWF Ribeye #4 | Bovine Meat | Grain |
| SA387768 | MWF Ribeye #3 | Bovine Meat | Grain |
| SA387769 | MWF Ribeye #1 | Bovine Meat | Grain |
| SA387770 | SBP Ribeye #3 | Bovine Meat | Grass |
| SA387771 | SPH Ribeye #2 | Bovine Meat | Grass |
| SA387772 | SPH Ribeye #1 | Bovine Meat | Grass |
| SA387773 | SBP Ribeye #2 | Bovine Meat | Grass |
| SA387774 | SBP Ribeye #1 | Bovine Meat | Grass |
| SA387775 | BLP Ribeye #3 | Bovine Meat | Grass |
| SA387776 | BLP Ribeye #2 | Bovine Meat | Grass |
| SA387777 | BLP Ribeye #1 | Bovine Meat | Grass |
| Showing results 1 to 33 of 33 |
Collection:
| Collection ID: | CO003668 |
| Collection Summary: | All cattle were processed in USDA-inspected slaughter facilities and the researchers worked with the producers to collect meat samples (Pectoralis profundus) from 8 individual animals (n=8) per group for both the grass-fed and grain-fed group. Upon arrival at the lab, all meat samples were stored in a -40°C freezer and processed for analysis within 3 weeks of arrival. The meat samples were ground individually in a commercial meat grinder. Thereafter ~2 grams sample was obtained (n = 8 pasture-finished beef; n = 8 for grain-finished beef), immediately frozen in liquid nitrogen, and stored at -80 degrees °C until further analysis. |
| Sample Type: | Beef Feed (Pasture forages & total mixed rations) and Beef Muscle |
| Collection Method: | Shipment on dry ice |
| Collection Location: | Surry and Buncombe County NC & Perry County, AL |
| Storage Conditions: | -20℃ |
Treatment:
| Treatment ID: | TR003684 |
| Treatment Summary: | All analyzed samples (grass-fed and grain-fed) were collected from cattle harvested in the fall of 2021 and were of a Black Angus genetic background. The grass-fed cattle were between 25-27 months old, while the grain-fed cattle ranged from 18-22 months of age at the time of slaughter. The grass-fed beef samples were sourced from three different farms in the Southern United States, specifically in Surry County, North Carolina; Buncombe County, North Carolina; and Perry County, Alabama. These farms practiced adaptive rotational grazing, where cattle were moved to new paddocks every 1-7 days. During the grazing season, the animals had access to diverse pasture species and rotated through various landscapes typical of their respective regions. The grain-fed beef samples, on the other hand, were obtained from a commercial feedlot in the Midwest. All meat samples were collected from the longissimus dorsi muscle and shipped to the Center for Human Nutrition Studies at Utah State University for analysis. |
Sample Preparation:
| Sampleprep ID: | SP003682 |
| Sampleprep Summary: | Samples analyzed for untargeted metabolomic profiling through collaborations with Metabolon (Morrisville, NC). One hundred (100 mg) was weighed out for each sample and recovery standards were added for quality control purposes. Proteins were subsequently precipitated with methanol under vigorous shaking for 2 min (Glen Mills Geno Grinder 2000, Clifton, NJ, USA) followed by centrifugation (15,000 × g). The resulting extract was divided into five fractions: two for analysis by separate reverse phase (RP)/UPLC-MS/MS methods with positive ion mode electrospray ionization (ESI), one for analysis by RP/UPLC-MS/MS with negative ion mode ESI, one for analysis by HILIC/UPLC-MS/MS with negative ion mode ESI, and one sample for backup. Sample extracts were placed briefly on a TurboVap (Zymark) to remove the organic solvent and reconstituted in mobile phases described below. The UPLC-MS/MS platform utilized a Waters Acquity UPLC with Waters UPLC BEH C18-2.1×100 mm, 1.7 μm columns and a Thermo Scientific Q-Exactive high resolution/accurate mass spectrometer interfaced with a heated electrospray ionization (HESI-II) source and Orbitrap mass analyzer. One aliquot was analyzed using acidic positive ion conditions, which was chromatographically optimized for more hydrophilic compounds. The extract was gradient eluted from a C18 column (Waters UPLC BEH C18-2.1x100 mm, 1.7 µm) using water and methanol, containing 0.05% perfluoropentanoic acid (PFPA) and 0.1% formic acid (FA). The second aliquot was also analyzed using acidic positive ion conditions; however, it was chromatographically optimized for more hydrophobic compounds. The extract was gradient eluted from the same C18 column using methanol, acetonitrile, water, 0.05% PFPA and 0.01% FA. The third aliquot was analyzed using basic negative ESI-optimized conditions using a separate dedicated C18 column. The basic extracts were gradient eluted from the column using methanol and water with 6.5 mmol/L Ammonium Bicarbonate at pH 8. The fourth aliquot was analyzed via negative ESI following elution from a HILIC column (Waters UPLC BEH Amide 2.1x150 mm, 1.7 µm) using a gradient consisting of water and acetonitrile with 10 mmol/L Ammonium Formate, pH 10.8. The MS analysis alternated between MS and data-dependent MSn scans using dynamic exclusion, while the scan range covered m/z 70–1000 at a resolving power of R=35,000 optimized at fifty percent of the maximum peak height (FWHM). Metabolites were identified by automated comparison of the ion features in the samples to a reference library of chemical standard entries that considered the retention time, molecular weight (m/z), preferred adducts, in-source fragments, and associated MS spectra77. The data were curated by visual inspection for quality control using Metabolon’s proprietary software. Library matches for each compound were checked for each sample and corrected if necessary. Peaks were quantified using area-under-the-curve. A data normalization step was performed to correct for variation resulting from instrument inter-day tuning differences by setting the medians to equal one (1.00) and normalizing each data point proportionately (termed “block correction”). This preserved variation between samples while allowing metabolites of different raw peak areas to be compared on a similar graphical scale. |
Combined analysis:
| Analysis ID | AN005825 | AN005826 | AN005827 | AN005828 |
|---|---|---|---|---|
| Analysis type | MS | MS | MS | MS |
| Chromatography type | Reversed phase | Reversed phase | Reversed phase | HILIC |
| Chromatography system | Waters Acquity | Waters Acquity | Waters Acquity | Waters Acquity |
| Column | Waters Acquity BEH C18 (100 x 2mm, 1.7um) | Waters Acquity BEH C18 (100 x 2mm, 1.7um) | Waters Acquity BEH C18 (100 x 2mm, 1.7um) | Waters Acquity BEH Amide (150 x 2.1mm, 1.7um) |
| MS Type | Other | Other | Other | Other |
| MS instrument type | Orbitrap | Orbitrap | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap |
| Ion Mode | POSITIVE | POSITIVE | NEGATIVE | NEGATIVE |
| Units | AU | AU | AU | AU |
Chromatography:
| Chromatography ID: | CH004426 |
| Chromatography Summary: | Low pH polar (LC/MS Pos early) |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity BEH C18 (100 x 2mm, 1.7um) |
| Column Temperature: | 40-50 |
| Flow Gradient: | Linear gradient from 5% B to 80% B over 3.35 minutes |
| Flow Rate: | 0.35 mL/min |
| Solvent A: | 100% water; 0.1% formic acid; 0.05% PFPA, pH ~2.5 |
| Solvent B: | 100% methanol; 0.1% formic acid; 0.05% PFPA, pH ~2.5 |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH004427 |
| Chromatography Summary: | Low pH Lipophilic (LC/MS Pos late) |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity BEH C18 (100 x 2mm, 1.7um) |
| Column Temperature: | 40-50 |
| Flow Gradient: | Linear gradient from 40% B to 99.5% B over 1.0 minute, hold 99.5% B for 2.4 minutes. |
| Flow Rate: | 0.60 mL/min |
| Solvent A: | 100% water; 0.1% formic acid; 0.05% PFPA, pH ~2.5 |
| Solvent B: | 50% methanol/50% acetonitrile; 0.1% formic acid; 0.05% PFPA, pH ~2.5 |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH004428 |
| Chromatography Summary: | High pH (LC/MS Neg) |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity BEH C18 (100 x 2mm, 1.7um) |
| Column Temperature: | 40-50 |
| Flow Gradient: | Linear gradient from 0.5 to 70% B over 4.0 minutes, then rapid gradient to 99% B in 0.5 minutes. |
| Flow Rate: | 0.35 mL/min |
| Solvent A: | 100% water; 6.5 mM ammonium bicarbonate, pH 8 |
| Solvent B: | 95% methanol/5% water; 6.5 mM ammonium bicarbonate |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH004429 |
| Chromatography Summary: | HILIC (LC/MS Polar Neg) |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity BEH Amide (150 x 2.1mm, 1.7um) |
| Column Temperature: | 40-50 |
| Flow Gradient: | Linear gradient from 5% B to 50% B in 3.5 minutes, then linear gradient from 50% B to 95% B in 2 minutes. |
| Flow Rate: | 0.50 mL/min |
| Solvent A: | 15% water/5% methanol/80% acetonitrile; 10 mM ammonium formate, (effective pH 10.16 with NH4OH) |
| Solvent B: | 50% water/50% acetonitrile; 10 mM ammonium formate, (effective pH 10.60 with NH4OH) |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS005545 |
| Analysis ID: | AN005825 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | Other |
| MS Comments: | Metabolon (LC/MS Pos early) |
| Ion Mode: | POSITIVE |
| MS ID: | MS005546 |
| Analysis ID: | AN005826 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | Other |
| MS Comments: | Metabolon (LC/MS Pos late) |
| Ion Mode: | POSITIVE |
| MS ID: | MS005547 |
| Analysis ID: | AN005827 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | Other |
| MS Comments: | Metabolon (LC/MS Neg) |
| Ion Mode: | NEGATIVE |
| MS ID: | MS005548 |
| Analysis ID: | AN005828 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | Other |
| MS Comments: | Metabolon (LC/MS Polar) |
| Ion Mode: | NEGATIVE |
