Summary of Study ST004384
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 PR002777. The data can be accessed directly via it's Project DOI: 10.21228/M8Q26C 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 | ST004384 |
| Study Title | Microbiome biogeography and ventral epithelial differences of rumen - vitamin profiling of rumen fluid from three ruminant species |
| Study Type | Targeted LC–MS/MS |
| Study Summary | This study aims to quantify and compare vitamin concentrations in the rumen liquid of three ruminant species—roe deer, sika deer, and sheep—using a targeted LC–MS/MS metabolomics approach. Rumen liquid samples were collected immediately after euthanasia and processed for vitamin extraction and analysis on a Triple Quad 4500MD mass spectrometer. The resulting dataset provides species-specific vitamin profiles that offer insights into rumen physiology, nutritional adaptation, and metabolic differentiation among ruminants. Targeted analysis revealed elevated levels of vitamins B3 and B6 in roe deer, increased vitamin B2 in sika deer, and higher concentrations of vitamins B1, B5, B7, and B12 in sheep. |
| Institute | Jilin Agricultural University |
| Department | College of Animal Science and Technology |
| Laboratory | Ruminant Nutrition Laboratory |
| Last Name | Li |
| First Name | Zhi Peng |
| Address | No. 2888 Xincheng Street |
| zhplicaas@163.com | |
| Phone | 18043213681 |
| Submit Date | 2025-11-17 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-12-15 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002777 |
| Project DOI: | doi: 10.21228/M8Q26C |
| Project Title: | Microbiome biogeography and ventral epithelial differences of rumen across different regions in three different ruminant species |
| Project Summary: | Ruminants thrive in diverse ecosystems by leveraging their rumen microbiome to ferment fibrous plants. However, the spatial biogeography of the rumen microbiome and genetic diversity of ventral rumen among the ruminants remain unknown. Here, we present a multi-omics integrating region-resolved microbiome across eleven ruminal sacs, metabolomics, and single-cell RNA sequencing, ATAC-seq, and bulk RNA-seq of ventral epithelium of roe deer, sika deer and sheep. Our results reveal species-specific rumen microbial compositions and metabolic capacities that contribute to differences in short-chain fatty acids and vitamin B production. We uncover functional divergence, genomic specialization and metabolic changes across distinct ruminal sacs microbiome. Single-cell profiling reveals changes of immune responses and structural remodeling in ventral rumen. We demonstrate that vitamin B12 promotes epithelial growth, and four novel genes that enhance stem cell differentiation. Our results highlight variation in microbial ecology and epithelial architecture among three ruminant species, offering insights to improve livestock productivity. |
| Institute: | Jilin Agricultural University |
| Department: | College of Animal Science and Technology |
| Laboratory: | Ruminant Nutrition Laboratory |
| Last Name: | Li |
| First Name: | Zhi Peng |
| Address: | No. 2888 Xincheng Street |
| Email: | zhplicaas@163.com |
| Phone: | 18043213681 |
Subject:
| Subject ID: | SU004543 |
| Subject Type: | Mammal |
| Subject Species: | Ovis aries, Capreolus pygargus, Cervus nippon |
| Taxonomy ID: | 9940, 48560, 9863 |
| Age Or Age Range: | 4 years |
| Gender: | Male |
| Animal Housing: | Each animal was housed in an individual pen (3 m × 3 m). |
| Animal Feed: | Roe deer, sika deer and sheep fed a total mixed ration consisting of alfalfa and concentrate (45:55, dry matter basis) for two months were used in this study. |
| Animal Water: | Free water |
Factors:
Subject type: Mammal; Subject species: Ovis aries, Capreolus pygargus, Cervus nippon (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Host |
|---|---|---|---|
| SA520446 | PLY02 | rumen liquid | Capreolus pygargus |
| SA520447 | PLY01 | rumen liquid | Capreolus pygargus |
| SA520448 | PLY03 | rumen liquid | Capreolus pygargus |
| SA520449 | PLY04 | rumen liquid | Capreolus pygargus |
| SA520450 | PLY05 | rumen liquid | Capreolus pygargus |
| SA520451 | MLY01 | rumen liquid | Cervus nippon |
| SA520452 | MLY02 | rumen liquid | Cervus nippon |
| SA520453 | MLY03 | rumen liquid | Cervus nippon |
| SA520454 | MLY04 | rumen liquid | Cervus nippon |
| SA520455 | MLY05 | rumen liquid | Cervus nippon |
| SA520456 | SLY01 | rumen liquid | Ovis aries |
| SA520457 | SLY02 | rumen liquid | Ovis aries |
| SA520458 | SLY03 | rumen liquid | Ovis aries |
| SA520459 | SLY04 | rumen liquid | Ovis aries |
| SA520460 | SLY05 | rumen liquid | Ovis aries |
| Showing results 1 to 15 of 15 |
Collection:
| Collection ID: | CO004536 |
| Collection Summary: | Rumen liquid samples were collected from three ruminant species—roe deer, sika deer, and sheep—immediately after euthanasia. Each animal was humanely euthanized 3 hours after morning feeding, followed by postmortem dissection. The rumen was opened through a midline abdominal incision, and rumen fluid was obtained by gently squeezing fresh digesta through four layers of cheesecloth to remove coarse particulate matter. The filtered rumen fluid was transferred into sterile tubes, kept on ice, and transported to the laboratory for subsequent vitamin extraction and LC–MS/MS analysis. |
| Sample Type: | rumen liquid |
| Collection Method: | Rumen liquid was obtained by filtering rumen digesta through four layers of cheesecloth. |
| Collection Location: | Liquid:Rumen liquid |
| Collection Frequency: | 15 |
| Collection Duration: | 1 year |
| Volumeoramount Collected: | 50ml |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR004552 |
| Treatment Summary: | Animals received no experimental treatment and were maintained under identical feeding and housing conditions. |
Sample Preparation:
| Sampleprep ID: | SP004549 |
| Sampleprep Summary: | Rumen liquid samples (200 μL) were transferred into 1.5-mL microcentrifuge tubes, and 20 μL of internal standard solution was added. The mixture was vortexed at 2,000 rpm for 10 min and then incubated at room temperature for 5 min. Protein precipitation was performed by adding 600 μL of precipitating reagent, followed by mixing at 2,000 rpm for 10 min at room temperature. Samples were centrifuged at 12,000 × g for 10 min, and 400 μL of the resulting supernatant was transferred into a V-shaped 96-well plate. The plate was dried under a gentle stream of nitrogen at 37°C. Dried residues were reconstituted in 60 μL of reconstitution solvent, sealed with a plate film, vortexed at 2,000 rpm for 5 min, and centrifuged at 2,811 × g for 5 min. Finally, 55 μL of the clarified extract from each well was transferred into a fresh V-shaped 96-well plate for LC–MS/MS analysis. |
| Processing Storage Conditions: | -80℃ |
| Extract Storage: | Room temperature |
Combined analysis:
| Analysis ID | AN007324 | AN007325 |
|---|---|---|
| Chromatography ID | CH005559 | CH005559 |
| MS ID | MS007018 | MS007019 |
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | AB Sciex Triple Quad 4500MD | AB Sciex Triple Quad 4500MD |
| Column | Waters XSelect HSS T3 XP (100 x 2.1mm, 2.5um) | Waters XSelect HSS T3 XP (100 x 2.1mm, 2.5um) |
| MS Type | ESI | ESI |
| MS instrument type | Triple quadrupole | Triple quadrupole |
| MS instrument name | ABI Sciex Triple Quad 4500MD | ABI Sciex Triple Quad 4500MD |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | ng/ml | ng/ml |
Chromatography:
| Chromatography ID: | CH005559 |
| Chromatography Summary: | Chromatographic separation of vitamins was performed using reversed-phase liquid chromatography on an LC system coupled to a SCIEX Triple Quad 4500MD mass spectrometer. Samples were injected onto the analytical column and eluted with a binary mobile phase under gradient conditions at a constant flow rate. The LC method was optimized to ensure efficient separation of water-soluble vitamins prior to MS/MS detection. |
| Instrument Name: | AB Sciex Triple Quad 4500MD |
| Column Name: | Waters XSelect HSS T3 XP (100 x 2.1mm, 2.5um) |
| Column Temperature: | 35℃ |
| Flow Gradient: | 0.00–1.00 min, 99% A / 1% B at 0.35 mL/min; 1.00–1.30 min, linear gradient from 99% A / 1% B to 60% A / 40% B at 0.35 mL/min; 1.30–2.80 min, 60% A / 40% B at 0.35 mL/min; 2.80–3.80 min, linear gradient from 60% A / 40% B to 1% A / 99% B at 0.35 mL/min; 3.80–4.30 min, 1% A / 99% B at 0.35 mL/min; 4.30–4.35 min, linear gradient from 1% A / 99% B back to 99% A / 1% B at 0.35 mL/min; 4.35–5.20 min, 99% A / 1% B at 0.35 mL/min (re-equilibration). |
| Flow Rate: | 0.35mL/min |
| Solvent A: | 100% Water; 0.1% formic acid |
| Solvent B: | 100% Methanol; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS007018 |
| Analysis ID: | AN007324 |
| Instrument Name: | ABI Sciex Triple Quad 4500MD |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | MS/MS data were acquired on a SCIEX Triple Quad™ 4500MD mass spectrometer in multiple reaction monitoring (MRM) mode. In MRM, the first quadrupole selects the precursor ion of each target analyte, which is then fragmented in the collision cell, and a characteristic product ion is selected by the third quadrupole for highly selective and reproducible quantification. Instrument parameters and MRM transitions were optimized based on authentic standards and the MWDB (Metware Database). Raw LC–MS/MS data were processed using the MWDB (Metware Database) and vendor software for peak detection and integration. Chromatographic peaks corresponding to target vitamins were integrated across all samples, and quantitative analysis was performed using internal and/or external standard calibration. Peak area (or peak area ratios of analyte to internal standard) was used to calculate the concentrations of each vitamin in rumen fluid. Qualitative assignment of vitamins was based on the MWDB (Metware Database) constructed from authentic standards, using matching of MRM transitions, retention time, and ion response patterns. Only compounds that matched the standard library criteria were retained as confidently identified targets. No untargeted feature discovery workflow was applied.No QC samples were included in this LC–MS/MS study because the targeted vitamin analysis was performed directly on individual rumen liquid samples without pooled biological or technical QC injections. All samples were processed and analyzed under identical conditions, and instrument stability was ensured through routine calibration, internal standard monitoring, and system suitability checks rather than dedicated QC runs. |
| Ion Mode: | POSITIVE |
| MS ID: | MS007019 |
| Analysis ID: | AN007325 |
| Instrument Name: | ABI Sciex Triple Quad 4500MD |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | MS/MS data were acquired on a SCIEX Triple Quad™ 4500MD mass spectrometer in multiple reaction monitoring (MRM) mode. In MRM, the first quadrupole selects the precursor ion of each target analyte, which is then fragmented in the collision cell, and a characteristic product ion is selected by the third quadrupole for highly selective and reproducible quantification. Instrument parameters and MRM transitions were optimized based on authentic standards and the MWDB (Metware Database). Raw LC–MS/MS data were processed using the MWDB (Metware Database) and vendor software for peak detection and integration. Chromatographic peaks corresponding to target vitamins were integrated across all samples, and quantitative analysis was performed using internal and/or external standard calibration. Peak area (or peak area ratios of analyte to internal standard) was used to calculate the concentrations of each vitamin in rumen fluid. Qualitative assignment of vitamins was based on the MWDB (Metware Database) constructed from authentic standards, using matching of MRM transitions, retention time, and ion response patterns. Only compounds that matched the standard library criteria were retained as confidently identified targets. No untargeted feature discovery workflow was applied.No QC samples were included in this LC–MS/MS study because the targeted vitamin analysis was performed directly on individual rumen liquid samples without pooled biological or technical QC injections. All samples were processed and analyzed under identical conditions, and instrument stability was ensured through routine calibration, internal standard monitoring, and system suitability checks rather than dedicated QC runs. |
| Ion Mode: | NEGATIVE |
