Summary of Study ST004383

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.

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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.

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Study IDST004383
Study TitleGC-FID based metabolomic profiling of rumen samples across different regions in three ruminant species - investigation of short-chain fatty acids
Study TypeGC-FID metabolomics
Study SummaryThis study investigates short-chain fatty acids (SCFAs) in the rumen of three ruminant species. Rumen contents and rumen fluid were collected from multiple anatomical regions, and SCFA concentrations were quantified using GC-FID. The analysis revealed species-specific fermentation patterns, with roe deer exhibiting elevated acetate levels, sika deer showing increased propionate, and sheep displaying higher concentrations of isobutyrate and isovalerate.
Institute
Jilin Agricultural University
DepartmentCollege of Animal Science and Technology
LaboratoryRuminant Nutrition Laboratory
Last NameLi
First NameZhi Peng
AddressNo. 2888 Xincheng Street
Emailzhplicaas@163.com
Phone18043213681
Submit Date2025-11-17
Raw Data AvailableYes
Raw Data File Type(s)cdf
Analysis Type DetailGC-MS
Release Date2025-12-15
Release Version1
Zhi Peng Li Zhi Peng Li
https://dx.doi.org/10.21228/M8Q26C
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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:SU004542
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 Regions Host
SA520269163_FIDIArumen content AR Capreolus pygargus
SA520270120_FIDIArumen content AR Capreolus pygargus
SA520271119_FIDIArumen content AR Capreolus pygargus
SA520272108_FIDIArumen content AR Capreolus pygargus
SA52027312_FIDIArumen content AR Cervus nippon
SA520274101_FIDIArumen content AR Cervus nippon
SA520275125_FIDIArumen content AR Cervus nippon
SA520276143_FIDIArumen content AR Cervus nippon
SA52027706_FIDIArumen content AR Cervus nippon
SA52027872_FIDIArumen content AR Ovis aries
SA520279115_FIDIArumen content AR Ovis aries
SA52028099_FIDIArumen content AR Ovis aries
SA52028127_FIDIArumen content AR Ovis aries
SA52028226_FIDIArumen content AR Ovis aries
SA520283112_FIDIArumen content DSR Capreolus pygargus
SA52028466_FIDIArumen content DSR Capreolus pygargus
SA52028593_FIDIArumen content DSR Capreolus pygargus
SA52028676_FIDIArumen content DSR Capreolus pygargus
SA520287130_FIDIArumen content DSR Capreolus pygargus
SA52028816_FIDIArumen content DSR Cervus nippon
SA52028933_FIDIArumen content DSR Cervus nippon
SA520290109_FIDIArumen content DSR Cervus nippon
SA52029121_FIDIArumen content DSR Cervus nippon
SA52029202_FIDIArumen content DSR Cervus nippon
SA52029315_FIDIArumen content DSR Ovis aries
SA520294105_FIDIArumen content DSR Ovis aries
SA520295135_FIDIArumen content DSR Ovis aries
SA52029665_FIDIArumen content DSR Ovis aries
SA52029728_FIDIArumen content DSR Ovis aries
SA520298136_FIDIArumen content IR Capreolus pygargus
SA520299156_FIDIArumen content IR Capreolus pygargus
SA52030052_FIDIArumen content IR Capreolus pygargus
SA52030163_FIDIArumen content IR Capreolus pygargus
SA52030280_FIDIArumen content IR Capreolus pygargus
SA520303139_FIDIArumen content IR Cervus nippon
SA52030468_FIDIArumen content IR Cervus nippon
SA52030525_FIDIArumen content IR Cervus nippon
SA520306153_FIDIArumen content IR Cervus nippon
SA52030723_FIDIArumen content IR Cervus nippon
SA52030831_FIDIArumen content IR Ovis aries
SA520309149_FIDIArumen content IR Ovis aries
SA52031056_FIDIArumen content IR Ovis aries
SA52031130_FIDIArumen content IR Ovis aries
SA520312141_FIDIArumen content IR Ovis aries
SA520313154_FIDIArumen content SAR Capreolus pygargus
SA52031445_FIDIArumen content SAR Capreolus pygargus
SA52031588_FIDIArumen content SAR Capreolus pygargus
SA52031678_FIDIArumen content SAR Capreolus pygargus
SA520317129_FIDIArumen content SAR Capreolus pygargus
SA520318132_FIDIArumen content SAR Cervus nippon
SA52031958_FIDIArumen content SAR Cervus nippon
SA52032053_FIDIArumen content SAR Cervus nippon
SA520321122_FIDIArumen content SAR Cervus nippon
SA52032275_FIDIArumen content SAR Cervus nippon
SA520323117_FIDIArumen content SAR Ovis aries
SA520324137_FIDIArumen content SAR Ovis aries
SA52032519_FIDIArumen content SAR Ovis aries
SA52032622_FIDIArumen content SAR Ovis aries
SA52032710_FIDIArumen content SAR Ovis aries
SA52032804_FIDIArumen content SASR Capreolus pygargus
SA52032935_FIDIArumen content SASR Capreolus pygargus
SA52033085_FIDIArumen content SASR Capreolus pygargus
SA52033117_FIDIArumen content SASR Capreolus pygargus
SA520332102_FIDIArumen content SASR Capreolus pygargus
SA520333161_FIDIArumen content SASR Cervus nippon
SA520334131_FIDIArumen content SASR Cervus nippon
SA52033539_FIDIArumen content SASR Cervus nippon
SA520336110_FIDIArumen content SASR Cervus nippon
SA52033784_FIDIArumen content SASR Cervus nippon
SA520338144_FIDIArumen content SASR Ovis aries
SA52033998_FIDIArumen content SASR Ovis aries
SA520340134_FIDIArumen content SASR Ovis aries
SA520341100_FIDIArumen content SASR Ovis aries
SA52034251_FIDIArumen content SASR Ovis aries
SA52034383_FIDIArumen content SCR Capreolus pygargus
SA520344147_FIDIArumen content SCR Capreolus pygargus
SA52034581_FIDIArumen content SCR Capreolus pygargus
SA52034657_FIDIArumen content SCR Capreolus pygargus
SA52034791_FIDIArumen content SCR Capreolus pygargus
SA520348126_FIDIArumen content SCR Cervus nippon
SA52034962_FIDIArumen content SCR Cervus nippon
SA520350151_FIDIArumen content SCR Cervus nippon
SA52035147_FIDIArumen content SCR Cervus nippon
SA52035241_FIDIArumen content SCR Cervus nippon
SA520353127_FIDIArumen content SCR Ovis aries
SA52035403_FIDIArumen content SCR Ovis aries
SA52035569_FIDIArumen content SCR Ovis aries
SA52035605_FIDIArumen content SCR Ovis aries
SA520357145_FIDIArumen content SCR Ovis aries
SA52035818_FIDIArumen content SCVR Capreolus pygargus
SA52035949_FIDIArumen content SCVR Capreolus pygargus
SA52036095_FIDIArumen content SCVR Capreolus pygargus
SA520361116_FIDIArumen content SCVR Capreolus pygargus
SA520362142_FIDIArumen content SCVR Cervus nippon
SA520363106_FIDIArumen content SCVR Cervus nippon
SA520364114_FIDIArumen content SCVR Cervus nippon
SA52036561_FIDIArumen content SCVR Cervus nippon
SA520366140_FIDIArumen content SCVR Cervus nippon
SA52036743_FIDIArumen content SCVR Ovis aries
SA52036860_FIDIArumen content SCVR Ovis aries
Showing page 1 of 2     Results:    1  2  Next     Showing results 1 to 100 of 177

Collection:

Collection ID:CO004535
Collection Summary:The contents from 11 rumen regions were collected: atrium ruminis (AR; n = 15), saccus dorsalis (DSR; n = 15), saccus ventralis (VSR; n = 15), saccus cecus caudodorsalis (SDR; n = 14), saccus cecus caudoventralis (SVR; n = 15), sulcus cranialis (SCR; n = 15), sulcus longitudinalis sinister (SLSR; n = 14), sulcus coronarius ventralis (SCVR; n = 15), sulcus caudalis (SAR; n = 15), sulcus accessorius sinister (SASR; n = 15), and insula ruminis (IR; n = 15). In addition, the rumen liquid (n = 15) filtered through four layers of cheesecloth were collected.
Sample Type:rumen content and liquid
Collection Method:Rumen content samples were manually collected from each anatomical region through dissection immediately after euthanasia. Rumen liquid was obtained by filtering rumen digesta through four layers of cheesecloth.
Collection Location:AR :Atrium ruminis; DSR:Saccus dorsalis; VSR:Saccus ventralis; SDR:Saccus cecus caudodorsalis;SVR:Saccus cecus caudoventralis;SCR:Sulcus cranialis; SLSR:Sulcus longitudinalis sinister ;SCVR :Sulcus coronarius ventralis; SAR :Sulcus caudalis :SASR :Sulcus accessorius sinister ; IR:Insula ruminis ; Liquid :Rumen liquid
Collection Frequency:15
Collection Duration:1 year
Volumeoramount Collected:5ml
Storage Conditions:-80℃

Treatment:

Treatment ID:TR004551
Treatment Summary:Animals received no experimental treatment and were maintained under identical feeding and housing conditions.

Sample Preparation:

Sampleprep ID:SP004548
Sampleprep Summary:Rumen content was homogenized and acidified to release short-chain fatty acids (SCFAs). Samples were centrifuged, and the supernatant was collected for analysis. Rumen liquid samples were filtered through four layers of cheesecloth, acidified, and centrifuged. All supernatants were transferred into GC vials for GC-FID analysis without further derivatization
Processing Storage Conditions:-80℃
Extract Storage:Room temperature

Combined analysis:

Analysis ID AN007323
Chromatography ID CH005558
MS ID MS007017
Analysis type MS
Chromatography type GC
Chromatography system Agilent 7890B
Column Agilent DB-FFAP (30m x 0.25mm, 0.25um)
MS Type None
MS instrument type None
MS instrument name None
Ion Mode None
Units mM

Chromatography:

Chromatography ID:CH005558
Chromatography Summary:Gas chromatography was performed using an Agilent 7890B GC system with a DB-FFAP capillary column. Samples (1 μL) were injected in split mode (20:1), nitrogen was used as the carrier gas, and the oven temperature was programmed from 60°C to 190°C. Detection was performed using a flame ionization detector at 250°C. Agilent DB-FFAP (30m x 0.25mm, 0.25um)
Instrument Name:Agilent 7890B
Column Name:Agilent DB-FFAP (30m x 0.25mm, 0.25um)
Column Temperature:the initial temperature was set at 60 °C (hold 0 min), followed by a temperature ramp of 20 °C/min to 190 °C, where it was held for 3 min before returning to initial conditions.
Flow Gradient:-
Flow Rate:-
Solvent A:-
Solvent B:-
Chromatography Type:GC

MS:

MS ID:MS007017
Analysis ID:AN007323
Instrument Name:None
Instrument Type:None
MS Type:None
MS Comments:No mass spectrometry was used in this study. Samples were analyzed by GC-FID, and therefore no MS acquisition, MS-based data processing, or feature-assignment procedures were performed. Peak identification and SCFA quantification were carried out using chromatographic software only, and no MS-related workflows were applied.No QC samples were included in this GC-FID SCFA analysis because the assay was performed directly on individual rumen content and rumen fluid samples without pooled biological QC or technical QC injections. All samples were prepared and analyzed under identical experimental conditions. Instrument performance and stability were ensured through routine calibration of the GC-FID system, consistent retention time monitoring, and system suitability checks rather than dedicated QC runs.
Ion Mode:None
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