Summary of Study ST002210
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 PR001411. The data can be accessed directly via it's Project DOI: 10.21228/M8BB0F 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 | ST002210 |
| Study Title | Revealing the Social Biomarkers of Residual Feed Intake by Using 16s rRNA and LC-MS/MS in Duroc Pig |
| Study Summary | Feed efficiency (FE) is a typical social affected trait. However, the mechanisms involved are not fully elucidated. According to the rank of residual feed intake (RFI)’s the social genetic effect (SGE), ten high and low pigs were selected, named LRI and HRI groups. The sampling of jejunal chyme after slaughter. 16S rRNA and LC-MS/MS were conducted to investigate the relationship between the gut microbiome or metabolites and the SGE of RFI. The results showed significant differences between HRI and LRI groups. Compared with the HRI group, Escherichia, Eubacterium, and Gemmiger were enriched in the LRI group (P < 0.01), whereas the abundance of Fusobacterium, Eubacterium, and Desulfovibrio in the HRI group were significantly higher than that in the LRI group (P < 0.01). In the metabolome, we found that Glycine, L-lysine, and L-tryptophan were positively correlated with RFI’s SGE. KEGG pathway analysis revealed that most differential metabolites were involved in amino acid metabolism. The Pearson correlation analysis of the candidate social biomarkers was carried out. Amino acid metabolites were discovered to have significant correlations with Escherichia and Fusobacterium. Therefore, Escherichia and Fusobacterium may influence the SGE of RFI through amino acid metabolism, thereby affecting feed efficiency. |
| Institute | Sichuan Agricultural University |
| Department | animal science and technology |
| Laboratory | Guoqing Tang Group |
| Last Name | Wang |
| First Name | Shujie |
| Address | Huimin Road, Chengdu, Sichuan, China |
| 670186296@qq.com | |
| Phone | 15680993607 |
| Submit Date | 2022-07-02 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2022-07-11 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001411 |
| Project DOI: | doi: 10.21228/M8BB0F |
| Project Title: | Revealing the Social Biomarkers of Residual Feed Intake by Using 16s rRNA and LC-MS/MS in Duroc Pig |
| Project Summary: | Feed efficiency (FE) is a typical social affected trait. However, the mechanisms involved are not fully elucidated. According to the rank of residual feed intake (RFI)’s the social genetic effect (SGE), ten high and low pigs were selected, named LRI and HRI groups. The sampling of jejunal chyme after slaughter. 16S rRNA and LC-MS/MS were conducted to investigate the relationship between the gut microbiome or metabolites and the SGE of RFI. The results showed significant differences between HRI and LRI groups. Compared with the HRI group, Escherichia, Eubacterium, and Gemmiger were enriched in the LRI group (P < 0.01), whereas the abundance of Fusobacterium, Eubacterium, and Desulfovibrio in the HRI group were significantly higher than that in the LRI group (P < 0.01). In the metabolome, we found that Glycine, L-lysine, and L-tryptophan were positively correlated with RFI’s SGE. KEGG pathway analysis revealed that most differential metabolites were involved in amino acid metabolism. The Pearson correlation analysis of the candidate social biomarkers was carried out. Amino acid metabolites were discovered to have significant correlations with Escherichia and Fusobacterium. Therefore, Escherichia and Fusobacterium may influence the SGE of RFI through amino acid metabolism, thereby affecting feed efficiency. |
| Institute: | Sichuan Agricultural University |
| Last Name: | Wang |
| First Name: | Shujie |
| Address: | Huimin Road, Chengdu, Sichuan, China |
| Email: | 670186296@qq.com |
| Phone: | 15680993607 |
Subject:
| Subject ID: | SU002296 |
| Subject Type: | Mammal |
| Subject Species: | Sus scrofa |
| Taxonomy ID: | 9823 |
| Age Or Age Range: | 174-196day |
| Weight Or Weight Range: | 110-120kg |
| Gender: | Female |
| Species Group: | Mammals |
Factors:
Subject type: Mammal; Subject species: Sus scrofa (Factor headings shown in green)
| mb_sample_id | local_sample_id | Factor |
|---|---|---|
| SA211516 | LRI9 | high SGE of RFI |
| SA211517 | LRI10 | high SGE of RFI |
| SA211518 | LRI1 | high SGE of RFI |
| SA211519 | LRI7 | high SGE of RFI |
| SA211520 | LRI8 | high SGE of RFI |
| SA211521 | LRI6 | high SGE of RFI |
| SA211522 | LRI2 | high SGE of RFI |
| SA211523 | LRI4 | high SGE of RFI |
| SA211524 | LRI3 | high SGE of RFI |
| SA211525 | LRI5 | high SGE of RFI |
| SA211526 | HRI8 | low SGE of RFI |
| SA211527 | HRI9 | low SGE of RFI |
| SA211528 | HRI10 | low SGE of RFI |
| SA211529 | HRI7 | low SGE of RFI |
| SA211530 | HRI1 | low SGE of RFI |
| SA211531 | HRI2 | low SGE of RFI |
| SA211532 | HRI3 | low SGE of RFI |
| SA211533 | HRI4 | low SGE of RFI |
| SA211534 | HRI5 | low SGE of RFI |
| SA211535 | HRI6 | low SGE of RFI |
| Showing results 1 to 20 of 20 |
Collection:
| Collection ID: | CO002289 |
| Collection Summary: | After ranking the RFI values of 294 pigs, the model equation was used to calculate RFI’s SGE. The top 10 highest RFI’s SGEs and 10 lowest RFI’s SGEs were selected as the LRI and HRI groups, respectively. The jejunal contents of 20 pigs were collected after being humanely slaughtered. Stores samples in liquid nitrogen immediately. Then, the samples were stored at − 80 °C refrigerators. |
| Sample Type: | Jejunum |
Treatment:
| Treatment ID: | TR002308 |
| Treatment Summary: | After ranking the RFI values of 294 pigs, the model equation was used to calculate RFI’s SGE. The top 10 highest RFI’s SGEs and 10 lowest RFI’s SGEs were selected as the LRI and HRI groups, respectively. The jejunal contents of 20 pigs were collected after being humanely slaughtered. Stores samples in liquid nitrogen immediately. Then, the samples were stored at − 80 °C refrigerators. |
Sample Preparation:
| Sampleprep ID: | SP002302 |
| Sampleprep Summary: | Weigh a 25 mg sample of jejunal content and add 400μl of extract (methanol: water = 4:1). Then, using the high-throughput tissue grinder, pulverize at -20 °C (60 Hz). After 30 minutes of vertexing at 40 kHz for 30 minutes at 5 °C for mixing and sonication, put the extracted samples at -20 °C for 30 minutes. After centrifuging the solution at 13,000 g for 15 minutes (4 °C), the supernatant was collected and fed into the LC-MS/MS apparatus for analysis. |
Combined analysis:
| Analysis ID | AN003613 | AN003614 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | HILIC | HILIC |
| Chromatography system | Waters 2D UPLC | Waters 2D UPLC |
| Column | Waters Acquity BEH C8 (100 x 2.1mm,1.7um) | Waters Acquity BEH C8 (100 x 2.1mm,1.7um) |
| MS Type | ESI | ESI |
| MS instrument type | Ion trap | Ion trap |
| MS instrument name | Thermo Q Exactive Focus | Thermo Q Exactive Focus |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | peak area | peak area |
Chromatography:
| Chromatography ID: | CH002669 |
| Instrument Name: | Waters 2D UPLC |
| Column Name: | Waters Acquity BEH C8 (100 x 2.1mm,1.7um) |
| Flow Gradient: | 0-1 min, 2% B; 1-9 min, 2%-98% B; 9-12 min, 98% B; 12-12.1 min, 98% B to 2% B; and 12.1-15min, 2% B |
| Flow Rate: | 0.35 mL/min |
| Solvent A: | Pos mode:100% water; 0.1% formic acid, Neg mode:100% water; 10 mM ammonium formate |
| Solvent B: | 100% acetonitrile |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS003364 |
| Analysis ID: | AN003613 |
| Instrument Name: | Thermo Q Exactive Focus |
| Instrument Type: | Ion trap |
| MS Type: | ESI |
| MS Comments: | The mobile phase consisted of 0.1% formic acid (A) and acetonitrile (B) in the positive mode, and in the negative mode, the mobile phase consisted of 10 mM ammonium formate (A) and acetonitrile (B). The gradient conditions were as follows: 0-1 min, 2% B; 1-9 min, 2%-98% B; 9-12 min, 98% B; 12-12.1 min, 98% B to 2% B; and 12.1-15min, 2% B. The flow rate was 0.35 mL/min and the injection volume was 5 μL. The mass spectrometric settings for positive/negative ionization modes were as follows: spray voltage, 3.8/−3.2 kV; sheath gas flow rate, 40 arbitrary units (arb); aux gas flow rate, 10 arb; aux gas heater temperature, 350 °C; capillary temperature, 320 °C. The full scan range was 70–1050 m/z with a resolution of 70000, and the automatic gain control (AGC) target for MS acquisitions was set to 3e6 with a maximum ion injection time of 100 ms. Top 3 precursors were selected for subsequent MSMS fragmentation with a maximum ion injection time of 50 ms and resolution of 17500, the AGC was 1e5. The stepped normalized collision energy was set to 20, 40 and 60 eV. |
| Ion Mode: | POSITIVE |
| MS ID: | MS003365 |
| Analysis ID: | AN003614 |
| Instrument Name: | Thermo Q Exactive Focus |
| Instrument Type: | Ion trap |
| MS Type: | ESI |
| MS Comments: | The mobile phase consisted of 0.1% formic acid (A) and acetonitrile (B) in the positive mode, and in the negative mode, the mobile phase consisted of 10 mM ammonium formate (A) and acetonitrile (B). The gradient conditions were as follows: 0-1 min, 2% B; 1-9 min, 2%-98% B; 9-12 min, 98% B; 12-12.1 min, 98% B to 2% B; and 12.1-15min, 2% B. The flow rate was 0.35 mL/min and the injection volume was 5 μL. The mass spectrometric settings for positive/negative ionization modes were as follows: spray voltage, 3.8/−3.2 kV; sheath gas flow rate, 40 arbitrary units (arb); aux gas flow rate, 10 arb; aux gas heater temperature, 350 °C; capillary temperature, 320 °C. The full scan range was 70–1050 m/z with a resolution of 70000, and the automatic gain control (AGC) target for MS acquisitions was set to 3e6 with a maximum ion injection time of 100 ms. Top 3 precursors were selected for subsequent MSMS fragmentation with a maximum ion injection time of 50 ms and resolution of 17500, the AGC was 1e5. The stepped normalized collision energy was set to 20, 40 and 60 eV. |
| Ion Mode: | NEGATIVE |
