Summary of Study ST004319
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 PR002733. The data can be accessed directly via it's Project DOI: 10.21228/M8CV8Z 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 | ST004319 |
| Study Title | Community structure and metabolite profiles of psychrophiles and thermophiles in bovine raw milk from arid inland areas |
| Study Summary | This project characterizes the bacterial communities and metabolomic signatures associated with psychrophilic and thermophilic isolates from raw cow’s milk collected across seven dairy farms in Xinjiang, China. We performed 16S rRNA gene sequencing on milk and associated environmental samples and carried out untargeted LC–MS metabolomics on isolates re-inoculated into sterilized milk (positive and negative ion modes). The dataset supports microbial source tracking, strain-specific metabolite profiling, and assessment of potential risks to milk quality and safety. We generated 16S rRNA amplicon sequencing data from 21 raw milk samples and associated environmental samples to profile microbial community composition and potential contamination sources. From these samples we isolated representative psychrophilic and thermophilic strains (7 + 7), re-inoculated them into sterilized milk, and performed untargeted LC–MS metabolomics in both positive and negative ion modes. The metabolomics data reveal strain-specific metabolic signatures and identify metabolites potentially relevant to milk spoilage and food safety. Data deposited include raw 16S reads, isolate metadata, and LC–MS raw data and processed metabolite tables. |
| Institute | Xinjiang University |
| Last Name | Yue |
| First Name | Haitao |
| Address | Yushugou Street, Shuimogou District, Urumqi City, Xinjiang Province |
| yuehaitao@tsinghua.org.cn | |
| Phone | 13639932226 |
| Submit Date | 2025-09-08 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML, raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-11-20 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002733 |
| Project DOI: | doi: 10.21228/M8CV8Z |
| Project Title: | Community structure and metabolite profiles of psychrophiles and thermophiles isolated from raw cow’s milk in Xinjiang, China. |
| Project Summary: | This project characterizes the bacterial communities and metabolomic signatures associated with psychrophilic and thermophilic isolates from raw cow’s milk collected across seven dairy farms in Xinjiang, China. We performed 16S rRNA gene sequencing on milk and associated environmental samples and carried out untargeted LC–MS metabolomics on isolates re-inoculated into sterilized milk (positive and negative ion modes). The dataset supports microbial source tracking, strain-specific metabolite profiling, and assessment of potential risks to milk quality and safety. |
| Institute: | Xinjiang University |
| Last Name: | Yue |
| First Name: | Haitao |
| Address: | Yushugou Street, Shuimogou District, Urumqi City, Xinjiang Province |
| Email: | yuehaitao@tsinghua.org.cn |
| Phone: | 13639932226 |
Subject:
| Subject ID: | SU004474 |
| Subject Type: | Food item |
Factors:
Subject type: Food item; Subject species: - (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Bacteria type |
|---|---|---|---|
| SA505854 | E63_neg | Raw milk isolate | Psychrophile |
| SA505855 | A40_neg | Raw milk isolate | Psychrophile |
| SA505856 | G5_neg | Raw milk isolate | Psychrophile |
| SA505857 | G5_pos | Raw milk isolate | Psychrophile |
| SA505858 | F22_neg | Raw milk isolate | Psychrophile |
| SA505859 | F22_pos | Raw milk isolate | Psychrophile |
| SA505860 | A40_pos | Raw milk isolate | Psychrophile |
| SA505861 | E63_pos | Raw milk isolate | Psychrophile |
| SA505862 | D73_pos | Raw milk isolate | Psychrophile |
| SA505863 | C5_neg | Raw milk isolate | Psychrophile |
| SA505864 | C5_pos | Raw milk isolate | Psychrophile |
| SA505865 | B61_neg | Raw milk isolate | Psychrophile |
| SA505866 | B61_pos | Raw milk isolate | Psychrophile |
| SA505867 | D73_neg | Raw milk isolate | Psychrophile |
| SA505868 | ER1_pos | Raw milk isolate | Thermophile |
| SA505869 | GR1_neg | Raw milk isolate | Thermophile |
| SA505870 | GR1_pos | Raw milk isolate | Thermophile |
| SA505871 | FR1_neg | Raw milk isolate | Thermophile |
| SA505872 | FR1_pos | Raw milk isolate | Thermophile |
| SA505873 | ER1_neg | Raw milk isolate | Thermophile |
| SA505874 | CR2_pos | Raw milk isolate | Thermophile |
| SA505875 | DR1_neg | Raw milk isolate | Thermophile |
| SA505876 | DR1_pos | Raw milk isolate | Thermophile |
| SA505877 | CR2_neg | Raw milk isolate | Thermophile |
| SA505878 | BR2_neg | Raw milk isolate | Thermophile |
| SA505879 | BR2_pos | Raw milk isolate | Thermophile |
| SA505880 | AR1_neg | Raw milk isolate | Thermophile |
| SA505881 | AR1_pos | Raw milk isolate | Thermophile |
| Showing results 1 to 28 of 28 |
Collection:
| Collection ID: | CO004467 |
| Collection Summary: | Bacterial isolation and culture methods: Raw milk samples (100 mL each) were collected from seven livestock farms (A–G) in July 2021. For isolation, 1 mL of each milk sample was serially diluted in sterile normal saline to 10^−7. Each dilution (100 µL) was spread onto MPC agar plates (n = 3 per dilution). Psychrophilic isolates were selected by incubation at 6.5 ± 0.5 °C for 10 days, while thermophilic isolates were selected by incubation at 55 ± 1 °C for 48 ± 2 h. Distinct colonies were picked randomly, purified twice on MPC medium, and propagated in TSB medium at 150 rpm for characterization. Purified strains used for downstream analyses were maintained in culture in the laboratory (see Methods for details). For taxonomic identification, genomic DNA from purified isolates was extracted using a bacterial DNA extraction kit and the 16S rRNA gene was PCR-amplified (27F / 1492R) and Sanger-sequenced for BLAST-based identification. |
| Sample Type: | Milk |
| Collection Method: | Milk collection and storage prior to inoculation/treatment: Raw milk (100 mL per sample) was aseptically collected from individual animals at seven farms (A–G) in July 2021. Collected samples were frozen in the field, transported to the laboratory on dry ice, and stored at −80 °C until downstream processing (DNA extraction for 16S sequencing and metabolite extraction for LC–MS). Aliquots of stored raw milk were later thawed as needed for culture isolation and follow-up experiments. |
Treatment:
| Treatment ID: | TR004483 |
| Treatment Summary: | Fourteen bacterial isolates (7 psychrophiles and 7 thermophiles) were obtained from raw cow’s milk collected in Xinjiang, China. Each isolate was re-inoculated into sterilized milk at 2% (v/v) and cultured under appropriate conditions (psychrophiles at 6.5 ± 0.5 °C for 10 days; thermophiles at 55 ± 1 °C for 48 ± 2 h). After incubation, metabolites were extracted from the culture supernatants and analyzed by untargeted LC–MS in both positive and negative ion modes. |
Sample Preparation:
| Sampleprep ID: | SP004480 |
| Sampleprep Summary: | Samples were thawed at 4 °C and vortexed for 1 min to ensure homogeneity. An aliquot of each sample was mixed with 200 µL methanol and 200 µL methyl tert-butyl ether, vortexed, and centrifuged at 12,000 rpm for 10 min at 4 °C. The supernatant was filtered through a 0.22 µm membrane and used for metabolite detection. A pooled quality control (QC) sample was prepared by combining 10 µL from each extract. |
Chromatography:
| Chromatography ID: | CH005466 |
| Methods Filename: | report_(2).pdf |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.8um) |
| Column Temperature: | 40 ℃ |
| Flow Gradient: | 0~1min, 2%B; 1~9min, 2%~50% B; 9~12min, 50%~98% B; 12~13.5min, 98% B;13.5~14min, 98%~2% B;14~20min, 2% B |
| Flow Rate: | 0.25 mL/min |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH005467 |
| Methods Filename: | report_(2).pdf |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.8um) |
| Column Temperature: | 40 ℃ |
| Flow Gradient: | 0~1min, 2% B;1~9min, 2%~50% B; 9~12min, 50%~98% B;12~13.5min, 98% B;13.5~14min, 98%~2% B;14~20min, 2% B |
| Flow Rate: | 0.3 mL/min |
| Solvent A: | 100% water; 5 mM ammonium formate |
| Solvent B: | 100% acetonitrile |
| Chromatography Type: | Reversed phase |
Analysis:
| Analysis ID: | AN007196 |
| Analysis Type: | MS |
| Analysis Protocol File: | report_(2).pdf |
| Chromatography ID: | CH005466 |
| Has Mz: | 1 |
| Has Rt: | 1 |
| Rt Units: | Seconds |
| Results File: | ST004319_AN007196_Results.txt |
| Units: | Peak intensity |
| Analysis ID: | AN007197 |
| Analysis Type: | MS |
| Analysis Protocol File: | report_(2).pdf |
| Chromatography ID: | CH005467 |
| Has Mz: | 1 |
| Has Rt: | 1 |
| Rt Units: | Seconds |
| Results File: | ST004319_AN007197_Results.txt |
| Units: | peak intensity |
