Summary of Study ST002770
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 PR001727. The data can be accessed directly via it's Project DOI: 10.21228/M8GD9S 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 | ST002770 |
| Study Title | Metabolomics and Molecular Networking-Guided Screening of Bacillus-Derived Bioactive Compounds Against a Highly Lethal Vibrio Species |
| Study Summary | During our search for active substances capable of inhibiting a newly discovered highly lethal Vibrio strain vp-HL causing highly lethal Vibrio disease in shrimp (HLVD), we found that the fermentation broth of multiple Bacillus strains exhibited antibacterial activity. However, the substances responsible for the activity remained unclear. Metabolomics was employed in conjunction with bioactivity screening to identify the antibacterial compounds from Bacillus strains. The Ethyl Acetate extracts of the broth of 20 Bacillus strains were analyzed using UPLC-MS/MS. Principal Component Analysis (PCA) and Orthogonal Partial Least Square - Discriminant Analysis (OPLS-DA) was used for pattern recognition. The strains fall into two groups in the scores plot from PCA. The S-plot from OPLS-DA offered information on biomarkers. |
| Institute | Third Institute of Oceanography, Ministry of Natural Resources |
| Last Name | Xia |
| First Name | Jinmei |
| Address | Daxue Rd, Xiamen, China. |
| xiajinmei@tio.org.cn | |
| Phone | 13003995626 |
| Submit Date | 2023-06-29 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-11-01 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001727 |
| Project DOI: | doi: 10.21228/M8GD9S |
| Project Title: | Bacillus-Derived Compounds Against a Vibrio |
| Project Summary: | Metabolomics was employed in conjunction with bioactivity screening to identify the antibacterial compounds from Bacillus strains against the highly lethal Vibrio strain vp-HL. |
| Institute: | Third Institute of Oceanography, Ministry of Natural Resources |
| Last Name: | Xia |
| First Name: | Jinmei |
| Address: | Daxue Rd, Xiamen, China. |
| Email: | xiajinmei@tio.org.cn |
| Phone: | 13003995626 |
Subject:
| Subject ID: | SU002877 |
| Subject Type: | Bacteria |
| Subject Species: | Bacillus pumilus |
Factors:
Subject type: Bacteria; Subject species: Bacillus pumilus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Group |
|---|---|---|
| SA294304 | 24 | B1 |
| SA294305 | 27 | B1 |
| SA294306 | 2 | B1 |
| SA294307 | 22 | B1 |
| SA294308 | 23 | B1 |
| SA294309 | 20 | B1 |
| SA294310 | 4 | B1 |
| SA294311 | 14 | B1 |
| SA294312 | 7 | B1 |
| SA294313 | 15 | B1 |
| SA294314 | 47 | B2 |
| SA294315 | 50 | B2 |
| SA294316 | 56 | B2 |
| SA294317 | 46 | B2 |
| SA294318 | 34 | B2 |
| SA294319 | 35 | B2 |
| SA294320 | 38 | B2 |
| SA294321 | 39 | B2 |
| SA294322 | 43 | B2 |
| SA294323 | 44 | B2 |
| Showing results 1 to 20 of 20 |
Collection:
| Collection ID: | CO002870 |
| Collection Summary: | The broth cultures were centrifuged at 7000 rpm for 10 min under 4 °C and the supernatants were collected. |
| Sample Type: | Bacterial cells |
Treatment:
| Treatment ID: | TR002886 |
| Treatment Summary: | The full-length 16S rRNA gene sequence was obtained for the studied Bacillus strains. The phylogenetic tree of the 16S rRNA gene showed that the strains formed two groups, which were defined as Group B1 and B2. The antagonistic activities of the Bacillus broth against the vp-HL strain were evaluated by the agar well diffusion method. The DI (diameters of the inhibition zones) values of the 20 Bacillus strains against the vp-HL strain were measured. All strains belonging to Group B2 showed DI values greater than those of strains from Group B1. |
Sample Preparation:
| Sampleprep ID: | SP002883 |
| Sampleprep Summary: | The broth cultures were centrifuged at 7000 rpm for 10 min under 4 °C and the supernatants were collected. Ethyl acetate (EtOAc) with 2 × volume was added and sonicated for 10 min. The samples were then centrifuged at 7000 rpm at 4 °C for 10 min and the organic phase was collected and dried using a rotary evaporator. The extracts were resuspended in 1:1 acetonitrile: H2O with 1% formic acid. These samples were diluted 20 times using methanol. All samples were filtrated through 0.22 µm syringe filters. |
Combined analysis:
| Analysis ID | AN004507 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Waters Acquity |
| Column | Waters ACQUITY UPLC BEH C18 (50 x 2.1mm,1.7um) |
| MS Type | ESI |
| MS instrument type | QTOF |
| MS instrument name | Waters Vion IMS QTof |
| Ion Mode | POSITIVE |
| Units | intensity |
Chromatography:
| Chromatography ID: | CH003387 |
| Chromatography Summary: | Low pH polar |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters ACQUITY UPLC BEH C18 (50 x 2.1mm,1.7um) |
| Column Temperature: | 30 |
| Flow Gradient: | 5%B was kept for 0.5 min, 0.5-2.5 min, 5% to 30% B; 2.5-3.5 min, 30% to 40% B; 3.5-9 min, 40% to 99% B; 9-10 min, 99% to 5% B; and 5%B was kept for 3 min. |
| Flow Rate: | 0.35 mL/min |
| Solvent A: | Water with 0.1% (vol/vol) formic acid |
| Solvent B: | Acetonitrile with 0.1% (vol/vol) formic acid |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS004254 |
| Analysis ID: | AN004507 |
| Instrument Name: | Waters Vion IMS QTof |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | UNIFI software (v. 1.8, Waters) |
| Ion Mode: | POSITIVE |
