Summary of Study ST002338
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 PR001501. The data can be accessed directly via it's Project DOI: 10.21228/M8P70H 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 | ST002338 |
| Study Title | Interplay Between Cruciferous Vegetables and the Gut Microbiome: A Multi-Omic Approach |
| Study Type | Ex Vivo Fecal Incubation |
| Study Summary | Cruciferous vegetable consumption has been associated with a decreased risk of multiple types of cancers, thus presenting a cost-effective, non-pharmacological approach to cancer prevention through dietary intervention. Broccoli sprouts and Brussels sprouts are among the leading cruciferous vegetables under study and contain some similar and some distinct phytochemicals which can activate different, but complementary, mechanisms to promote health. While the cancer-preventative effects of cruciferous vegetables are typically attributed to glucosinolates and their metabolic products, isothiocyanates and indoles, other components of cruciferous vegetables could play a synergistic role in conferring cancer-protective and health promoting effects. Additionally, metabolism of phytochemicals from cruciferous vegetables by the gut microbiome could further lead to the production, inactivation, or clearance of bioactive dietary components. The gut microbiome is essential to the production of bioactive compounds from various food sources. For example, with soy isoflavones and pomegranate urolithins, the presence or absence of specific microbial taxa directly dictates which metabolites are produced (resulting in a metabotype). A similar paradigm could be extended to cruciferous vegetables in which the gut microbiome may play an important role in driving inter-individual metabolism of glucosinolates and isothiocyanates. We recently reported (Bouranis et. al, 2021, Nutrients) that the gut microbiome composition can influence production of glucosinolate-derived nitriles from cruciferous vegetables, showing that the presence or absence of specific microbes can influence the abundance of a single metabolite. Thus, we sought to take an untargeted approach to investigate other phytochemicals from cruciferous vegetables which the gut microbiome could play a role in generating. To investigate plant- and microbe-derived metabolites of cruciferous vegetable digestion and capture information about the microbiome, we utilized an ex vivo fecal incubation system. Broccoli sprouts and Brussels sprouts were in vitro digested using an oral, gastric, and intestinal phase. For fecal bacterial cultivation a 20% fecal slurry (w/v) was made from fecal material from 10 healthy volunteers (6 female, and 4 male, age 17-51, Lee Biosolutions) and sterile PBS (0.1 M pH 7). 500 µL of fecal slurry was mixed with 10 mL of Brain Heart Infusion Broth (BHI) with hemin and vitamin K, per the manufacturer’s recommendation, and either 500 µl of filter sterilized in vitro digested broccoli sprouts (Broc), 500 µL of filter sterilized in vitro digested Brussels sprouts (Brus), 500 µL of Broc and 500 µL of Brus were added (Combo) or a negative control in vitro digestion (NC). NC contained reverse osmosis water, equivalent in volume to the water content of broccoli sprouts and underwent the same in vitro digestion procedure as described above with the same enzymes, chemicals and equipment. Broc and Brus digests were scaled to be equivalent in concentration to a human consuming ½ cup of broccoli or Brussels sprouts, or in the case of the combination, ½ cup of broccoli sprouts and ½ cup of Brussels sprouts. This combination was included as Broc and Brus contain many similar but also some distinct phytochemicals and thus by combining the vegetables we increased the dose and broadened the range of phytochemicals from cruciferous vegetables which can be achieved in the kitchen as a mixed vegetable dish. Fecal cultures were incubated at 37°C for 24 h in anaerobic conditions. |
| Institute | Oregon State University |
| Department | Linus Pauling Institute |
| Laboratory | Emily Ho |
| Last Name | Bouranis |
| First Name | John |
| Address | 371 Linus Pauling Science Center, 2900 SW Campus Way, Corvallis, OR, 97331, USA |
| bouranij@oregonstate.edu | |
| Phone | 5417375049 |
| Submit Date | 2022-10-27 |
| Num Groups | 4 |
| Total Subjects | 10 |
| Num Males | 4 |
| Num Females | 6 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzXML |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-01-02 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001501 |
| Project DOI: | doi: 10.21228/M8P70H |
| Project Title: | Interplay Between Cruciferous Vegetables and the Gut Microbiome: A Multi-Omic Approach |
| Project Type: | Untargeted Metabolomics |
| Project Summary: | Untargeted metabolomics analysis of human fecal cultures following incubation with in vitro digested cruciferous vegetables. The goal of this study was to identify microbial- and plant-dervied metabolites of cruciferous vegetables. An ex vivo fecal incubation system reflecting the digestive metabolome was used. Accompanying 16S data can be retrieved in the NCBI SRA under BioProject PRJNA895102. |
| Institute: | Oregon State University |
| Department: | Linus Pauling Institute |
| Laboratory: | Emily Ho |
| Last Name: | Bouranis |
| First Name: | John |
| Address: | 371 Linus Pauling Science Center, 2900 SW Campus Way, Corvallis, OR, 97331, USA |
| Email: | bouranij@oregonstate.edu |
| Phone: | 5417375049 |
| Funding Source: | United States Department of Agriculture National Institute of Food and Agriculture (NI-FA-2020-67001-31214; NIFA-2022-67011-36576), National Institutes of Health (P30ES030287; S10RR027878), Oregon Agricultural Experimental Station (W4002; OR00735) |
Subject:
| Subject ID: | SU002427 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Age Or Age Range: | 17-51 |
| Gender: | Male and female |
| Cell Biosource Or Supplier: | Lee Biosolutions |
| Subject Comments: | Human fecal cultures |
| Species Group: | Mammals |
Factors:
Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | treatment | group |
|---|---|---|---|
| SA234988 | ms_33 | broc | C_Type |
| SA234989 | ms_41 | broc | C_Type |
| SA234990 | ms_45 | broc | C_Type |
| SA234991 | ms_17 | broc | C_Type |
| SA234992 | ms_21 | broc | C_Type |
| SA234993 | ms_25 | broc | E_Type |
| SA234994 | ms_49 | broc | E_Type |
| SA234995 | ms_13 | broc | E_Type |
| SA234996 | ms_29 | broc | E_Type |
| SA234997 | ms_37 | broc | E_Type |
| SA234998 | ms_22 | brus | C_Type |
| SA234999 | ms_18 | brus | C_Type |
| SA235000 | ms_34 | brus | C_Type |
| SA235001 | ms_42 | brus | C_Type |
| SA235002 | ms_46 | brus | C_Type |
| SA235003 | ms_50 | brus | E_Type |
| SA235004 | ms_30 | brus | E_Type |
| SA235005 | ms_38 | brus | E_Type |
| SA235006 | ms_14 | brus | E_Type |
| SA235007 | ms_26 | brus | E_Type |
| SA235008 | ms_47 | combo | C_Type |
| SA235009 | ms_19 | combo | C_Type |
| SA235010 | ms_35 | combo | C_Type |
| SA235011 | ms_43 | combo | C_Type |
| SA235012 | ms_23 | combo | C_Type |
| SA235013 | ms_31 | combo | E_Type |
| SA235014 | ms_39 | combo | E_Type |
| SA235015 | ms_51 | combo | E_Type |
| SA235016 | ms_27 | combo | E_Type |
| SA235017 | ms_15 | combo | E_Type |
| SA234978 | ms_20 | NC | C_Type |
| SA234979 | ms_32 | NC | C_Type |
| SA234980 | ms_44 | NC | C_Type |
| SA234981 | ms_40 | NC | C_Type |
| SA234982 | ms_16 | NC | C_Type |
| SA234983 | ms_28 | NC | E_Type |
| SA234984 | ms_12 | NC | E_Type |
| SA234985 | ms_48 | NC | E_Type |
| SA234986 | ms_24 | NC | E_Type |
| SA234987 | ms_36 | NC | E_Type |
| Showing results 1 to 40 of 40 |
Collection:
| Collection ID: | CO002420 |
| Collection Summary: | Fecal culture medium was then vortexed, sampled, centrifuged (13,000 g, 10 min) and supernatants frozen in liquid nitrogen. |
| Sample Type: | Feces |
Treatment:
| Treatment ID: | TR002439 |
| Treatment Summary: | Broccoli sprouts and Brussels sprouts were in vitro digested using an oral, gastric, and intestinal phase. For fecal bacterial cultivation a 20% fecal slurry (w/v) was made from fecal material from 10 healthy volunteers (6 female, and 4 male, age 17-51, Lee Biosolutions) and sterile PBS (0.1 M pH 7). 500 µL of fecal slurry was mixed with 10 mL of Brain Heart Infusion Broth (BHI) with hemin and vitamin K, per the manufacturer’s recommendation, and either 500 µl of filter sterilized in vitro digested broccoli sprouts (Broc), 500 µL of filter sterilized in vitro digested Brussels sprouts (Brus), 500 µL of Broc and 500 µL of Brus were added (Combo) or a negative control in vitro digestion (NC). NC contained reverse osmosis water, equivalent in volume to the water content of broccoli sprouts and underwent the same in vitro digestion procedure as described above with the same enzymes, chemicals and equipment. Broc and Brus digests were scaled to be equivalent in concentration to a human consuming ½ cup of broccoli or Brussels sprouts, or in the case of the combination, ½ cup of broccoli sprouts and ½ cup of Brussels sprouts. This combination was included as Broc and Brus contain many similar but also some distinct phytochemicals and thus by combining the vegetables we increased the dose and broadened the range of phytochemicals from cruciferous vegetables which can be achieved in the kitchen as a mixed vegetable dish. Fecal cultures were incubated at 37°C for 24 h in anaerobic conditions |
| Treatment Protocol Filename: | MWB_Protocol.pdf |
Sample Preparation:
| Sampleprep ID: | SP002433 |
| Sampleprep Summary: | Metabolites from fecal culture medium were extracted (100 μL culture/100 μL ice cold 80:20, v/v, methanol:water), mixed vigorously, and clarified by centrifugation (13,000× g for 10 min). The supernatants were further diluted 1:10 (v/v) with ice cold 80:20 methanol:water (v/v) and transferred to mass spectrometry (MS) vials |
Combined analysis:
| Analysis ID | AN003820 | AN003821 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Shimadzu Nexera | Shimadzu Nexera |
| Column | GL Sciences Inertsil1 Phenyl-3 (4.6 x 150mm,5um) | GL Sciences Inertsil1 Phenyl-3 (4.6 x 150mm,5um) |
| MS Type | ESI | ESI |
| MS instrument type | Triple TOF | Triple TOF |
| MS instrument name | ABI Sciex 5600 TripleTOF | ABI Sciex 5600 TripleTOF |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | Intensity | Intensity |
Chromatography:
| Chromatography ID: | CH002827 |
| Chromatography Summary: | Ultra-high pressure liquid chromatography (UPLC) was performed on a Shimadzu Nexera™ system (Shimadzu, Columbia, MD) coupled to a quadrupole time-of-flight mass spectrometer (AB SCIEX TripleTOF 5600). Chromatographic separations were conducted on an Inertsil1 Phenyl-3 column (4.6 × 150 mm, GL Sciences, Torrance, CA). Elution was achieved using a binary gradient employing as solvent A water, and solvent B methanol, both containing 0.1% formic acid (v/ v), as described previously. The gradient started with 5% Band was held for 1 min at 5% B, followed by a 11-min linear gradient from 5% to 30% B. The gradient was increased linearly to 100% B at 23 min, held for 5 min at 100% B and, finally, stepped back to 5% B to equilibrate the column. The flow rate was 0.4 mL/min. The auto-sampler temperature was held at 10 ̊C, the column oven temperature at 50 ̊C, and the injection volume was 5 μL. Time-of-flight (TOF) mass spectrometry (MS) was operated with an acquisition time of 0.25 s and a scan range of 70–1200 Da. Tandem mass spectrometry (MS/MS) acquisition was performed with collision energy set at 35 V and collision energy spread of 15 V. Each MS/MS scan had an accumulation time of 0.17 sand a range of 50–1250 Da using information-dependent MS/MS acquisition (IDA). Ion source gas 1and 2and curtain gas (all nitrogen) were set at 50, 40, and 25, respectively. The source temperature was set at 500 ̊C and the ion spray voltage at 4.5 kV in positive ion mode. The mass calibration was automatically performed every 2 injections using a calibration solution (AB SCIEX) via a calibration delivery system (CDS). |
| Instrument Name: | Shimadzu Nexera |
| Column Name: | GL Sciences Inertsil1 Phenyl-3 (4.6 x 150mm,5um) |
| Column Temperature: | 50 |
| Flow Gradient: | The gradient started with 5% B and was held for 1 min at 5% B, followed by a 11-min linear gradient from 5% to 30% B. The gradient was increased linearly to 100% B at 23 min, held for 5 min at 100% B and, finally, stepped back to 5% B to equilibrate the column. |
| Flow Rate: | 0.4ml/min |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% methanol; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS003562 |
| Analysis ID: | AN003820 |
| Instrument Name: | ABI Sciex 5600 TripleTOF |
| Instrument Type: | Triple TOF |
| MS Type: | ESI |
| MS Comments: | The samples were randomized, auto-calibration was performed every two samples, and a quality control sample, composed of a pooled aliquot from each sample, was analyzed every 10 samples. MS/MS information was obtained for all samples using information dependent acquisition (IDA), while sequential window acquisition of all theoretical spectra (SWATH) was performed only on quality control samples. Spectral data were processed using Progenesis QI (NonLinear Dynamics v2.4). Peak deconvolution for [M + H]+, [M + Na]+, and [M + NH4]+ adducts in positive ionization mode, and [M−H]-, [M + FA-H]-, and [M−H2O−H]- in negative ionization mode was performed in Progenesis QI. Feature intensities were normalized in Progenesis QI across samples by total ion current of all features. |
| Ion Mode: | POSITIVE |
| Analysis Protocol File: | MWB_Protocol.pdf |
| MS ID: | MS003563 |
| Analysis ID: | AN003821 |
| Instrument Name: | ABI Sciex 5600 TripleTOF |
| Instrument Type: | Triple TOF |
| MS Type: | ESI |
| MS Comments: | The samples were randomized, auto-calibration was performed every two samples, and a quality control sample, composed of a pooled aliquot from each sample, was analyzed every 10 samples. MS/MS information was obtained for all samples using information dependent acquisition (IDA), while sequential window acquisition of all theoretical spectra (SWATH) was performed only on quality control samples. Spectral data were processed using Progenesis QI (NonLinear Dynamics v2.4). Peak deconvolution for [M + H]+, [M + Na]+, and [M + NH4]+ adducts in positive ionization mode, and [M−H]-, [M + FA-H]-, and [M−H2O−H]- in negative ionization mode was performed in Progenesis QI. Feature intensities were normalized in Progenesis QI across samples by total ion current of all features. |
| Ion Mode: | NEGATIVE |
| Analysis Protocol File: | MWB_Protocol.pdf |
