Summary of Study ST004112
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 PR002566. The data can be accessed directly via it's Project DOI: 10.21228/M8ZK1T 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 | ST004112 |
| Study Title | Nutrient competition predicts gut microbiome restructuring under drug perturbations |
| Study Summary | To interrogate community-level responses to perturbations, we screened stool-derived in vitro communities with 707 clinically relevant drugs, and anlyzed the exometabolomics data of the resulting communities along with their growth and compositional changes. Compositional and metabolomic responses were predictably impacted by nutrient competition, and each bacterial species in the community maintains most of its nutrient niche. Finally, in defined, simplified communities, the response to drug perturbations of each species are quantitatively predicted from their drug susceptibility and metabolic profiles. Our study reveals that quantitative understanding of the interaction landscape, particularly nutrient competition, can be used to anticipate and potentially mitigate side effects of drug treatment on the gut microbiota. |
| Institute | Stanford University |
| Last Name | Shi |
| First Name | Handuo |
| Address | 443 Via Ortega, Stanford, CA 94305, USA |
| handuo@stanford.edu | |
| Phone | 6505615314 |
| Submit Date | 2025-07-28 |
| Study Comments | Study 1 of 2. The other part of this study has been uploaded as datatrack_id: 6218 and assigned study ID ST004087 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML, raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-08-14 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002566 |
| Project DOI: | doi: 10.21228/M8ZK1T |
| Project Title: | Nutrient competition predicts gut microbiome restructuring under drug perturbations |
| Project Summary: | Human gut bacteria are routinely exposed to stresses, and collateral effects are difficult to predict. To interrogate community-level responses to perturbations, we screened stool-derived in vitro communities with 707 clinically relevant drugs, and anlyzed the exometabolomics data of the resulting communities along with their growth and compositional changes. Drug bioaccumulation and degradation are rare. Compositional and metabolomic responses were predictably impacted by nutrient competition, and each bacterial species in the community maintains most of its nutrient niche. Finally, in defined, simplified communities, the response to drug perturbations of each species are quantitatively predicted from their drug susceptibility and metabolic profiles. Our study reveals that quantitative understanding of the interaction landscape, particularly nutrient competition, can be used to anticipate and potentially mitigate side effects of drug treatment on the gut microbiota. |
| Institute: | Stanford University |
| Last Name: | Shi |
| First Name: | Handuo |
| Address: | 443 Via Ortega, Stanford University, Stanford, CA 94305, USA |
| Email: | handuo@stanford.edu |
| Phone: | 6505615314 |
Subject:
| Subject ID: | SU004259 |
| Subject Type: | Bacteria |
| Subject Species: | Bacteroides thetaiotaomicron |
| Taxonomy ID: | 8188 |
Factors:
Subject type: Bacteria; Subject species: Bacteroides thetaiotaomicron (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | ||
|---|---|---|---|---|
| SA476030 | P7_1_B5__cis_Diltiazem_hydrochloride | Bacterial cells (using spent media for exometabolomics) | cis_Diltiazem_hydrochloride | |
| SA475056 | P7_1_G10_11_Deoxycortisol | Bacterial cells (using spent media for exometabolomics) | 11_Deoxycortisol | |
| SA475060 | P9_1_F8_1_1_Dimethyl_4_phenylpiperazinium_iodide | Bacterial cells (using spent media for exometabolomics) | 1_1_Dimethyl_4_phenylpiperazinium_iodide | |
| SA475057 | P6_1_F11_19_Norethindrone | Bacterial cells (using spent media for exometabolomics) | 19_Norethindrone | |
| SA475058 | P3_1_G9_19_Norethindrone_acetate | Bacterial cells (using spent media for exometabolomics) | 19_Norethindrone_acetate | |
| SA475059 | P4_1_C6_19_Nortestosterone | Bacterial cells (using spent media for exometabolomics) | 19_Nortestosterone | |
| SA475061 | P8_1_G8_2_Chloroadenosine | Bacterial cells (using spent media for exometabolomics) | 2_Chloroadenosine | |
| SA475062 | P8_1_D3_2_Pyridylethylamine | Bacterial cells (using spent media for exometabolomics) | 2_Pyridylethylamine | |
| SA475063 | P1_1_D10_3_5_3_Triiodothyronine | Bacterial cells (using spent media for exometabolomics) | 3_5_3_Triiodothyronine | |
| SA475064 | P2_1_D5_3_Deoxydenosine | Bacterial cells (using spent media for exometabolomics) | 3_Deoxydenosine | |
| SA475065 | P2_1_G4_3_Pyridinemethanol | Bacterial cells (using spent media for exometabolomics) | 3_Pyridinemethanol | |
| SA475066 | P4_1_C2_4_Phenylbutyric_acid | Bacterial cells (using spent media for exometabolomics) | 4_Phenylbutyric_acid | |
| SA475068 | P5_1_F5_5_Azacytidine | Bacterial cells (using spent media for exometabolomics) | 5_Azacytidine | |
| SA475069 | P11_2_B7_5_Azacytidine | Bacterial cells (using spent media for exometabolomics) | 5_Azacytidine | |
| SA475070 | P9_1_F4_5_Fluoro_2_pyrimidone | Bacterial cells (using spent media for exometabolomics) | 5_Fluoro_2_pyrimidone | |
| SA475071 | P11_2_C6_5_Fluorouracil | Bacterial cells (using spent media for exometabolomics) | 5_Fluorouracil | |
| SA475072 | P5_1_A6_5_Fluorouracil | Bacterial cells (using spent media for exometabolomics) | 5_Fluorouracil | |
| SA475073 | P5_1_A8_5_Methoxytryptamine | Bacterial cells (using spent media for exometabolomics) | 5_Methoxytryptamine | |
| SA475067 | P1_1_F07_5-Nonyloxytryptamine_hydrochloride | Bacterial cells (using spent media for exometabolomics) | 5-Nonyloxytryptamine_hydrochloride | |
| SA475074 | P4_1_G1_5_Nonyloxytryptamine_hydrochloride | Bacterial cells (using spent media for exometabolomics) | 5_Nonyloxytryptamine_hydrochloride | |
| SA475075 | P6_1_G1_5_Nonyloxytryptamine_hydrochloride | Bacterial cells (using spent media for exometabolomics) | 5_Nonyloxytryptamine_hydrochloride | |
| SA475077 | P4_1_B6_6_Aminoindazole | Bacterial cells (using spent media for exometabolomics) | 6_Aminoindazole | |
| SA475076 | P1_1_B04_6-Azauridine | Bacterial cells (using spent media for exometabolomics) | 6-Azauridine | |
| SA475078 | P8_1_E5_7_Nitroindazole | Bacterial cells (using spent media for exometabolomics) | 7_Nitroindazole | |
| SA475081 | P3_1_E2_Acarbose | Bacterial cells (using spent media for exometabolomics) | Acarbose | |
| SA475082 | P7_1_A2_Acebutolol_hydrochloride | Bacterial cells (using spent media for exometabolomics) | Acebutolol_hydrochloride | |
| SA475083 | P6_1_D8_Acetazolamide | Bacterial cells (using spent media for exometabolomics) | Acetazolamide | |
| SA475084 | P7_1_B2_Acetylcholine_chloride | Bacterial cells (using spent media for exometabolomics) | Acetylcholine_chloride | |
| SA475085 | P3_1_F7_Acitretin | Bacterial cells (using spent media for exometabolomics) | Acitretin | |
| SA475086 | P4_1_F5_Actarit | Bacterial cells (using spent media for exometabolomics) | Actarit | |
| SA475087 | P3_1_B8_Acyclovir | Bacterial cells (using spent media for exometabolomics) | Acyclovir | |
| SA475088 | P10_1_D1_Agate_red | Bacterial cells (using spent media for exometabolomics) | Agate_red | |
| SA475089 | P10_1_A2_Ai_Ye_dist | Bacterial cells (using spent media for exometabolomics) | Ai_Ye_dist | |
| SA475090 | P6_1_A11_Albendazole | Bacterial cells (using spent media for exometabolomics) | Albendazole | |
| SA475091 | P5_1_H10_Alfuzosin | Bacterial cells (using spent media for exometabolomics) | Alfuzosin | |
| SA475092 | P6_1_C8_Allopurinol | Bacterial cells (using spent media for exometabolomics) | Allopurinol | |
| SA475093 | P9_1_A5_Alosetron_monohydrochloride | Bacterial cells (using spent media for exometabolomics) | Alosetron_monohydrochloride | |
| SA476031 | P5_1_C7_alpha_Methyl_L_tyrosine | Bacterial cells (using spent media for exometabolomics) | alpha_Methyl_L_tyrosine | |
| SA475094 | P4_1_G6_Alprazolam | Bacterial cells (using spent media for exometabolomics) | Alprazolam | |
| SA475095 | P4_1_D8_Altanserin_hydrochloride | Bacterial cells (using spent media for exometabolomics) | Altanserin_hydrochloride | |
| SA475096 | P3_1_E10_Altretamine | Bacterial cells (using spent media for exometabolomics) | Altretamine | |
| SA475079 | P8_1_A3_AM_251 | Bacterial cells (using spent media for exometabolomics) | AM_251 | |
| SA475080 | P9_1_E3_AM_404 | Bacterial cells (using spent media for exometabolomics) | AM_404 | |
| SA475097 | P1_1_G06_Amcinonide | Bacterial cells (using spent media for exometabolomics) | Amcinonide | |
| SA475098 | P8_1_B9_Amiloride_hydrochloride_hydrate | Bacterial cells (using spent media for exometabolomics) | Amiloride_hydrochloride_hydrate | |
| SA475099 | P3_1_B7_Aminoglutethimide | Bacterial cells (using spent media for exometabolomics) | Aminoglutethimide | |
| SA475100 | P2_1_E6_Aminolevulinic_acid | Bacterial cells (using spent media for exometabolomics) | Aminolevulinic_acid | |
| SA475101 | P6_1_D3_Amiodarone_hydrochloride | Bacterial cells (using spent media for exometabolomics) | Amiodarone_hydrochloride | |
| SA475102 | P11_2_F8_Amiodarone_hydrochloride | Bacterial cells (using spent media for exometabolomics) | Amiodarone_hydrochloride | |
| SA475103 | P5_1_F7_Amisulpride | Bacterial cells (using spent media for exometabolomics) | Amisulpride | |
| SA475104 | P6_1_F10_Amitriptyline_hydrochloride | Bacterial cells (using spent media for exometabolomics) | Amitriptyline_hydrochloride | |
| SA475105 | P4_1_H11_Amlexanox | Bacterial cells (using spent media for exometabolomics) | Amlexanox | |
| SA475106 | P4_1_G10_Amlodipine | Bacterial cells (using spent media for exometabolomics) | Amlodipine | |
| SA475107 | P11_2_A10_Amoxapine | Bacterial cells (using spent media for exometabolomics) | Amoxapine | |
| SA475108 | P7_1_F5_Amoxapine | Bacterial cells (using spent media for exometabolomics) | Amoxapine | |
| SA475109 | P5_1_H5_Amoxicillin | Bacterial cells (using spent media for exometabolomics) | Amoxicillin | |
| SA475110 | P11_2_F7_Amoxicillin | Bacterial cells (using spent media for exometabolomics) | Amoxicillin | |
| SA475111 | P5_1_B6_Ampicillin_sodium | Bacterial cells (using spent media for exometabolomics) | Ampicillin_sodium | |
| SA475112 | P11_2_E6_Ampicillin_sodium | Bacterial cells (using spent media for exometabolomics) | Ampicillin_sodium | |
| SA475113 | P8_1_B6_Ampiroxicam | Bacterial cells (using spent media for exometabolomics) | Ampiroxicam | |
| SA475114 | P8_1_B11_Anagrelide_hydrochloride | Bacterial cells (using spent media for exometabolomics) | Anagrelide_hydrochloride | |
| SA475115 | P2_1_D9_Anastrozole | Bacterial cells (using spent media for exometabolomics) | Anastrozole | |
| SA475116 | P4_1_H4_Argatroban | Bacterial cells (using spent media for exometabolomics) | Argatroban | |
| SA475117 | P4_1_F6_Aripiprazole | Bacterial cells (using spent media for exometabolomics) | Aripiprazole | |
| SA475118 | P8_1_E6_Artemether | Bacterial cells (using spent media for exometabolomics) | Artemether | |
| SA475119 | P5_1_F8_Artesunate | Bacterial cells (using spent media for exometabolomics) | Artesunate | |
| SA475120 | P7_1_B8_Atenolol | Bacterial cells (using spent media for exometabolomics) | Atenolol | |
| SA475121 | P9_1_H7_Atomoxetine_hydrochloride | Bacterial cells (using spent media for exometabolomics) | Atomoxetine_hydrochloride | |
| SA475122 | P2_1_B4_Atracurium_besylate | Bacterial cells (using spent media for exometabolomics) | Atracurium_besylate | |
| SA475123 | P3_1_A5_Atropine | Bacterial cells (using spent media for exometabolomics) | Atropine | |
| SA475124 | P4_1_G7_Azasetron_hydrochloride | Bacterial cells (using spent media for exometabolomics) | Azasetron_hydrochloride | |
| SA475125 | P2_1_F10_Azathioprine | Bacterial cells (using spent media for exometabolomics) | Azathioprine | |
| SA475126 | P1_1_D06_Azelastine_hydrochloride | Bacterial cells (using spent media for exometabolomics) | Azelastine_hydrochloride | |
| SA475127 | P2_1_E8_Azithromycin | Bacterial cells (using spent media for exometabolomics) | Azithromycin | |
| SA475128 | P11_2_H2_Azithromycin | Bacterial cells (using spent media for exometabolomics) | Azithromycin | |
| SA475129 | P10_1_B2_Bai_Dou_Kou_CO2 | Bacterial cells (using spent media for exometabolomics) | Bai_Dou_Kou_CO2 | |
| SA475130 | P10_1_C2_Bai_Yu_Lan_Ye_dist | Bacterial cells (using spent media for exometabolomics) | Bai_Yu_Lan_Ye_dist | |
| SA475131 | P10_1_D2_Bai_Zhi_CO2 | Bacterial cells (using spent media for exometabolomics) | Bai_Zhi_CO2 | |
| SA475132 | P10_1_E2_Bai_Zi_Ren_CO2 | Bacterial cells (using spent media for exometabolomics) | Bai_Zi_Ren_CO2 | |
| SA475133 | P4_1_E5_Balsalazide | Bacterial cells (using spent media for exometabolomics) | Balsalazide | |
| SA475134 | P6_1_H4_Beclomethasone | Bacterial cells (using spent media for exometabolomics) | Beclomethasone | |
| SA475135 | P3_1_F1_Beclomethasone_dipropionate | Bacterial cells (using spent media for exometabolomics) | Beclomethasone_dipropionate | |
| SA475136 | P1_1_G05_Beclomethasone_dipropionate | Bacterial cells (using spent media for exometabolomics) | Beclomethasone_dipropionate | |
| SA475137 | P4_1_C8_Benactyzine_hydrochloride | Bacterial cells (using spent media for exometabolomics) | Benactyzine_hydrochloride | |
| SA475138 | P6_1_E4_Benazepril_hydrochloride | Bacterial cells (using spent media for exometabolomics) | Benazepril_hydrochloride | |
| SA475139 | P1_1_D02_Bendrofluazide | Bacterial cells (using spent media for exometabolomics) | Bendrofluazide | |
| SA475140 | P9_1_A7_Benidipine_hydrochloride | Bacterial cells (using spent media for exometabolomics) | Benidipine_hydrochloride | |
| SA475141 | P1_1_H07_Benproperine_phosphate | Bacterial cells (using spent media for exometabolomics) | Benproperine_phosphate | |
| SA475142 | P5_1_C11_Benzbromarone | Bacterial cells (using spent media for exometabolomics) | Benzbromarone | |
| SA475143 | P1_1_D04_Benztropine_mesylate | Bacterial cells (using spent media for exometabolomics) | Benztropine_mesylate | |
| SA475144 | P7_1_B11_Benzylimidazole | Bacterial cells (using spent media for exometabolomics) | Benzylimidazole | |
| SA475145 | P1_1_A06_Bestatin | Bacterial cells (using spent media for exometabolomics) | Bestatin | |
| SA475146 | P9_1_D3_Beta_estradiol | Bacterial cells (using spent media for exometabolomics) | Beta_estradiol | |
| SA475147 | P8_1_D6_Betaxolol_hydrochloride | Bacterial cells (using spent media for exometabolomics) | Betaxolol_hydrochloride | |
| SA475148 | P3_1_G4_Bethanechol_chloride | Bacterial cells (using spent media for exometabolomics) | Bethanechol_chloride | |
| SA475150 | P2_1_C6_Bicalutamide | Bacterial cells (using spent media for exometabolomics) | Bicalutamide | |
| SA475149 | P10_1_F2_Bi_Cheng_Qie_dist | Bacterial cells (using spent media for exometabolomics) | Bi_Cheng_Qie_dist | |
| SA475151 | P9_1_B5_Bifemelane_hydrochloride | Bacterial cells (using spent media for exometabolomics) | Bifemelane_hydrochloride | |
| SA475152 | P11_2_E11_Bifonazole | Bacterial cells (using spent media for exometabolomics) | Bifonazole | |
| SA475153 | P9_1_D7_Bifonazole | Bacterial cells (using spent media for exometabolomics) | Bifonazole |
Collection:
| Collection ID: | CO004252 |
| Collection Summary: | Stool-derived in vitro communities were revived from glycerol stocks, as previously described (Cell Host & Microbe (2022). https://doi.org/https://doi.org/10.1016/j.chom.2021.12.008) into 3 mL of Brain Heart Infusion (BHI) (BD #2237500). All culturing was performed at 37 °C without shaking in an anaerobic chamber (Coy). To minimize potential physiological changes from freeze-thaw cycles and changes in growth medium, cultures were diluted 1:200 after 48 h of growth into 96-well polystyrene plates (Greiner Bio-One #655161) filled with 200 µL of growth medium. 20 µM of small molecule drugs were added to the growth medium, and the plates were incubated at 37 °C with shaking for 48 hour. |
| Sample Type: | Bacterial cells |
Treatment:
| Treatment ID: | TR004268 |
| Treatment Summary: | Samples were spun down at 4000g for 10 min at 4 °C, then the supernatant was immediately frozen at -70 °C and only thawed upon analyzing. Details of the chemical conditions can be found in the publicly available preprint: https://doi.org/10.1101/2024.08.06.606863 |
Sample Preparation:
| Sampleprep ID: | SP004265 |
| Sampleprep Summary: | Spent media were collected as described above and immediately stored at -70 °C. Samples were thawed only once, immediately before LC-MS/MS. Thawed samples were kept on ice, each sample was homogenized by pipetting prior to dispensing. Two 20-µL aliquots of supernatant were removed from each sample well and dispensed into two shallow 96-well polypropylene plates, maintained on ice. Additionally, 5 µL were removed from each sample and combined into a homogenous pool; this pool was dispensed in 20-µL aliquots and prepared in parallel with samples. These pooled samples were used for in-run quality control, injected at predefined intervals over the course of analysis to ensure consistent instrument performance over time. Samples were analyzed using hydrophilic interaction chromatography (HILIC). All samples were analyzed by positive and negative mode electrospray ionization (ESI+, ESI-). Sample analysis order was randomized to minimize potential bias in data acquisition. Procedural blanks were prepared by extracting 20 µL of water in place of bacterial supernatant. Procedural blanks were inserted throughout the run as additional quality control. |
Chromatography:
| Chromatography ID: | CH005178 |
| Chromatography Summary: | Bacterial supernatant were analyzed via hydrophilic interaction liquid chromatography (HILIC) coupled to a Thermo Q-Exactive HF high resolution mass spectrometer. Each sample was analyzed in both positive and negative ionization modes (ESI+, ESI-) via subsequent injections. Full MS-ddMS2 data was collected, an inclusion list was used to prioritize MS2 selection of metabolites from our in-house ‘local’ library, when additional scan bandwidth was available MS2 was collected in a data-dependent manner. Mass range was 60-900 mz, resolution was 60k (MS1) and 15k (MS2), centroid data was collected, loop count was 4, isolation window was 1.5 Da. Metabolomics data was processed using MS-DIAL v4.60 (https://www.nature.com/articles/s41587-020-0531-2) and queried against a combination of our in-house MS2 library (https://www.nature.com/articles/s41586-021-03707-9) and MassBank of North America, the largest freely available spectral repository (https://doi.org/10.1002/mas.21535). Annotations were scored using guidelines from the metabolomics standards initiative (https://www.nature.com/articles/nbt0807-846b). Features were excluded from analysis if peak height was not at least 5-fold greater in one or more samples compared to the procedural blank average. |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um) |
| Column Temperature: | 45 |
| Flow Gradient: | Gradient elution was performed from 100% (B) at 0–2 min to 70% (B) at 7.7 min, 40% (B) at 9.5 min, 30% (B) at 10.25 min, 100% (B) at 12.75 min, isocratic until 16.75 min |
| Flow Rate: | 0.4 mL/min |
| Solvent A: | 100% Water; 10mM ammonium formate; 0.125% formic acid |
| Solvent B: | 95% acetonitrile/5%water; 10mM ammonium formate; 0.125% formic acid |
| Chromatography Type: | HILIC |
Analysis:
| Analysis ID: | AN006815 |
| Analysis Type: | MS |
| Chromatography ID: | CH005178 |
| Has Mz: | 1 |
| Has Rt: | 1 |
| Rt Units: | Minutes |
| Results File: | ST004112_AN006815_Results.txt |
| Units: | peak height |
| Analysis ID: | AN006816 |
| Analysis Type: | MS |
| Chromatography ID: | CH005178 |
| Has Mz: | 1 |
| Has Rt: | 1 |
| Rt Units: | Minutes |
| Results File: | ST004112_AN006816_Results.txt |
| Units: | peak height |
