Summary of Study ST004087

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.

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Study IDST004087
Study TitleBioaccumulation and degradation of drugs in stool-derived communities
Study SummaryWe analyzed bacterial culturing medium, Brain Heart Infusion, with addition of various drugs. We then compared these results with the other study with drug-treated stool-derived communities. The drugs remain largely intact after the growth of the communities, suggesting that drug bioaccumulation and degradation are rare in this context.
Institute
Stanford University
Last NameShi
First NameHanduo
Address443 Via Ortega, Stanford University, Stanford, CA 94305, USA
Emailhanduo@stanford.edu
Phone6505615314
Submit Date2025-07-26
Study CommentsStudy 2 of 2. This part of study contains small molecule drugs directly added to the base bacterial growth media. No biological samples were involved. See Study part 1 of 2 for the bacterial data.
Raw Data AvailableYes
Raw Data File Type(s)mzML, raw(Thermo)
Analysis Type DetailLC-MS
Release Date2025-08-01
Release Version1
Handuo Shi Handuo Shi
https://dx.doi.org/10.21228/M8ZK1T
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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:SU004233
Subject Type:Other abiotic sample

Factors:

Subject type: Other abiotic sample; Subject species: - (Factor headings shown in green)

mb_sample_id local_sample_id Sample source Factor
SA473665Acebutololhydrochloride_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Neg_014075_KCHU023_QE2bacterial growth media Acebutololhydrochloride
SA473666Acebutololhydrochloride_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Pos_014074_KCHU023_QE2bacterial growth media Acebutololhydrochloride
SA473667Alosetronmonohydrochloride_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Neg_014125_KCHU023_QE2bacterial growth media Alosetronmonohydrochloride
SA473668Alosetronmonohydrochloride_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Pos_014124_KCHU023_QE2bacterial growth media Alosetronmonohydrochloride
SA473669Alprazolam_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Neg_014213_KCHU023_QE2bacterial growth media Alprazolam
SA473670Alprazolam_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Pos_014212_KCHU023_QE2bacterial growth media Alprazolam
SA473671Amisulpride_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Neg_014171_KCHU023_QE2bacterial growth media Amisulpride
SA473672Amisulpride_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Pos_014170_KCHU023_QE2bacterial growth media Amisulpride
SA473673Amoxapine_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Neg_014103_KCHU023_QE2bacterial growth media Amoxapine
SA473674Amoxapine_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Pos_014102_KCHU023_QE2bacterial growth media Amoxapine
SA473675Anastrozole_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Neg_014203_KCHU023_QE2bacterial growth media Anastrozole
SA473676Anastrozole_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Pos_014202_KCHU023_QE2bacterial growth media Anastrozole
SA473677Aripiprazole_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Neg_014157_KCHU023_QE2bacterial growth media Aripiprazole
SA473678Aripiprazole_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Pos_014156_KCHU023_QE2bacterial growth media Aripiprazole
SA473679Atropine_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Pos_014004_KCHU023_QE2bacterial growth media Atropine
SA473680Atropine_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Neg_014005_KCHU023_QE2bacterial growth media Atropine
SA473681Azithromycin_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Pos_014108_KCHU023_QE2bacterial growth media Azithromycin
SA473682Azithromycin_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Neg_014109_KCHU023_QE2bacterial growth media Azithromycin
SA473683Betaxololhydrochloride_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Neg_014059_KCHU023_QE2bacterial growth media Betaxololhydrochloride
SA473684Betaxololhydrochloride_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Pos_014058_KCHU023_QE2bacterial growth media Betaxololhydrochloride
SA473685Bicalutamide_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Pos_014168_KCHU023_QE2bacterial growth media Bicalutamide
SA473686Bicalutamide_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Neg_014169_KCHU023_QE2bacterial growth media Bicalutamide
SA473687Bifonazole_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Pos_014046_KCHU023_QE2bacterial growth media Bifonazole
SA473688Bifonazole_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Neg_014047_KCHU023_QE2bacterial growth media Bifonazole
SA473689Blank_NotUsed_F1_R3_T1_Untargeted_DDA_HILICshort_Neg_014039_KCHU023_QE2bacterial growth media Blank
SA473690Blank_NotUsed_F1_R5_T1_Untargeted_DDA_HILICshort_Pos_014086_KCHU023_QE2bacterial growth media Blank
SA473691Blank_NotUsed_F1_R3_T1_Untargeted_DDA_HILICshort_Pos_014038_KCHU023_QE2bacterial growth media Blank
SA473692Blank_NotUsed_F1_R9_T1_Untargeted_DDA_HILICshort_Pos_014182_KCHU023_QE2bacterial growth media Blank
SA473693Blank_NotUsed_F1_R7_T1_Untargeted_DDA_HILICshort_Neg_014135_KCHU023_QE2bacterial growth media Blank
SA473694Blank_NotUsed_F1_R7_T1_Untargeted_DDA_HILICshort_Pos_014134_KCHU023_QE2bacterial growth media Blank
SA473695Blank_NotUsed_F1_R10_T1_Untargeted_DDA_HILICshort_Neg_014207_KCHU023_QE2bacterial growth media Blank
SA473696Blank_NotUsed_F1_R2_T1_Untargeted_DDA_HILICshort_Neg_014015_KCHU023_QE2bacterial growth media Blank
SA473697Blank_NotUsed_F1_R2_T1_Untargeted_DDA_HILICshort_Pos_014014_KCHU023_QE2bacterial growth media Blank
SA473698Blank_NotUsed_F1_R10_T1_Untargeted_DDA_HILICshort_Pos_014206_KCHU023_QE2bacterial growth media Blank
SA473699Blank_NotUsed_F1_R8_T1_Untargeted_DDA_HILICshort_Pos_014158_KCHU023_QE2bacterial growth media Blank
SA473700Blank_NotUsed_F1_R8_T1_Untargeted_DDA_HILICshort_Neg_014159_KCHU023_QE2bacterial growth media Blank
SA473701Blank_NotUsed_F1_R11_T1_Untargeted_DDA_HILICshort_Pos_014224_KCHU023_QE2bacterial growth media Blank
SA473702Blank_NotUsed_F1_R11_T1_Untargeted_DDA_HILICshort_Neg_014225_KCHU023_QE2bacterial growth media Blank
SA473703Blank_NotUsed_F1_R9_T1_Untargeted_DDA_HILICshort_Neg_014183_KCHU023_QE2bacterial growth media Blank
SA473704Blank_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Pos_013992_KCHU023_QE2bacterial growth media Blank
SA473705Blank_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Neg_013993_KCHU023_QE2bacterial growth media Blank
SA473706Blank_NotUsed_F1_R4_T1_Untargeted_DDA_HILICshort_Neg_014063_KCHU023_QE2bacterial growth media Blank
SA473707Blank_NotUsed_F1_R4_T1_Untargeted_DDA_HILICshort_Pos_014062_KCHU023_QE2bacterial growth media Blank
SA473708Blank_NotUsed_F1_R6_T1_Untargeted_DDA_HILICshort_Pos_014110_KCHU023_QE2bacterial growth media Blank
SA473709Blank_NotUsed_F1_R5_T1_Untargeted_DDA_HILICshort_Neg_014087_KCHU023_QE2bacterial growth media Blank
SA473710Blank_NotUsed_F1_R6_T1_Untargeted_DDA_HILICshort_Neg_014111_KCHU023_QE2bacterial growth media Blank
SA473711Buflomedilhydrochloride_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Neg_014001_KCHU023_QE2bacterial growth media Buflomedilhydrochloride
SA473712Buflomedilhydrochloride_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Pos_014000_KCHU023_QE2bacterial growth media Buflomedilhydrochloride
SA473713Buspironehydrochloride_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Neg_014011_KCHU023_QE2bacterial growth media Buspironehydrochloride
SA473714Buspironehydrochloride_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Pos_014010_KCHU023_QE2bacterial growth media Buspironehydrochloride
SA473717Carbinoxaminemaleate_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Neg_014083_KCHU023_QE2bacterial growth media Carbinoxaminemaleate
SA473718Carbinoxaminemaleate_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Pos_014082_KCHU023_QE2bacterial growth media Carbinoxaminemaleate
SA473719Carisoprodol_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Pos_014080_KCHU023_QE2bacterial growth media Carisoprodol
SA473720Carisoprodol_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Neg_014081_KCHU023_QE2bacterial growth media Carisoprodol
SA473715CGS12066Bdimaleate_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Pos_014164_KCHU023_QE2bacterial growth media CGS12066Bdimaleate
SA473716CGS12066Bdimaleate_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Neg_014165_KCHU023_QE2bacterial growth media CGS12066Bdimaleate
SA473721Chlorpheniraminemaleate_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Neg_014121_KCHU023_QE2bacterial growth media Chlorpheniraminemaleate
SA473722Chlorpheniraminemaleate_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Pos_014120_KCHU023_QE2bacterial growth media Chlorpheniraminemaleate
SA473723Chlorpromazinehydrochloride_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Pos_014024_KCHU023_QE2bacterial growth media Chlorpromazinehydrochloride
SA473724Chlorpromazinehydrochloride_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Neg_014025_KCHU023_QE2bacterial growth media Chlorpromazinehydrochloride
SA473725Clarithromycin_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Pos_014008_KCHU023_QE2bacterial growth media Clarithromycin
SA473726Clarithromycin_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Neg_014009_KCHU023_QE2bacterial growth media Clarithromycin
SA473727Clonidinehydrochloride_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Neg_014049_KCHU023_QE2bacterial growth media Clonidinehydrochloride
SA473728Clonidinehydrochloride_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Pos_014048_KCHU023_QE2bacterial growth media Clonidinehydrochloride
SA473729Clotrimazole_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Pos_014146_KCHU023_QE2bacterial growth media Clotrimazole
SA473730Clotrimazole_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Neg_014147_KCHU023_QE2bacterial growth media Clotrimazole
SA473743Desipraminehydrochloride_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Neg_014145_KCHU023_QE2bacterial growth media Desipraminehydrochloride
SA473744Desipraminehydrochloride_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Pos_014144_KCHU023_QE2bacterial growth media Desipraminehydrochloride
SA473745Dexchlorpheniraminemaleate_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Neg_014175_KCHU023_QE2bacterial growth media Dexchlorpheniraminemaleate
SA473746Dexchlorpheniraminemaleate_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Pos_014174_KCHU023_QE2bacterial growth media Dexchlorpheniraminemaleate
SA473747Dextromethorphanhydrobromidemonohydrate_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Neg_014141_KCHU023_QE2bacterial growth media Dextromethorphanhydrobromidemonohydrate
SA473748Dextromethorphanhydrobromidemonohydrate_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Pos_014140_KCHU023_QE2bacterial growth media Dextromethorphanhydrobromidemonohydrate
SA473749DextrorphanDtartrate_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Pos_014032_KCHU023_QE2bacterial growth media DextrorphanDtartrate
SA473750DextrorphanDtartrate_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Neg_014033_KCHU023_QE2bacterial growth media DextrorphanDtartrate
SA473751Diazepam_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Neg_014095_KCHU023_QE2bacterial growth media Diazepam
SA473752Diazepam_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Pos_014094_KCHU023_QE2bacterial growth media Diazepam
SA473753Dicyclominehydrochloride_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Pos_014172_KCHU023_QE2bacterial growth media Dicyclominehydrochloride
SA473754Dicyclominehydrochloride_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Neg_014173_KCHU023_QE2bacterial growth media Dicyclominehydrochloride
SA473755Disopyramidephosphate_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Pos_014060_KCHU023_QE2bacterial growth media Disopyramidephosphate
SA473756Disopyramidephosphate_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Neg_014061_KCHU023_QE2bacterial growth media Disopyramidephosphate
SA473731DMSO1_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Pos_014166_KCHU023_QE2bacterial growth media DMSO1
SA473732DMSO1_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Neg_014167_KCHU023_QE2bacterial growth media DMSO1
SA473733DMSO2_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Pos_014150_KCHU023_QE2bacterial growth media DMSO2
SA473734DMSO2_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Neg_014151_KCHU023_QE2bacterial growth media DMSO2
SA473735DMSO3_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Pos_014070_KCHU023_QE2bacterial growth media DMSO3
SA473736DMSO3_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Neg_014071_KCHU023_QE2bacterial growth media DMSO3
SA473737DMSO4_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Neg_014105_KCHU023_QE2bacterial growth media DMSO4
SA473738DMSO4_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Pos_014104_KCHU023_QE2bacterial growth media DMSO4
SA473739DMSO5_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Pos_014020_KCHU023_QE2bacterial growth media DMSO5
SA473740DMSO5_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Neg_014021_KCHU023_QE2bacterial growth media DMSO5
SA473741DMSO6_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Pos_014126_KCHU023_QE2bacterial growth media DMSO6
SA473742DMSO6_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Neg_014127_KCHU023_QE2bacterial growth media DMSO6
SA473757Dofetilide_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Neg_014205_KCHU023_QE2bacterial growth media Dofetilide
SA473758Dofetilide_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Pos_014204_KCHU023_QE2bacterial growth media Dofetilide
SA473759Doxapramhydrochloride_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Neg_014077_KCHU023_QE2bacterial growth media Doxapramhydrochloride
SA473760Doxapramhydrochloride_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Pos_014076_KCHU023_QE2bacterial growth media Doxapramhydrochloride
SA473761Econazolenitrate_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Neg_014195_KCHU023_QE2bacterial growth media Econazolenitrate
SA473762Econazolenitrate_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Pos_014194_KCHU023_QE2bacterial growth media Econazolenitrate
SA473763Enalaprilmaleate_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Pos_014084_KCHU023_QE2bacterial growth media Enalaprilmaleate
SA473764Enalaprilmaleate_NotUsed_F1_R1_T1_Untargeted_DDA_HILICshort_Neg_014085_KCHU023_QE2bacterial growth media Enalaprilmaleate
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Collection:

Collection ID:CO004226
Collection Summary:Chemical stocks at 64 mM in DMSO were added to Brain Heart Infusion (BHI) (BD #2237500) at a final concentration of 20 µM. These samples were then frozen at -70°C and proceeded directly for LC/MS analyses. No biological samples were involved in this part of the study.
Sample Type:Media

Treatment:

Treatment ID:TR004242
Treatment Summary:Samples were immediately frozen at -70°C and thawed upon analyzing.

Sample Preparation:

Sampleprep ID:SP004239
Sampleprep Summary: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:CH005145
Instrument Name:Thermo Vanquish
Column Name:Waters ACQUITY UPLC BEH Amide (150 x 2.1 mm, 1.7 µm)
Column Temperature:45°C
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 with a column flow of
Flow Rate:0.4 mL/min
Solvent A:100% Water; 10mM Ammonium formate; 0.125% formic acid
Solvent B:95% Acetonitrile; 10mM Ammonium formate; 0.125% formic acid
Chromatography Type:HILIC

Analysis:

Analysis ID:AN006774
Analysis Type:MS
Chromatography ID:CH005145
Has Mz:1
Has Rt:1
Rt Units:Minutes
Results File:ST004087_AN006774_Results.txt
Units:peak height
  
Analysis ID:AN006775
Analysis Type:MS
Chromatography ID:CH005145
Has Mz:1
Has Rt:1
Rt Units:Minutes
Results File:ST004087_AN006775_Results.txt
Units:peak height
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