Isolation:Article Title: Identifying transient and stable bacteria- metabolite interactions from longitudinal multi-omics data
Article Snippet: .. Batch cultures Frozen glycerol stocks of Ruminococcus gnavus (DSMZ 108212), Blautia obeum and Ruminococcus luti (both isolated from human faecal material) were grown anaerobically at 37oC (Don Whitley Scienti c Limited, containing 80% N2, 10% H2 and 10% CO2) for 24 hrs on brain-heart infusion (BHI; Sigma-Aldrich) agar supplemented with 3% L-cysteine hydrochloride monohydrate, D-(+)-Cellobiose, D-(+)-Maltose and 0.5% yeast extract. .. The identity of bacteria isolates was validated using Sanger sequencing (16S rRNA gene V1-V9), following bacterial DNA extraction (E.Z.N.A Omega Bio-Tek).
Modification:Article Title: Impact of drugs and environmental contaminants on amine production by gut bacteria.
Article Snippet: .. Reagent and tools table Reagent/resource Reference or source Identifier or catalogue number Experimental models Clostridium sporogenes DSMZ DSM 1664 Escherichia coli Denamur Lab, INSERM IAI1 Klebsiella aerogenes DSMZ DSM 30053 Ruminococcus gnavus DSMZ DSM 108212 Chemicals, enzymes and other reagents Modified Gifu anaerobic medium (mGAM) Nissui Pharmaceuticals (sold by HyServe, Germany) 1005433-001 Clear untreated sterile 96-well polystyrene plates, u-bottom Corning 3795 Pharmaceutical drug library Prestwick Chemical Libraries Dataset EV2 Pesticide library EMBL Chemical Biology core facility Dataset EV2 Industrial chemicals library Lindell et al, 2024 Dataset EV2 Sweeteners library Blasche et al, 2025 Dataset EV2 Ampicillin Sigma-Aldrich/Merck A9518 Reagent/resource Reference or source Identifier or catalogue number Cefixime Cayman Chemical Company 17176 Ceftazidime MedChemExpress HY-B0593/ CS-2810 Levofloxacin Cayman Chemical Company 20382 Tetracycline Sigma-Aldrich/Merck 87128 Paroxetine TargetMOI T1636L Didanosine Cayman Chemical Company 23715 Fenazaflor Sigma-Aldrich/Merck 36504 Acetonitrile VWR 83640.320 Methanol VWR 83638.320 Formic acid Fisher A117-50 Ammonium formate VWR 84884.180 Caffeine Fluka 56396 Amoxicillin Sigma-Aldrich/Merck A8523 Putrescine MetaSci Complete Metabolite Library Cadaverine Sigma-Aldrich/Merck C8561-1G Histamine MetaSci Complete Metabolite Library Tryptamine MetaSci Complete Metabolite Library 2-Phenylethylamine MetaSci Complete Metabolite Library Software MassHunter Workstation Agilent v10.1 SkanIt Microplate Reader Software ThermoFischer v 6.1.1 Python v 3.11.5 pandas package McKinney, 2010 v. 2.2.0 scipy package Virtanen et al, 2020 v. 1.11.3 numpy package Harris et al, 2020 v. 1.26.0 scikit-learn package Pedregosa et al, 2012 v. 1.3.2 matplotlib package Hunter, 2007 v. 3.8.0 seaborn package Waskom, 2021 v. 0.13.1 Other Analytical column: ACQUITY BEH Amide 1.7 μm, 2.1 × 50mm Waters 186009504 Analytical column: InfinityLab Poroshell 120 EC-C18 1.9 μm, 2.1 × 50mm Agilent 699675-902 Triple-quadrupole mass spectrometer Agilent 6470 Ultra-high performance liquid chromatography instrument Agilent 1290 Infinity II © The Author(s) Molecular Systems Biology 9 D ow nloaded from https://w w w .em bopress.org on July 2, 2025 from IP 120.188.94.94. .. Reagent/resource Reference or source Identifier or catalogue number Biomek Automated Workstation Beckman Coulter i7 Microplate reader ThermoFisher Multiskan FC, 51119100
Sterility:Article Title: Impact of drugs and environmental contaminants on amine production by gut bacteria.
Article Snippet: .. Reagent and tools table Reagent/resource Reference or source Identifier or catalogue number Experimental models Clostridium sporogenes DSMZ DSM 1664 Escherichia coli Denamur Lab, INSERM IAI1 Klebsiella aerogenes DSMZ DSM 30053 Ruminococcus gnavus DSMZ DSM 108212 Chemicals, enzymes and other reagents Modified Gifu anaerobic medium (mGAM) Nissui Pharmaceuticals (sold by HyServe, Germany) 1005433-001 Clear untreated sterile 96-well polystyrene plates, u-bottom Corning 3795 Pharmaceutical drug library Prestwick Chemical Libraries Dataset EV2 Pesticide library EMBL Chemical Biology core facility Dataset EV2 Industrial chemicals library Lindell et al, 2024 Dataset EV2 Sweeteners library Blasche et al, 2025 Dataset EV2 Ampicillin Sigma-Aldrich/Merck A9518 Reagent/resource Reference or source Identifier or catalogue number Cefixime Cayman Chemical Company 17176 Ceftazidime MedChemExpress HY-B0593/ CS-2810 Levofloxacin Cayman Chemical Company 20382 Tetracycline Sigma-Aldrich/Merck 87128 Paroxetine TargetMOI T1636L Didanosine Cayman Chemical Company 23715 Fenazaflor Sigma-Aldrich/Merck 36504 Acetonitrile VWR 83640.320 Methanol VWR 83638.320 Formic acid Fisher A117-50 Ammonium formate VWR 84884.180 Caffeine Fluka 56396 Amoxicillin Sigma-Aldrich/Merck A8523 Putrescine MetaSci Complete Metabolite Library Cadaverine Sigma-Aldrich/Merck C8561-1G Histamine MetaSci Complete Metabolite Library Tryptamine MetaSci Complete Metabolite Library 2-Phenylethylamine MetaSci Complete Metabolite Library Software MassHunter Workstation Agilent v10.1 SkanIt Microplate Reader Software ThermoFischer v 6.1.1 Python v 3.11.5 pandas package McKinney, 2010 v. 2.2.0 scipy package Virtanen et al, 2020 v. 1.11.3 numpy package Harris et al, 2020 v. 1.26.0 scikit-learn package Pedregosa et al, 2012 v. 1.3.2 matplotlib package Hunter, 2007 v. 3.8.0 seaborn package Waskom, 2021 v. 0.13.1 Other Analytical column: ACQUITY BEH Amide 1.7 μm, 2.1 × 50mm Waters 186009504 Analytical column: InfinityLab Poroshell 120 EC-C18 1.9 μm, 2.1 × 50mm Agilent 699675-902 Triple-quadrupole mass spectrometer Agilent 6470 Ultra-high performance liquid chromatography instrument Agilent 1290 Infinity II © The Author(s) Molecular Systems Biology 9 D ow nloaded from https://w w w .em bopress.org on July 2, 2025 from IP 120.188.94.94. .. Reagent/resource Reference or source Identifier or catalogue number Biomek Automated Workstation Beckman Coulter i7 Microplate reader ThermoFisher Multiskan FC, 51119100
Drug discovery:Article Title: Impact of drugs and environmental contaminants on amine production by gut bacteria.
Article Snippet: .. Reagent and tools table Reagent/resource Reference or source Identifier or catalogue number Experimental models Clostridium sporogenes DSMZ DSM 1664 Escherichia coli Denamur Lab, INSERM IAI1 Klebsiella aerogenes DSMZ DSM 30053 Ruminococcus gnavus DSMZ DSM 108212 Chemicals, enzymes and other reagents Modified Gifu anaerobic medium (mGAM) Nissui Pharmaceuticals (sold by HyServe, Germany) 1005433-001 Clear untreated sterile 96-well polystyrene plates, u-bottom Corning 3795 Pharmaceutical drug library Prestwick Chemical Libraries Dataset EV2 Pesticide library EMBL Chemical Biology core facility Dataset EV2 Industrial chemicals library Lindell et al, 2024 Dataset EV2 Sweeteners library Blasche et al, 2025 Dataset EV2 Ampicillin Sigma-Aldrich/Merck A9518 Reagent/resource Reference or source Identifier or catalogue number Cefixime Cayman Chemical Company 17176 Ceftazidime MedChemExpress HY-B0593/ CS-2810 Levofloxacin Cayman Chemical Company 20382 Tetracycline Sigma-Aldrich/Merck 87128 Paroxetine TargetMOI T1636L Didanosine Cayman Chemical Company 23715 Fenazaflor Sigma-Aldrich/Merck 36504 Acetonitrile VWR 83640.320 Methanol VWR 83638.320 Formic acid Fisher A117-50 Ammonium formate VWR 84884.180 Caffeine Fluka 56396 Amoxicillin Sigma-Aldrich/Merck A8523 Putrescine MetaSci Complete Metabolite Library Cadaverine Sigma-Aldrich/Merck C8561-1G Histamine MetaSci Complete Metabolite Library Tryptamine MetaSci Complete Metabolite Library 2-Phenylethylamine MetaSci Complete Metabolite Library Software MassHunter Workstation Agilent v10.1 SkanIt Microplate Reader Software ThermoFischer v 6.1.1 Python v 3.11.5 pandas package McKinney, 2010 v. 2.2.0 scipy package Virtanen et al, 2020 v. 1.11.3 numpy package Harris et al, 2020 v. 1.26.0 scikit-learn package Pedregosa et al, 2012 v. 1.3.2 matplotlib package Hunter, 2007 v. 3.8.0 seaborn package Waskom, 2021 v. 0.13.1 Other Analytical column: ACQUITY BEH Amide 1.7 μm, 2.1 × 50mm Waters 186009504 Analytical column: InfinityLab Poroshell 120 EC-C18 1.9 μm, 2.1 × 50mm Agilent 699675-902 Triple-quadrupole mass spectrometer Agilent 6470 Ultra-high performance liquid chromatography instrument Agilent 1290 Infinity II © The Author(s) Molecular Systems Biology 9 D ow nloaded from https://w w w .em bopress.org on July 2, 2025 from IP 120.188.94.94. .. Reagent/resource Reference or source Identifier or catalogue number Biomek Automated Workstation Beckman Coulter i7 Microplate reader ThermoFisher Multiskan FC, 51119100
Software:Article Title: Impact of drugs and environmental contaminants on amine production by gut bacteria.
Article Snippet: .. Reagent and tools table Reagent/resource Reference or source Identifier or catalogue number Experimental models Clostridium sporogenes DSMZ DSM 1664 Escherichia coli Denamur Lab, INSERM IAI1 Klebsiella aerogenes DSMZ DSM 30053 Ruminococcus gnavus DSMZ DSM 108212 Chemicals, enzymes and other reagents Modified Gifu anaerobic medium (mGAM) Nissui Pharmaceuticals (sold by HyServe, Germany) 1005433-001 Clear untreated sterile 96-well polystyrene plates, u-bottom Corning 3795 Pharmaceutical drug library Prestwick Chemical Libraries Dataset EV2 Pesticide library EMBL Chemical Biology core facility Dataset EV2 Industrial chemicals library Lindell et al, 2024 Dataset EV2 Sweeteners library Blasche et al, 2025 Dataset EV2 Ampicillin Sigma-Aldrich/Merck A9518 Reagent/resource Reference or source Identifier or catalogue number Cefixime Cayman Chemical Company 17176 Ceftazidime MedChemExpress HY-B0593/ CS-2810 Levofloxacin Cayman Chemical Company 20382 Tetracycline Sigma-Aldrich/Merck 87128 Paroxetine TargetMOI T1636L Didanosine Cayman Chemical Company 23715 Fenazaflor Sigma-Aldrich/Merck 36504 Acetonitrile VWR 83640.320 Methanol VWR 83638.320 Formic acid Fisher A117-50 Ammonium formate VWR 84884.180 Caffeine Fluka 56396 Amoxicillin Sigma-Aldrich/Merck A8523 Putrescine MetaSci Complete Metabolite Library Cadaverine Sigma-Aldrich/Merck C8561-1G Histamine MetaSci Complete Metabolite Library Tryptamine MetaSci Complete Metabolite Library 2-Phenylethylamine MetaSci Complete Metabolite Library Software MassHunter Workstation Agilent v10.1 SkanIt Microplate Reader Software ThermoFischer v 6.1.1 Python v 3.11.5 pandas package McKinney, 2010 v. 2.2.0 scipy package Virtanen et al, 2020 v. 1.11.3 numpy package Harris et al, 2020 v. 1.26.0 scikit-learn package Pedregosa et al, 2012 v. 1.3.2 matplotlib package Hunter, 2007 v. 3.8.0 seaborn package Waskom, 2021 v. 0.13.1 Other Analytical column: ACQUITY BEH Amide 1.7 μm, 2.1 × 50mm Waters 186009504 Analytical column: InfinityLab Poroshell 120 EC-C18 1.9 μm, 2.1 × 50mm Agilent 699675-902 Triple-quadrupole mass spectrometer Agilent 6470 Ultra-high performance liquid chromatography instrument Agilent 1290 Infinity II © The Author(s) Molecular Systems Biology 9 D ow nloaded from https://w w w .em bopress.org on July 2, 2025 from IP 120.188.94.94. .. Reagent/resource Reference or source Identifier or catalogue number Biomek Automated Workstation Beckman Coulter i7 Microplate reader ThermoFisher Multiskan FC, 51119100
Targeted Proteomics:Article Title: Impact of drugs and environmental contaminants on amine production by gut bacteria.
Article Snippet: .. Reagent and tools table Reagent/resource Reference or source Identifier or catalogue number Experimental models Clostridium sporogenes DSMZ DSM 1664 Escherichia coli Denamur Lab, INSERM IAI1 Klebsiella aerogenes DSMZ DSM 30053 Ruminococcus gnavus DSMZ DSM 108212 Chemicals, enzymes and other reagents Modified Gifu anaerobic medium (mGAM) Nissui Pharmaceuticals (sold by HyServe, Germany) 1005433-001 Clear untreated sterile 96-well polystyrene plates, u-bottom Corning 3795 Pharmaceutical drug library Prestwick Chemical Libraries Dataset EV2 Pesticide library EMBL Chemical Biology core facility Dataset EV2 Industrial chemicals library Lindell et al, 2024 Dataset EV2 Sweeteners library Blasche et al, 2025 Dataset EV2 Ampicillin Sigma-Aldrich/Merck A9518 Reagent/resource Reference or source Identifier or catalogue number Cefixime Cayman Chemical Company 17176 Ceftazidime MedChemExpress HY-B0593/ CS-2810 Levofloxacin Cayman Chemical Company 20382 Tetracycline Sigma-Aldrich/Merck 87128 Paroxetine TargetMOI T1636L Didanosine Cayman Chemical Company 23715 Fenazaflor Sigma-Aldrich/Merck 36504 Acetonitrile VWR 83640.320 Methanol VWR 83638.320 Formic acid Fisher A117-50 Ammonium formate VWR 84884.180 Caffeine Fluka 56396 Amoxicillin Sigma-Aldrich/Merck A8523 Putrescine MetaSci Complete Metabolite Library Cadaverine Sigma-Aldrich/Merck C8561-1G Histamine MetaSci Complete Metabolite Library Tryptamine MetaSci Complete Metabolite Library 2-Phenylethylamine MetaSci Complete Metabolite Library Software MassHunter Workstation Agilent v10.1 SkanIt Microplate Reader Software ThermoFischer v 6.1.1 Python v 3.11.5 pandas package McKinney, 2010 v. 2.2.0 scipy package Virtanen et al, 2020 v. 1.11.3 numpy package Harris et al, 2020 v. 1.26.0 scikit-learn package Pedregosa et al, 2012 v. 1.3.2 matplotlib package Hunter, 2007 v. 3.8.0 seaborn package Waskom, 2021 v. 0.13.1 Other Analytical column: ACQUITY BEH Amide 1.7 μm, 2.1 × 50mm Waters 186009504 Analytical column: InfinityLab Poroshell 120 EC-C18 1.9 μm, 2.1 × 50mm Agilent 699675-902 Triple-quadrupole mass spectrometer Agilent 6470 Ultra-high performance liquid chromatography instrument Agilent 1290 Infinity II © The Author(s) Molecular Systems Biology 9 D ow nloaded from https://w w w .em bopress.org on July 2, 2025 from IP 120.188.94.94. .. Reagent/resource Reference or source Identifier or catalogue number Biomek Automated Workstation Beckman Coulter i7 Microplate reader ThermoFisher Multiskan FC, 51119100
Mass Spectrometry:Article Title: Impact of drugs and environmental contaminants on amine production by gut bacteria.
Article Snippet: .. Reagent and tools table Reagent/resource Reference or source Identifier or catalogue number Experimental models Clostridium sporogenes DSMZ DSM 1664 Escherichia coli Denamur Lab, INSERM IAI1 Klebsiella aerogenes DSMZ DSM 30053 Ruminococcus gnavus DSMZ DSM 108212 Chemicals, enzymes and other reagents Modified Gifu anaerobic medium (mGAM) Nissui Pharmaceuticals (sold by HyServe, Germany) 1005433-001 Clear untreated sterile 96-well polystyrene plates, u-bottom Corning 3795 Pharmaceutical drug library Prestwick Chemical Libraries Dataset EV2 Pesticide library EMBL Chemical Biology core facility Dataset EV2 Industrial chemicals library Lindell et al, 2024 Dataset EV2 Sweeteners library Blasche et al, 2025 Dataset EV2 Ampicillin Sigma-Aldrich/Merck A9518 Reagent/resource Reference or source Identifier or catalogue number Cefixime Cayman Chemical Company 17176 Ceftazidime MedChemExpress HY-B0593/ CS-2810 Levofloxacin Cayman Chemical Company 20382 Tetracycline Sigma-Aldrich/Merck 87128 Paroxetine TargetMOI T1636L Didanosine Cayman Chemical Company 23715 Fenazaflor Sigma-Aldrich/Merck 36504 Acetonitrile VWR 83640.320 Methanol VWR 83638.320 Formic acid Fisher A117-50 Ammonium formate VWR 84884.180 Caffeine Fluka 56396 Amoxicillin Sigma-Aldrich/Merck A8523 Putrescine MetaSci Complete Metabolite Library Cadaverine Sigma-Aldrich/Merck C8561-1G Histamine MetaSci Complete Metabolite Library Tryptamine MetaSci Complete Metabolite Library 2-Phenylethylamine MetaSci Complete Metabolite Library Software MassHunter Workstation Agilent v10.1 SkanIt Microplate Reader Software ThermoFischer v 6.1.1 Python v 3.11.5 pandas package McKinney, 2010 v. 2.2.0 scipy package Virtanen et al, 2020 v. 1.11.3 numpy package Harris et al, 2020 v. 1.26.0 scikit-learn package Pedregosa et al, 2012 v. 1.3.2 matplotlib package Hunter, 2007 v. 3.8.0 seaborn package Waskom, 2021 v. 0.13.1 Other Analytical column: ACQUITY BEH Amide 1.7 μm, 2.1 × 50mm Waters 186009504 Analytical column: InfinityLab Poroshell 120 EC-C18 1.9 μm, 2.1 × 50mm Agilent 699675-902 Triple-quadrupole mass spectrometer Agilent 6470 Ultra-high performance liquid chromatography instrument Agilent 1290 Infinity II © The Author(s) Molecular Systems Biology 9 D ow nloaded from https://w w w .em bopress.org on July 2, 2025 from IP 120.188.94.94. .. Reagent/resource Reference or source Identifier or catalogue number Biomek Automated Workstation Beckman Coulter i7 Microplate reader ThermoFisher Multiskan FC, 51119100
Liquid Chromatography:Article Title: Impact of drugs and environmental contaminants on amine production by gut bacteria.
Article Snippet: .. Reagent and tools table Reagent/resource Reference or source Identifier or catalogue number Experimental models Clostridium sporogenes DSMZ DSM 1664 Escherichia coli Denamur Lab, INSERM IAI1 Klebsiella aerogenes DSMZ DSM 30053 Ruminococcus gnavus DSMZ DSM 108212 Chemicals, enzymes and other reagents Modified Gifu anaerobic medium (mGAM) Nissui Pharmaceuticals (sold by HyServe, Germany) 1005433-001 Clear untreated sterile 96-well polystyrene plates, u-bottom Corning 3795 Pharmaceutical drug library Prestwick Chemical Libraries Dataset EV2 Pesticide library EMBL Chemical Biology core facility Dataset EV2 Industrial chemicals library Lindell et al, 2024 Dataset EV2 Sweeteners library Blasche et al, 2025 Dataset EV2 Ampicillin Sigma-Aldrich/Merck A9518 Reagent/resource Reference or source Identifier or catalogue number Cefixime Cayman Chemical Company 17176 Ceftazidime MedChemExpress HY-B0593/ CS-2810 Levofloxacin Cayman Chemical Company 20382 Tetracycline Sigma-Aldrich/Merck 87128 Paroxetine TargetMOI T1636L Didanosine Cayman Chemical Company 23715 Fenazaflor Sigma-Aldrich/Merck 36504 Acetonitrile VWR 83640.320 Methanol VWR 83638.320 Formic acid Fisher A117-50 Ammonium formate VWR 84884.180 Caffeine Fluka 56396 Amoxicillin Sigma-Aldrich/Merck A8523 Putrescine MetaSci Complete Metabolite Library Cadaverine Sigma-Aldrich/Merck C8561-1G Histamine MetaSci Complete Metabolite Library Tryptamine MetaSci Complete Metabolite Library 2-Phenylethylamine MetaSci Complete Metabolite Library Software MassHunter Workstation Agilent v10.1 SkanIt Microplate Reader Software ThermoFischer v 6.1.1 Python v 3.11.5 pandas package McKinney, 2010 v. 2.2.0 scipy package Virtanen et al, 2020 v. 1.11.3 numpy package Harris et al, 2020 v. 1.26.0 scikit-learn package Pedregosa et al, 2012 v. 1.3.2 matplotlib package Hunter, 2007 v. 3.8.0 seaborn package Waskom, 2021 v. 0.13.1 Other Analytical column: ACQUITY BEH Amide 1.7 μm, 2.1 × 50mm Waters 186009504 Analytical column: InfinityLab Poroshell 120 EC-C18 1.9 μm, 2.1 × 50mm Agilent 699675-902 Triple-quadrupole mass spectrometer Agilent 6470 Ultra-high performance liquid chromatography instrument Agilent 1290 Infinity II © The Author(s) Molecular Systems Biology 9 D ow nloaded from https://w w w .em bopress.org on July 2, 2025 from IP 120.188.94.94. .. Reagent/resource Reference or source Identifier or catalogue number Biomek Automated Workstation Beckman Coulter i7 Microplate reader ThermoFisher Multiskan FC, 51119100
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