Pure standards were used for method development, compound identification and calibration.
"],"repository":["MetaboLights"],"study_status":["Public"],"ptm_modification":[""],"instrument_platform":["Liquid Chromatography MS - negative - reverse phase","Liquid Chromatography MS - positive - reverse phase"],"chromatography_protocol":["15 min reverse-phase LC-method used with QTOF in positive ionization mode:
The separation was performed on an Agilent 1290 Infinity II LC system using a ZORBAX RRHD Eclipse Plus column (C18, 2.1
Å~ 100 mm, 1.8 μm; Agilent 858700-902) with a ZOBRAX Eclipse Plus guard column (C18, 2.1 Å~ 5 mm, 1.8 μm; Agilent 821725-901) at 40 °C. The multisampler was kept at a temperature of 4 °C. The injection volume was 1 μL and the flow rate was 0.4 mL/min. The mobile phases consisted of A: water + 0.1 % formic acid + 5 mM ammonium formate; B: methanol + 0.1 % formic acid + 5 mM ammonium formate. The 15 min gradient started with 5 % solvent B, which was increased to 30 % over 1 min and then further increased to 100 % by 7 min and held for 3 min, before returning to 5 % solvent B for a 5 min re-equilibration.
13 min reverse-phase LC-method used with QTOF in negative ionization mode:
The separation was performed on an Agilent 1290 Infinity II LC system using a ZORBAX RRHD Eclipse Plus column (C18, 2.1 Å~ 100 mm, 1.8 μm; Agilent 858700-902) with a ZOBRAX Eclipse Plus guard column (C18, 2.1 Å~ 5 mm, 1.8 μm; Agilent 821725-901) at 40 °C. The multisampler was kept at a temperature of 4 °C. The injection volume was 1 μL and the flow rate was 0.4 mL/min. The 13 min gradient started with 35 % solvent B, which was increased to 100 % over 9 min and held for 1 min, before returning to 35 % solvent B for a 3 min reequilibration. Mobile phases for BPA, BPB, BPF and catechol analysis consisted of A: water and B: methanol; Mobile phases for BPAF, BPS, PFNA, PFOA, patulin and 2- nitrofluorene analysis consisted of A: water + 5 mM ammonium acetate + 0.03 % acetic acid and B: methanol + 5 mM ammonium acetate + 0.03 % acetic acid.
"],"publication":["Extensive PFAS accumulation by human gut bacteria."],"submitter_affiliation":["MRC Toxicology Unit"],"submitter_name":["Anna Elisabeth Lindell"],"organism_part":["calibration curve","Control Analyte","control sample role","Vehicle Control","solvent blank","Supernatant","Quality Control"],"technology_type":["mass spectrometry"],"disease":[""],"extraction_protocol":["70 μl sample was extracted with 140 μl of ice-cold methanol:acetonitrile (1:1) containing the internal standard (20 µM caffeine, 60 µM ibuprofen) and incubated at 4 ºC for 30 min. Plates were then centrifuged at 4 ºC and 4000 rpm for 10 min. Supernatants were transferred to 96-well plates for LC-MS analysis. Samples for concentration calibration and bacteria-free compound controls were processed in the same way.
"],"organism":["calibration curve","Control Analyte","Anaerobic Bacteria","experimental blank","Quality Control"],"full_dataset_link":["https://www.ebi.ac.uk/metabolights/MTBLS9756"],"author":["Anna Lindell.","Kiran Patil. kp533@mrc-tox.cam.ac.uk."],"data_transformation_protocol":["The Agilent MassHunter Qualitative Analysis 10.0 software was used to qualify the selected xenobiotic standards. TIC, EIC and EIC-fragment graphs were extracted for each compound. The Agilent MassHunter TOF Quantitative Analysis (Version 10.1) was used to quantify the xenobiotic compounds in each sample.
Calibration curves based on pure compound standards were used to estimate the concentrations of target compounds. Data analysis was performed in RStudio Version 1.3.1093. The median of each sample group was compared to the median of the compound controls and an appropriate reduction of more than 20 % was chosen as cut-off, to ensure relevant reduction compared to the compound control distribution.
"],"study_factor":["Internal standard","Compound","Compound concentration micromolar","Bacterial community","Technical replicate","Biological replicate"],"submitter_email":["annalindell08@gmail.com"],"sample_collection_protocol":["On the day of the screen communities were assembled by pooling together second passages of individual strains according to their OD600 values. Assembled communities were then centrifuged at 25 ºC and 4000 rpm for 15 min and the pellet was resuspended in PBS buffer to create a community with OD600 of 7.5. Each well was inoculated 1:1 with community in PBS to reach a starting OD600 of 3.75 and a compound concentration of 20 µM (1 % DMSO). For compound control wells bacteria-free PBS was added to the respective wells. Plates were incubated at 37 ºC for 4 h, after which they were centrifuged at 21 ºC and 4000 rpm for 15 min. The supernatant and compound controls were transferred to fresh 96-well plates and stored at -80 °C until extraction.
Community 1: Bacteroides caccae, Bacteroides dorei, Bacteroides thetaiotaomicron, Bacteroides uniformis, Bacteroides vulgatus, Colinsella aerofaciens, Coprococcus comes, Eubacterium rectale, Parabacteroides merdae, Roseburia intestinalis
Community 2: Akkermansia muciniphila, Bacteroides clarus, Bacteroides stercoris, Clostridium difficile, Eggerthella lenta, Eubacterium eligens, Fusobacterium nucleatum subsp. animalis, Odoribacter splanchnicus, Parabacteroides distastonis, Ruminococcus bromii
"],"omics_type":["Metabolomics"],"study_design":["Microbiota","Environmental Pollutants","polyfluoroalkyl substance","Liquid chromatography mass spectrometry","targeted metabolites"],"curator_keywords":["Microbiota","Environmental Pollutants","polyfluoroalkyl substance","Liquid chromatography mass spectrometry","targeted metabolites"],"mass_spectrometry_protocol":["LC-MS analysis was performed on an Agilent 1290 Infinity II LC system coupled with an Agilent 6546 LC/Q-TOF equipped with an with ESI ion source. The QTOF MS scan was operated in positive or negative MS mode using four different collision energies (0V, 10V, 20V, 40V) (30-1500 m/z), depending on the xenobiotic targeted for measurement. The source parameters were as
follows: gas temperature: 200 °C, drying gas: 9 L/min, nebulizer: 20 psi, sheath gas temperature: 400 °C, sheath gas flow: 12 L/min, VCap: 3000 V, nozzle voltage: 0 V, fragmentor: 110 V, skimmer 45 V, Oct RF Vpp: 750 V. The online mass calibration was performed using a reference solution (positive: 121.05 and 922.01 m/z; negative: 112.99 and 1033.99 m/z). The compounds were identified based on their retention time, accurate mass and fragmentation patterns. For all measured compounds, pure standards were used for method development, compound identification and calibration.
"],"metabolite_name":["3,4-methylenedioxymethamphetamine","Propiconazole","Zearalenone","Ochratoxin A","Pyrimethanil","Fluopyram","Tributyl phosphate","Fludioxonil","Thiamethoxam","Azoxystrobin","Pyraclostrobin","Carbendazim","Heroin","Triphenyl phosphate","Caffeine","Imazalil","Serotonin","Tebuconazole","Melamine","o-Anisidine","Methamphetamine","Chlorantraniliprole","T-2 toxin","Malathion","Deoxynivalenol","N-itrosomorpholine","Acetamiprid","Cocaine","Imidacloprid","Boscalid","Nicotine","Thiabendazole"],"additional_accession":[]},"is_claimable":false,"name":"Pollutant depletion by gut bacterial communities","description":"Per- and polyfluoroalkyl Substances (PFAS) – the so-called ‘forever chemicals’ – are a major cause of environmental and health concern due to their toxicity and long-term persistence. Yet, no efficient mechanisms for their removal have been identified. Here we report the potential of two communities of human gut bacteria to bioaccumulate or degrade common environmental pollutants.","dates":{"publication":"2025-06-30","submission":"2024-07-05"},"accession":"MTBLS9756","cross_references":{"MetaboLights":["MTBLC33216","MTBLC72754","MTBLC34581","MTBLC34575","MTBLC22901","MTBLC18135","MTBLC5855","MTBLC74926","MTBLC38397","MTBLC35549","MTBLC39163","MTBLC40909","MTBLC81822","MTBLC27732","MTBLC3392","MTBLC67113","MTBLC27958","MTBLC10022","MTBLC81763","MTBLC83070","MTBLC27808","MTBLC83831","MTBLC5870","MTBLC6651","MTBLC1391","MTBLC27915","MTBLC6809","MTBLC18723","MTBLC76326","MTBLC82288","MTBLC7719","MTBLC8489","MTBLC78780","MTBLC8674","MTBLC28790","MTBLC9381","MTBLC81781","MTBLC45979","MTBLC39185","MTBLC35019","MTBLC35033","MTBLC10106"],"ChEBI":["CHEBI:33216","CHEBI:72754","CHEBI:34581","CHEBI:34575","CHEBI:22901","CHEBI:18135","CHEBI:5855","CHEBI:74926","CHEBI:38397","CHEBI:35549","CHEBI:39163","CHEBI:40909","CHEBI:81822","CHEBI:27732","CHEBI:3392","CHEBI:67113","CHEBI:27958","CHEBI:10022","CHEBI:81763","CHEBI:83070","CHEBI:27808","CHEBI:83831","CHEBI:5870","CHEBI:6651","CHEBI:1391","CHEBI:27915","CHEBI:6809","CHEBI:18723","CHEBI:76326","CHEBI:82288","CHEBI:7719","CHEBI:8489","CHEBI:78780","CHEBI:8674","CHEBI:28790","CHEBI:9381","CHEBI:81781","CHEBI:45979","CHEBI:39185","CHEBI:35019","CHEBI:35033","CHEBI:10106"]}}