{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002004","ANALYSIS_ID":"AN003267","VERSION":"1","CREATED_ON":"November 27, 2021, 8:57 am"},

"PROJECT":{"PROJECT_TITLE":"A longitudinal study of the effect of temperature modification in full-scale anaerobic digesters","PROJECT_SUMMARY":"In order to identify metabolites descriptive of alterations of the working themperature during the process of anaerobic digestion, we performed untargeted metabolomics on samples of sewage sludge collected from two reactors working in parallel but with different temperature settings.","INSTITUTE":"INRAE","DEPARTMENT":"Microbiology and the food chain","LABORATORY":"PRocédés biOtechnologiques au Service de l'Environnement","LAST_NAME":"Chapleur","FIRST_NAME":"Olivier","ADDRESS":"1 rue Pierre-Gilles de Gennes, 92761 Antony Cedex, FRANCE","EMAIL":"olivier.chapleur@inrae.fr","PHONE":"+33 0140966506","FUNDING_SOURCE":"ANR"},

"STUDY":{"STUDY_TITLE":"Metabolomics analysis of anaerobic digesters","STUDY_SUMMARY":"In order to identify metabolites descriptive of alterations of the working themperature during the process of anaerobic digestion, we performed untargeted metabolomics on samples of sewage sludge collected from two reactors working in parallel but with different temperature settings.","INSTITUTE":"INRAE","LAST_NAME":"Chapleur","FIRST_NAME":"Olivier","ADDRESS":"1 rue Pierre-Gilles de Gennes, 92761 Antony Cedex, FRANCE","EMAIL":"olivier.chapleur@inrae.fr","PHONE":"+33 0140966506","NUM_GROUPS":"14"},

"SUBJECT":{"SUBJECT_TYPE":"Other abiotic sample","SUBJECT_SPECIES":"None"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"a01",
"Factors":{"Reactor":"A","Day":"-"},
"Additional sample data":{"RAW_FILE_NAME":"a01","ExperimentDescription":"full-digester","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"a02",
"Factors":{"Reactor":"B","Day":"-"},
"Additional sample data":{"RAW_FILE_NAME":"a02","ExperimentDescription":"full-digester","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"a03",
"Factors":{"Reactor":"A","Day":"218"},
"Additional sample data":{"RAW_FILE_NAME":"a03","ExperimentDescription":"full-digester","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"a04",
"Factors":{"Reactor":"B","Day":"218"},
"Additional sample data":{"RAW_FILE_NAME":"a04","ExperimentDescription":"full-digester","Temperature":"25"}
},
{
"Subject ID":"-",
"Sample ID":"a05",
"Factors":{"Reactor":"A","Day":"353"},
"Additional sample data":{"RAW_FILE_NAME":"a05","ExperimentDescription":"full-digester","Temperature":"32"}
},
{
"Subject ID":"-",
"Sample ID":"a06",
"Factors":{"Reactor":"B","Day":"353"},
"Additional sample data":{"RAW_FILE_NAME":"a06","ExperimentDescription":"full-digester","Temperature":"25"}
},
{
"Subject ID":"-",
"Sample ID":"a07",
"Factors":{"Reactor":"A","Day":"80"},
"Additional sample data":{"RAW_FILE_NAME":"a07","ExperimentDescription":"full-digester","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"a08",
"Factors":{"Reactor":"B","Day":"80"},
"Additional sample data":{"RAW_FILE_NAME":"a08","ExperimentDescription":"full-digester","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"a09",
"Factors":{"Reactor":"A","Day":"177"},
"Additional sample data":{"RAW_FILE_NAME":"a09","ExperimentDescription":"full-digester","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"a10",
"Factors":{"Reactor":"B","Day":"177"},
"Additional sample data":{"RAW_FILE_NAME":"a10","ExperimentDescription":"full-digester","Temperature":"30"}
},
{
"Subject ID":"-",
"Sample ID":"a11",
"Factors":{"Reactor":"A","Day":"281"},
"Additional sample data":{"RAW_FILE_NAME":"a11","ExperimentDescription":"full-digester","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"a12",
"Factors":{"Reactor":"B","Day":"281"},
"Additional sample data":{"RAW_FILE_NAME":"a12","ExperimentDescription":"full-digester","Temperature":"25"}
},
{
"Subject ID":"-",
"Sample ID":"a13",
"Factors":{"Reactor":"A","Day":"462"},
"Additional sample data":{"RAW_FILE_NAME":"a13","ExperimentDescription":"full-digester","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"a14",
"Factors":{"Reactor":"B","Day":"462"},
"Additional sample data":{"RAW_FILE_NAME":"a14","ExperimentDescription":"full-digester","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"b01",
"Factors":{"Reactor":"A","Day":"-"},
"Additional sample data":{"RAW_FILE_NAME":"b01","ExperimentDescription":"full-digester","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"b02",
"Factors":{"Reactor":"B","Day":"-"},
"Additional sample data":{"RAW_FILE_NAME":"b02","ExperimentDescription":"full-digester","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"b03",
"Factors":{"Reactor":"A","Day":"218"},
"Additional sample data":{"RAW_FILE_NAME":"b03","ExperimentDescription":"full-digester","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"b04",
"Factors":{"Reactor":"B","Day":"218"},
"Additional sample data":{"RAW_FILE_NAME":"b04","ExperimentDescription":"full-digester","Temperature":"25"}
},
{
"Subject ID":"-",
"Sample ID":"b05",
"Factors":{"Reactor":"A","Day":"353"},
"Additional sample data":{"RAW_FILE_NAME":"b05","ExperimentDescription":"full-digester","Temperature":"32"}
},
{
"Subject ID":"-",
"Sample ID":"b06",
"Factors":{"Reactor":"B","Day":"353"},
"Additional sample data":{"RAW_FILE_NAME":"b06","ExperimentDescription":"full-digester","Temperature":"25"}
},
{
"Subject ID":"-",
"Sample ID":"b07",
"Factors":{"Reactor":"A","Day":"80"},
"Additional sample data":{"RAW_FILE_NAME":"b07","ExperimentDescription":"full-digester","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"b08",
"Factors":{"Reactor":"B","Day":"80"},
"Additional sample data":{"RAW_FILE_NAME":"b08","ExperimentDescription":"full-digester","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"b09",
"Factors":{"Reactor":"A","Day":"177"},
"Additional sample data":{"RAW_FILE_NAME":"b09","ExperimentDescription":"full-digester","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"b10",
"Factors":{"Reactor":"B","Day":"177"},
"Additional sample data":{"RAW_FILE_NAME":"b10","ExperimentDescription":"full-digester","Temperature":"30"}
},
{
"Subject ID":"-",
"Sample ID":"b11",
"Factors":{"Reactor":"A","Day":"281"},
"Additional sample data":{"RAW_FILE_NAME":"b11","ExperimentDescription":"full-digester","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"b12",
"Factors":{"Reactor":"B","Day":"281"},
"Additional sample data":{"RAW_FILE_NAME":"b12","ExperimentDescription":"full-digester","Temperature":"25"}
},
{
"Subject ID":"-",
"Sample ID":"b13",
"Factors":{"Reactor":"A","Day":"462"},
"Additional sample data":{"RAW_FILE_NAME":"b13","ExperimentDescription":"full-digester","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"b14",
"Factors":{"Reactor":"B","Day":"462"},
"Additional sample data":{"RAW_FILE_NAME":"b14","ExperimentDescription":"full-digester","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"blank_200603195159",
"Factors":{"Reactor":"-","Day":"-"},
"Additional sample data":{"RAW_FILE_NAME":"blank_200603195159","ExperimentDescription":"blank","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"blank_200603235248",
"Factors":{"Reactor":"-","Day":"-"},
"Additional sample data":{"RAW_FILE_NAME":"blank_200603235248","ExperimentDescription":"blank","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"blank_200604045400",
"Factors":{"Reactor":"-","Day":"-"},
"Additional sample data":{"RAW_FILE_NAME":"blank_200604045400","ExperimentDescription":"blank","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"blank_200604095509",
"Factors":{"Reactor":"-","Day":"-"},
"Additional sample data":{"RAW_FILE_NAME":"blank_200604095509","ExperimentDescription":"blank","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"blank_200604145613",
"Factors":{"Reactor":"-","Day":"-"},
"Additional sample data":{"RAW_FILE_NAME":"blank_200604145613","ExperimentDescription":"blank","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"blank_200604195714",
"Factors":{"Reactor":"-","Day":"-"},
"Additional sample data":{"RAW_FILE_NAME":"blank_200604195714","ExperimentDescription":"blank","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"blank_200605005825",
"Factors":{"Reactor":"-","Day":"-"},
"Additional sample data":{"RAW_FILE_NAME":"blank_200605005825","ExperimentDescription":"blank","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"blank_200605055939",
"Factors":{"Reactor":"-","Day":"-"},
"Additional sample data":{"RAW_FILE_NAME":"blank_200605055939","ExperimentDescription":"blank","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"blank_200605090020",
"Factors":{"Reactor":"-","Day":"-"},
"Additional sample data":{"RAW_FILE_NAME":"blank_200605090020","ExperimentDescription":"blank","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"blank_200605100030",
"Factors":{"Reactor":"-","Day":"-"},
"Additional sample data":{"RAW_FILE_NAME":"blank_200605100030","ExperimentDescription":"blank","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"blank",
"Factors":{"Reactor":"-","Day":"-"},
"Additional sample data":{"RAW_FILE_NAME":"blank","ExperimentDescription":"blank","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"c01",
"Factors":{"Reactor":"A","Day":"-"},
"Additional sample data":{"RAW_FILE_NAME":"c01","ExperimentDescription":"full-digester","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"c02",
"Factors":{"Reactor":"B","Day":"-"},
"Additional sample data":{"RAW_FILE_NAME":"c02","ExperimentDescription":"full-digester","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"c03",
"Factors":{"Reactor":"A","Day":"218"},
"Additional sample data":{"RAW_FILE_NAME":"c03","ExperimentDescription":"full-digester","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"c04",
"Factors":{"Reactor":"B","Day":"218"},
"Additional sample data":{"RAW_FILE_NAME":"c04","ExperimentDescription":"full-digester","Temperature":"25"}
},
{
"Subject ID":"-",
"Sample ID":"c05",
"Factors":{"Reactor":"A","Day":"353"},
"Additional sample data":{"RAW_FILE_NAME":"c05","ExperimentDescription":"full-digester","Temperature":"32"}
},
{
"Subject ID":"-",
"Sample ID":"c06",
"Factors":{"Reactor":"B","Day":"353"},
"Additional sample data":{"RAW_FILE_NAME":"c06","ExperimentDescription":"full-digester","Temperature":"25"}
},
{
"Subject ID":"-",
"Sample ID":"c07",
"Factors":{"Reactor":"A","Day":"80"},
"Additional sample data":{"RAW_FILE_NAME":"c07","ExperimentDescription":"full-digester","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"c08",
"Factors":{"Reactor":"B","Day":"80"},
"Additional sample data":{"RAW_FILE_NAME":"c08","ExperimentDescription":"full-digester","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"c09",
"Factors":{"Reactor":"A","Day":"177"},
"Additional sample data":{"RAW_FILE_NAME":"c09","ExperimentDescription":"full-digester","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"c10",
"Factors":{"Reactor":"B","Day":"177"},
"Additional sample data":{"RAW_FILE_NAME":"c10","ExperimentDescription":"full-digester","Temperature":"30"}
},
{
"Subject ID":"-",
"Sample ID":"c11",
"Factors":{"Reactor":"A","Day":"281"},
"Additional sample data":{"RAW_FILE_NAME":"c11","ExperimentDescription":"full-digester","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"c12",
"Factors":{"Reactor":"B","Day":"281"},
"Additional sample data":{"RAW_FILE_NAME":"c12","ExperimentDescription":"full-digester","Temperature":"25"}
},
{
"Subject ID":"-",
"Sample ID":"c13",
"Factors":{"Reactor":"A","Day":"462"},
"Additional sample data":{"RAW_FILE_NAME":"c13","ExperimentDescription":"full-digester","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"c14",
"Factors":{"Reactor":"B","Day":"462"},
"Additional sample data":{"RAW_FILE_NAME":"c14","ExperimentDescription":"full-digester","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"d01",
"Factors":{"Reactor":"A","Day":"-"},
"Additional sample data":{"RAW_FILE_NAME":"d01","ExperimentDescription":"full-digester","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"d02",
"Factors":{"Reactor":"B","Day":"-"},
"Additional sample data":{"RAW_FILE_NAME":"d02","ExperimentDescription":"full-digester","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"d03",
"Factors":{"Reactor":"A","Day":"218"},
"Additional sample data":{"RAW_FILE_NAME":"d03","ExperimentDescription":"full-digester","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"d04",
"Factors":{"Reactor":"B","Day":"218"},
"Additional sample data":{"RAW_FILE_NAME":"d04","ExperimentDescription":"full-digester","Temperature":"25"}
},
{
"Subject ID":"-",
"Sample ID":"d05",
"Factors":{"Reactor":"A","Day":"353"},
"Additional sample data":{"RAW_FILE_NAME":"d05","ExperimentDescription":"full-digester","Temperature":"32"}
},
{
"Subject ID":"-",
"Sample ID":"d06",
"Factors":{"Reactor":"B","Day":"353"},
"Additional sample data":{"RAW_FILE_NAME":"d06","ExperimentDescription":"full-digester","Temperature":"25"}
},
{
"Subject ID":"-",
"Sample ID":"d07",
"Factors":{"Reactor":"A","Day":"80"},
"Additional sample data":{"RAW_FILE_NAME":"d07","ExperimentDescription":"full-digester","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"d08",
"Factors":{"Reactor":"B","Day":"80"},
"Additional sample data":{"RAW_FILE_NAME":"d08","ExperimentDescription":"full-digester","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"d09",
"Factors":{"Reactor":"A","Day":"177"},
"Additional sample data":{"RAW_FILE_NAME":"d09","ExperimentDescription":"full-digester","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"d10",
"Factors":{"Reactor":"B","Day":"177"},
"Additional sample data":{"RAW_FILE_NAME":"d10","ExperimentDescription":"full-digester","Temperature":"30"}
},
{
"Subject ID":"-",
"Sample ID":"d11",
"Factors":{"Reactor":"A","Day":"281"},
"Additional sample data":{"RAW_FILE_NAME":"d11","ExperimentDescription":"full-digester","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"d12",
"Factors":{"Reactor":"B","Day":"281"},
"Additional sample data":{"RAW_FILE_NAME":"d12","ExperimentDescription":"full-digester","Temperature":"25"}
},
{
"Subject ID":"-",
"Sample ID":"d13",
"Factors":{"Reactor":"A","Day":"462"},
"Additional sample data":{"RAW_FILE_NAME":"d13","ExperimentDescription":"full-digester","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"d14",
"Factors":{"Reactor":"B","Day":"462"},
"Additional sample data":{"RAW_FILE_NAME":"d14","ExperimentDescription":"full-digester","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"pool08",
"Factors":{"Reactor":"-","Day":"-"},
"Additional sample data":{"RAW_FILE_NAME":"pool08","ExperimentDescription":"pool","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"pool09",
"Factors":{"Reactor":"-","Day":"-"},
"Additional sample data":{"RAW_FILE_NAME":"pool09","ExperimentDescription":"pool","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"pool1",
"Factors":{"Reactor":"-","Day":"-"},
"Additional sample data":{"RAW_FILE_NAME":"pool1","ExperimentDescription":"pool","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"pool2",
"Factors":{"Reactor":"-","Day":"-"},
"Additional sample data":{"RAW_FILE_NAME":"pool2","ExperimentDescription":"pool","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"pool3",
"Factors":{"Reactor":"-","Day":"-"},
"Additional sample data":{"RAW_FILE_NAME":"pool3","ExperimentDescription":"pool","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"pool4",
"Factors":{"Reactor":"-","Day":"-"},
"Additional sample data":{"RAW_FILE_NAME":"pool4","ExperimentDescription":"pool","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"pool5",
"Factors":{"Reactor":"-","Day":"-"},
"Additional sample data":{"RAW_FILE_NAME":"pool5","ExperimentDescription":"pool","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"pool6",
"Factors":{"Reactor":"-","Day":"-"},
"Additional sample data":{"RAW_FILE_NAME":"pool6","ExperimentDescription":"pool","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"pool7",
"Factors":{"Reactor":"-","Day":"-"},
"Additional sample data":{"RAW_FILE_NAME":"pool7","ExperimentDescription":"pool","Temperature":"35"}
},
{
"Subject ID":"-",
"Sample ID":"pool",
"Factors":{"Reactor":"-","Day":"-"},
"Additional sample data":{"RAW_FILE_NAME":"pool","ExperimentDescription":"pool","Temperature":"35"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Sludge samples from two reactors were collected at days 0, 80, 177, 218, 281, 353, and 462. Sludge was collected in 50-mL sterile Falcon tubes and immediately transported on dry ice to INRAE, where they were frozen at -80 °C.","SAMPLE_TYPE":"Sewage sludge"},

"TREATMENT":{"TREATMENT_SUMMARY":"During the time of the experiment, both reactors (3,000 m3 each) worked at half capacity due to a constraint in the availability of substrate to treat. On average, the full-scale digesters were operated at a mean hydraulic retention time (HRT) of 34 days and a mean organic loading rate of 0.82 kg of volatile solids m-3 day-1. For the first four months of study, the two reactors operated at 35 °C. Reactor A was kept at this temperature during all the experiment. For digester B, the temperature was decreased abruptly to 30 °C on the 123th day and maintained at this level for 2 HRTs until the 190th day. Then, the temperature was modified to 25 °C and maintained for 3 HRTs (between the 191st and the 373th days). Finally, the heating of reactor B was increased from day 374 onwards to reach the initial temperature of 35 °C."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"For every sample, four aliquots with 0.75 mL of sludge were prepared in 2-mL Eppendorf tubes. Then, 1 mL of phosphate buffer saline was added into each tube and the sludge volumes were washed by centrifuging them at 15500 rcf for 3 min at 4 °C. This process was repeated once. The samples were freeze-dried overnight and, for every sample, 20 mg of dried sludge were transferred in new Eppendorf tubes. Then, the dried sludge powders were resuspended in 1 mL of a cold ddH2O: MeOH mixture (1:1) containing 2.5 mM PIPES. The samples were sonicated for 6 min, and submerged in liquid nitrogen. After one minute, the samples were thawed in ice. The cold-shock step was repeated twice. Afterwards, the samples were agitated for 15 min at 420 rpm in an orbital shaker. Following this, the samples were centrifuged at 15500 rcf for 3 min at 4 °C and the supernatants were collected. The supernatants were immediately filtered with 0.45 μM Nylon filters and freeze-dried overnight. The dried extracts were left at -80°C until the HPLC-MS analyses."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"HILIC","INSTRUMENT_NAME":"Thermo Accela 1250","COLUMN_NAME":"Macherey Nagel Nucleodur HILIC (100 x 2 mm, 1.8 µm)","FLOW_GRADIENT":"95% B: 3 min, 95% - 60% B: 3 - 14 min, 60% - 95 % B: 14 -24 min, 95% B: 24 - 29 min","FLOW_RATE":"0.4 mL/min","SOLVENT_A":"Ammonium acetate 50 Mm at pH 5","SOLVENT_B":"Acetonitrile","SAMPLE_INJECTION":"10 µL"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Thermo LTQ XL","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"XCMS online for assignment METLIN, HMDB","CAPILLARY_TEMPERATURE":"320 °C","MS_RESULTS_FILE":"ST002004_AN003267_Results.txt UNITS:Peak areas Has m/z:Yes Has RT:Yes RT units:Minutes"}

}