{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002535","ANALYSIS_ID":"AN004170","VERSION":"1","CREATED_ON":"March 31, 2023, 7:39 am"},
"PROJECT":{"PROJECT_TITLE":"Metabolomic Profiling of Human Faecal Samples","PROJECT_SUMMARY":"Targeted analysis of SCFAs and polar metabolites in samples from human faeces.","INSTITUTE":"South Australian Health and Medical Research Institute","DEPARTMENT":"Lifelong Health","LABORATORY":"Microbiome and Host Health Programme","LAST_NAME":"Shoubridge","FIRST_NAME":"Andrew","ADDRESS":"North Terrace, Adelaide, South Australia, 5000, Australia","EMAIL":"andrew.shoubridge@sahmri.com","PHONE":"+61405041977"},
"STUDY":{"STUDY_TITLE":"Relationships between the gut microbiome and cognitive impairment in residents of long-term aged care.","STUDY_SUMMARY":"Ageing-associated cognitive decline affects more than half of those in long-term residential aged care. Emerging evidence suggests that gut microbiome-host interactions influence the effects of modifiable risk factors. We investigated the relationship between gut microbiome characteristics and severity of cognitive impairment (CI) in 159 residents of long-term aged care. Severe CI was associated with a significantly increased abundance of proinflammatory bacterial species, including Methanobrevibacter smithii and Alistipes finegoldii, and decreased relative abundance of beneficial bacterial clades. Severe CI was associated with increased microbial capacity for methanogenesis, and reduced capacity for synthesis of short-chain fatty acids, neurotransmitters glutamate and gamma-aminobutyric acid, and amino acids required for neuro-protective lysosomal activity. These relationships were independent of age, sex, antibiotic exposure, and diet. Our findings implicate multiple gut microbiome-brain pathways in ageing-associated cognitive decline, including inflammation, neurotransmission, and autophagy, and highlight the potential to predict and prevent cognitive decline through microbiome-targeted strategies.","INSTITUTE":"South Australian Health and Medical Research Institute","LAST_NAME":"Shoubridge","FIRST_NAME":"Andrew","ADDRESS":"North Terrace, Adelaide, South Australia, 5000, Australia","EMAIL":"andrew.shoubridge@sahmri.com","PHONE":"+61405041977"},
"SUBJECT":{"SUBJECT_TYPE":"Human","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606","GENDER":"Male and female"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"01-01-012",
"Sample ID":"AS_01",
"Factors":{"CI_group":"4"},
"Additional sample data":{"RAW_FILE_NAME":"AS_01.mzML AS_001.mzML"}
},
{
"Subject ID":"01-01-017",
"Sample ID":"AS_02",
"Factors":{"CI_group":"4"},
"Additional sample data":{"RAW_FILE_NAME":"AS_02.mzML AS_002.mzML"}
},
{
"Subject ID":"02-02-001",
"Sample ID":"AS_03",
"Factors":{"CI_group":"2"},
"Additional sample data":{"RAW_FILE_NAME":"AS_03.mzML AS_003.mzML"}
},
{
"Subject ID":"02-02-002",
"Sample ID":"AS_04",
"Factors":{"CI_group":"3"},
"Additional sample data":{"RAW_FILE_NAME":"AS_04.mzML AS_004.mzML"}
},
{
"Subject ID":"02-02-009",
"Sample ID":"AS_05",
"Factors":{"CI_group":"2"},
"Additional sample data":{"RAW_FILE_NAME":"AS_05.mzML AS_005.mzML"}
},
{
"Subject ID":"02-02-014",
"Sample ID":"AS_06",
"Factors":{"CI_group":"2"},
"Additional sample data":{"RAW_FILE_NAME":"AS_06.mzML AS_006.mzML"}
},
{
"Subject ID":"02-02-018",
"Sample ID":"AS_07",
"Factors":{"CI_group":"4"},
"Additional sample data":{"RAW_FILE_NAME":"AS_07.mzML AS_007.mzML"}
},
{
"Subject ID":"02-03-002",
"Sample ID":"AS_08",
"Factors":{"CI_group":"2"},
"Additional sample data":{"RAW_FILE_NAME":"AS_08.mzML AS_008.mzML"}
},
{
"Subject ID":"02-03-018",
"Sample ID":"AS_09",
"Factors":{"CI_group":"4"},
"Additional sample data":{"RAW_FILE_NAME":"AS_09.mzML AS_009.mzML"}
},
{
"Subject ID":"02-03-020",
"Sample ID":"AS_10",
"Factors":{"CI_group":"3"},
"Additional sample data":{"RAW_FILE_NAME":"AS_10.mzML AS_010.mzML"}
},
{
"Subject ID":"02-03-031",
"Sample ID":"AS_11",
"Factors":{"CI_group":"4"},
"Additional sample data":{"RAW_FILE_NAME":"AS_11.mzML AS_011.mzML"}
},
{
"Subject ID":"02-03-033",
"Sample ID":"AS_12",
"Factors":{"CI_group":"3"},
"Additional sample data":{"RAW_FILE_NAME":"AS_12.mzML AS_012.mzML"}
},
{
"Subject ID":"02-03-046",
"Sample ID":"AS_13",
"Factors":{"CI_group":"2"},
"Additional sample data":{"RAW_FILE_NAME":"AS_13.mzML AS_013.mzML"}
},
{
"Subject ID":"02-03-063",
"Sample ID":"AS_14",
"Factors":{"CI_group":"4"},
"Additional sample data":{"RAW_FILE_NAME":"AS_14.mzML AS_014.mzML"}
},
{
"Subject ID":"02-03-069",
"Sample ID":"AS_15",
"Factors":{"CI_group":"4"},
"Additional sample data":{"RAW_FILE_NAME":"AS_15.mzML AS_015.mzML"}
},
{
"Subject ID":"02-03-095",
"Sample ID":"AS_16",
"Factors":{"CI_group":"3"},
"Additional sample data":{"RAW_FILE_NAME":"AS_16.mzML AS_016.mzML"}
},
{
"Subject ID":"02-03-096",
"Sample ID":"AS_17",
"Factors":{"CI_group":"3"},
"Additional sample data":{"RAW_FILE_NAME":"AS_17.mzML AS_017.mzML"}
},
{
"Subject ID":"02-03-105",
"Sample ID":"AS_18",
"Factors":{"CI_group":"4"},
"Additional sample data":{"RAW_FILE_NAME":"AS_18.mzML AS_018.mzML"}
},
{
"Subject ID":"02-03-108",
"Sample ID":"AS_19",
"Factors":{"CI_group":"3"},
"Additional sample data":{"RAW_FILE_NAME":"AS_19.mzML AS_019.mzML"}
},
{
"Subject ID":"02-03-109",
"Sample ID":"AS_20",
"Factors":{"CI_group":"2"},
"Additional sample data":{"RAW_FILE_NAME":"AS_20.mzML AS_020.mzML"}
},
{
"Subject ID":"02-03-110",
"Sample ID":"AS_21",
"Factors":{"CI_group":"2"},
"Additional sample data":{"RAW_FILE_NAME":"AS_21.mzML AS_021.mzML"}
},
{
"Subject ID":"02-03-112",
"Sample ID":"AS_22",
"Factors":{"CI_group":"3"},
"Additional sample data":{"RAW_FILE_NAME":"AS_22.mzML AS_022.mzML"}
},
{
"Subject ID":"02-03-114",
"Sample ID":"AS_23",
"Factors":{"CI_group":"3"},
"Additional sample data":{"RAW_FILE_NAME":"AS_23.mzML AS_023.mzML"}
},
{
"Subject ID":"02-03-137",
"Sample ID":"AS_24",
"Factors":{"CI_group":"4"},
"Additional sample data":{"RAW_FILE_NAME":"AS_24.mzML AS_024.mzML"}
},
{
"Subject ID":"02-03-141",
"Sample ID":"AS_25",
"Factors":{"CI_group":"4"},
"Additional sample data":{"RAW_FILE_NAME":"AS_25.mzML AS_025.mzML"}
},
{
"Subject ID":"03-04-007",
"Sample ID":"AS_26",
"Factors":{"CI_group":"2"},
"Additional sample data":{"RAW_FILE_NAME":"AS_26.mzML AS_026.mzML"}
},
{
"Subject ID":"03-04-016",
"Sample ID":"AS_27",
"Factors":{"CI_group":"3"},
"Additional sample data":{"RAW_FILE_NAME":"AS_27.mzML AS_027.mzML"}
},
{
"Subject ID":"03-04-017",
"Sample ID":"AS_28",
"Factors":{"CI_group":"2"},
"Additional sample data":{"RAW_FILE_NAME":"AS_28.mzML AS_028.mzML"}
},
{
"Subject ID":"03-04-028",
"Sample ID":"AS_29",
"Factors":{"CI_group":"4"},
"Additional sample data":{"RAW_FILE_NAME":"AS_29.mzML AS_029.mzML"}
},
{
"Subject ID":"03-04-029",
"Sample ID":"AS_30",
"Factors":{"CI_group":"4"},
"Additional sample data":{"RAW_FILE_NAME":"AS_30.mzML AS_030.mzML"}
},
{
"Subject ID":"03-04-030",
"Sample ID":"AS_31",
"Factors":{"CI_group":"3"},
"Additional sample data":{"RAW_FILE_NAME":"AS_31.mzML AS_031.mzML"}
},
{
"Subject ID":"03-05-002",
"Sample ID":"AS_32",
"Factors":{"CI_group":"3"},
"Additional sample data":{"RAW_FILE_NAME":"AS_32.mzML AS_032.mzML"}
},
{
"Subject ID":"03-05-017",
"Sample ID":"AS_33",
"Factors":{"CI_group":"2"},
"Additional sample data":{"RAW_FILE_NAME":"AS_33.mzML AS_033.mzML"}
},
{
"Subject ID":"03-05-020",
"Sample ID":"AS_34",
"Factors":{"CI_group":"2"},
"Additional sample data":{"RAW_FILE_NAME":"AS_34.mzML AS_034.mzML"}
},
{
"Subject ID":"03-05-040",
"Sample ID":"AS_35",
"Factors":{"CI_group":"2"},
"Additional sample data":{"RAW_FILE_NAME":"AS_35.mzML AS_035.mzML"}
},
{
"Subject ID":"Norgen_buffer_blank",
"Sample ID":"AS_36",
"Factors":{"CI_group":"-"},
"Additional sample data":{"RAW_FILE_NAME":"AS_36.mzML AS_036.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"PBQC_001",
"Factors":{"CI_group":"-"},
"Additional sample data":{"RAW_FILE_NAME":"PBQC_001.mzML PBQC_001 (2)..mzML"}
},
{
"Subject ID":"-",
"Sample ID":"PBQC_002",
"Factors":{"CI_group":"-"},
"Additional sample data":{"RAW_FILE_NAME":"PBQC_002.mzML PBQC_002 (2)..mzML"}
},
{
"Subject ID":"-",
"Sample ID":"PBQC_003",
"Factors":{"CI_group":"-"},
"Additional sample data":{"RAW_FILE_NAME":"PBQC_003.mzML PBQC_003 (2)..mzML"}
},
{
"Subject ID":"-",
"Sample ID":"PBQC_004",
"Factors":{"CI_group":"-"},
"Additional sample data":{"RAW_FILE_NAME":"PBQC_004.mzML PBQC_004 (2)..mzML"}
},
{
"Subject ID":"-",
"Sample ID":"PBQC_005",
"Factors":{"CI_group":"-"},
"Additional sample data":{"RAW_FILE_NAME":"PBQC_005.mzML PBQC_005 (2)..mzML"}
},
{
"Subject ID":"-",
"Sample ID":"PBQC_006",
"Factors":{"CI_group":"-"},
"Additional sample data":{"RAW_FILE_NAME":"PBQC_006.mzML PBQC_006 (2)..mzML"}
},
{
"Subject ID":"-",
"Sample ID":"PBQC_007",
"Factors":{"CI_group":"-"},
"Additional sample data":{"RAW_FILE_NAME":"PBQC_007.mzML PBQC_007 (2)..mzML"}
},
{
"Subject ID":"-",
"Sample ID":"PBQC_008",
"Factors":{"CI_group":"-"},
"Additional sample data":{"RAW_FILE_NAME":"PBQC_008.mzML PBQC_008 (2)..mzML"}
},
{
"Subject ID":"-",
"Sample ID":"PBQC_009",
"Factors":{"CI_group":"-"},
"Additional sample data":{"RAW_FILE_NAME":"PBQC_009.mzML PBQC_009 (2)..mzML"}
},
{
"Subject ID":"-",
"Sample ID":"R_Blank_01",
"Factors":{"CI_group":"-"},
"Additional sample data":{"RAW_FILE_NAME":"R_Blank_01.mzML R_Blank_01.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"R_Blank_02",
"Factors":{"CI_group":"-"},
"Additional sample data":{"RAW_FILE_NAME":"R_Blank_02.mzML R_Blank_02.mzML"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Stool was collected and stored using Norgen Stool Nucleic Acid Collection and Preservation Tubes (Norgen Biotek, ON, Canada).","SAMPLE_TYPE":"Feces","STORAGE_CONDITIONS":"-80℃"},
"TREATMENT":{"TREATMENT_SUMMARY":"Stool samples containing buffer were vortexed vigorously and 1 ml was transferred to a clean 2 ml tube. Samples were centrifuged for 20 min at 13,000 xg at 4°C and the supernatant was transferred to a clean 2 ml screw-cap tube for storage."},
"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"SCFA analysis was performed using an Agilent 6490 series triple quadrupole mass spectrometer (Agilent Technologies) with chromatographic separation on an Agilent 1200 series high-performance liquid chromatography system (HPLC) (Agilent Technologies). SCFAs were extracted by adding 360μL of 50% acetonitrile with 10μM 4-methylvaleric acid internal standard to 40μL of biological sample supernatant. Samples were then vortexed for 30 seconds, incubated at 10oC for 30 minutes at 950RPM, centrifuged at 14,000RPM for five minutes at 4oC, followed by supernatant collection. Derivatisation for SCFA analysis was performed by first adding 20μL of 20μM 13C6-nitrophenylhydrazine as internal standard to 40μL of the extracted supernatant, followed by 20μL each of 200mM nitrophenylhydrazine and 120mM 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC), incubated at 40oC for 30 minutes at 950RPM, quenched with 20μL of 200mM quinic acid, and incubated at 40oC for a further 30 minutes at 950RPM. Lastly, the samples were reconstituted with 1.9mL of 15% acetonitrile and 1μL was injected onto the column. Pooled biological quality controls (PBQCs) were created by pooling extracts (20μL) from individual biological samples and injected onto the column in five sample intervals. A reagent and procedural blank of the original sample preservation buffer was included for analysis to perform background correction. Polar metabolite analysis was performed using an Agilent 6545 series quadrupole time-of-flight mass spectrometer (Agilent Technologies) with chromatographic separation on an Agilent 1200 series HPLC system (Agilent Technologies). Metabolite extraction was performed by first adding a solvent mixture of acetonitrile, methanol and water to 20μL of biological sample, followed by vortexing, sonication and agitation. Samples were then centrifuged and supernatant collected and mixed with an internal standard mixture containing 13C5, 15N-valine, 13C6-leucine, and 13C6-sorbitol, and 14μL of sample was injected onto the column. Samples were injected in a randomised order and PBQCs were injected onto the column in five sample intervals. Data matrices were imported to the web-based platform MetaboAnalyst (v5.0) for quality control checks by multivariate statistics. SCFA data were normalised to internal standards, and polar metabolite data were log-transformed and median-normalised."},
"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"HILIC","INSTRUMENT_NAME":"Agilent 1200","COLUMN_NAME":"Merck SeQuant ZIC-HILIC (150 x 2.1mm,5um)","SOLVENT_A":"100% water; 20 mM ammonium carbonate (pH 9.0)","SOLVENT_B":"100% acetonitrile","FLOW_GRADIENT":"time = 0 min, 90% B; t = 0.5 min, 90% B; t = 12 min, 40% B; t = 14 min, 40% B; t = 15 min, 5%; t = 18 min, 5% B; and t = 19 min, 90%.","FLOW_RATE":"250 ul/min","COLUMN_TEMPERATURE":"40"},
"ANALYSIS":{"ANALYSIS_TYPE":"MS"},
"MS":{"INSTRUMENT_NAME":"Agilent 6545 QTOF","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"ESI","ION_MODE":"NEGATIVE","MS_COMMENTS":"Negative mode LC-MS data were collected in centroid mode with a scan range of 50 to 1700 mass-to-charge ratio (m/z) and an acquisition rate of 1.2 spectra/s. Samples were analyzed in the same analytical batch and randomized with a quality control every five samples. Authentic standards were also run to generate the library for targeted analysis. Level 1 metabolite identification [according to the Metabolite Standard Initiative] was based on matching accurate mass, retention time, and tandem MS (MS/MS) spectra to the 550 authentic standards in the MA in-house library. Metabolite abundance based on area under the curve (AUC) was obtained using Agilent Masshunter Quantitative Analysis B 0.7.00. Statistical analysis was performed applying the web-based platform MetaboAnalyst applying no missing value imputation, normalization to median peak area, and no scaling or transformation. RAW_FILE_NAME=AS_01.mzML to AS_35.mzML refer to metabolite detection of short-chain fatty acids, and RAW_FILE_NAME=AS_001.mzML to AS_035.mzML refer the polar metabolites."},
"MS_METABOLITE_DATA":{
"Units":"ng/ml",
"Data":[{"Metabolite":"Isocaproate (4-MVA) ISTD","AS_01":"14318","AS_02":"14102","AS_03":"15283","AS_04":"16411","AS_05":"16564","AS_06":"16792","AS_07":"14318","AS_08":"16317","AS_09":"17010","AS_10":"18045","AS_11":"18373","AS_12":"16419","AS_13":"17079","AS_14":"17989","AS_15":"15145","AS_16":"21745","AS_17":"19185","AS_18":"18562","AS_19":"16442","AS_20":"17294","AS_21":"17226","AS_22":"20150","AS_23":"16324","AS_24":"18113","AS_25":"15250","AS_26":"20650","AS_27":"30661","AS_28":"15396","AS_29":"17556","AS_30":"17787","AS_31":"21068","AS_32":"16013","AS_33":"18235","AS_34":"13109","AS_35":"15231","AS_36":"14916","PBQC_001":"16559","PBQC_002":"16486","PBQC_003":"16959","PBQC_004":"17018","PBQC_005":"17838","PBQC_006":"18817","PBQC_007":"18700","PBQC_008":"18913","PBQC_009":"18483"},{"Metabolite":"Acetate","AS_01":"31158","AS_02":"103871","AS_03":"108276","AS_04":"39190","AS_05":"17164","AS_06":"3728","AS_07":"57806","AS_08":"238686","AS_09":"166431","AS_10":"139864","AS_11":"92181","AS_12":"150570","AS_13":"68690","AS_14":"106157","AS_15":"69352","AS_16":"221459","AS_17":"123517","AS_18":"211038","AS_19":"168265","AS_20":"285030","AS_21":"64725","AS_22":"118773","AS_23":"12479","AS_24":"15476","AS_25":"24829","AS_26":"75440","AS_27":"65820","AS_28":"92022","AS_29":"50597","AS_30":"32284","AS_31":"232804","AS_32":"106373","AS_33":"101435","AS_34":"44720","AS_35":"298110","AS_36":"1505","PBQC_001":"94720","PBQC_002":"109050","PBQC_003":"117431","PBQC_004":"110994","PBQC_005":"87231","PBQC_006":"114560","PBQC_007":"95972","PBQC_008":"97694","PBQC_009":"111309"},{"Metabolite":"ACETATE - 6C13NPH (ISTD)","AS_01":"16614","AS_02":"20289","AS_03":"19032","AS_04":"19043","AS_05":"27595","AS_06":"18829","AS_07":"20011","AS_08":"30430","AS_09":"19183","AS_10":"18808","AS_11":"20498","AS_12":"18380","AS_13":"20113","AS_14":"21823","AS_15":"25770","AS_16":"17375","AS_17":"19613","AS_18":"20199","AS_19":"16980","AS_20":"21092","AS_21":"17633","AS_22":"17644","AS_23":"20298","AS_24":"18906","AS_25":"14723","AS_26":"16203","AS_27":"13405","AS_28":"16155","AS_29":"15441","AS_30":"16692","AS_31":"32461","AS_32":"33630","AS_33":"16983","AS_34":"31142","AS_35":"19130","AS_36":"16107","PBQC_001":"17506","PBQC_002":"19488","PBQC_003":"21932","PBQC_004":"21275","PBQC_005":"16958","PBQC_006":"21514","PBQC_007":"18268","PBQC_008":"19204","PBQC_009":"22377"},{"Metabolite":"Propionate","AS_01":"76260","AS_02":"295088","AS_03":"388872","AS_04":"94806","AS_05":"37184","AS_06":"8881","AS_07":"159874","AS_08":"763216","AS_09":"310618","AS_10":"516366","AS_11":"141267","AS_12":"275801","AS_13":"209309","AS_14":"222866","AS_15":"214621","AS_16":"815832","AS_17":"252493","AS_18":"422959","AS_19":"710688","AS_20":"596027","AS_21":"289213","AS_22":"566362","AS_23":"63615","AS_24":"43246","AS_25":"128654","AS_26":"330153","AS_27":"376263","AS_28":"272748","AS_29":"217885","AS_30":"160465","AS_31":"593947","AS_32":"300209","AS_33":"402726","AS_34":"61969","AS_35":"834497","AS_36":"1756","PBQC_001":"300298","PBQC_002":"329640","PBQC_003":"346914","PBQC_004":"339821","PBQC_005":"327184","PBQC_006":"347449","PBQC_007":"345696","PBQC_008":"342567","PBQC_009":"349652"},{"Metabolite":"Propionate 6C13NPH (ISTD)","AS_01":"60125","AS_02":"66594","AS_03":"60877","AS_04":"63249","AS_05":"70144","AS_06":"61929","AS_07":"63615","AS_08":"68191","AS_09":"61441","AS_10":"62424","AS_11":"65337","AS_12":"65184","AS_13":"64934","AS_14":"65273","AS_15":"64769","AS_16":"63360","AS_17":"64287","AS_18":"64084","AS_19":"60680","AS_20":"65766","AS_21":"60958","AS_22":"63803","AS_23":"64313","AS_24":"63175","AS_25":"55723","AS_26":"60003","AS_27":"53752","AS_28":"60952","AS_29":"56729","AS_30":"57755","AS_31":"69210","AS_32":"71579","AS_33":"60358","AS_34":"66620","AS_35":"61850","AS_36":"59411","PBQC_001":"62107","PBQC_002":"67278","PBQC_003":"68449","PBQC_004":"69084","PBQC_005":"65099","PBQC_006":"70495","PBQC_007":"68235","PBQC_008":"67904","PBQC_009":"70255"},{"Metabolite":"Isobutyrate","AS_01":"110951","AS_02":"582591","AS_03":"717646","AS_04":"252963","AS_05":"59652","AS_06":"13778","AS_07":"293815","AS_08":"905331","AS_09":"738067","AS_10":"175520","AS_11":"192308","AS_12":"507871","AS_13":"485601","AS_14":"462022","AS_15":"220242","AS_16":"634592","AS_17":"458178","AS_18":"1225376","AS_19":"283506","AS_20":"1573380","AS_21":"463201","AS_22":"896569","AS_23":"61631","AS_24":"63911","AS_25":"126298","AS_26":"427694","AS_27":"361621","AS_28":"651614","AS_29":"316534","AS_30":"256053","AS_31":"1484116","AS_32":"446640","AS_33":"1057877","AS_34":"182651","AS_35":"865668","AS_36":"917","PBQC_001":"475676","PBQC_002":"512862","PBQC_003":"538028","PBQC_004":"539712","PBQC_005":"539344","PBQC_006":"536223","PBQC_007":"537831","PBQC_008":"541363","PBQC_009":"532950"},{"Metabolite":"Isobutyrate-6C13 NPH 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}
}