{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001757","ANALYSIS_ID":"AN002862","VERSION":"1","CREATED_ON":"April 28, 2021, 7:00 pm"},

"PROJECT":{"PROJECT_TITLE":"High-coverage metabolomics annotation uncovers microbiota-driven biochemical landscape of interorgan transport and gut-brain communication","PROJECT_TYPE":"untargeted metabolomics","PROJECT_SUMMARY":"The mammalian gut harbors a complex and dynamic microbial ecosystem: the microbiota. While emerging studies support that microbiota regulates brain function with a few molecular cues suggested, the overall biochemical landscape of the “microbiota-gut-brain axis” remains largely unclear. Using high coverage metabolomics, we profiled feces, blood sera and cerebral cortical brain tissues of germ-free C57BL/6 mice and their age-matched conventionally raised counterparts. Results revealed for all three sample matrices metabolomic signatures owing to microbiota, yielding hundreds of identified metabolites including 533 altered for feces, 231 for sera and 58 for brain tissues with numerous significantly enriched pathways involving aromatic amino acids and neurotransmitters. Multicompartmental comparative analyses singled out microbiota-derived metabolites potentially implicated in interorgan transport and the gut-brain axis, exemplified by indoxyl sulfate and trimethylamine-N-oxide. Gender-specific characteristics of these landscapes were discussed. Our findings may be valuable for future research probing microbial influences on host metabolism and gut-brain communication.","INSTITUTE":"University of North Carolina at Chapel Hill","DEPARTMENT":"Department of Environmental Sciences and Engineering","LAST_NAME":"Lai","FIRST_NAME":"Yunjia","ADDRESS":"1104 MHRC, 135 Dauer Dr., Chapel Hill, NC, 27599, USA","EMAIL":"yunjia.lai@outlook.com","PHONE":"9194805489","FUNDING_SOURCE":"NIEHS"},

"STUDY":{"STUDY_TITLE":"Metabolomics of mouse blood sera comparing GF and CONV-R mice","STUDY_TYPE":"untargeted metabolomics","STUDY_SUMMARY":"Using high coverage metabolomics, we profiled feces, blood sera and cerebral cortical brain tissues of germ-free C57BL/6 mice and their age-matched conventionally raised counterparts. Results revealed for all three sample matrices metabolomic signatures owing to microbiota, yielding hundreds of identified metabolites including 533 altered for feces, 231 for sera and 58 for brain tissues with numerous significantly enriched pathways involving aromatic amino acids and neurotransmitters.","INSTITUTE":"University of North Carolina at Chapel Hill","DEPARTMENT":"Department of Environmental Sciences and Engineering","LAST_NAME":"Lai","FIRST_NAME":"Yunjia","ADDRESS":"1104 MHRC, 135 Dauer Dr., Chapel Hill, NC 27599","EMAIL":"yunjia.lai@outlook.com","PHONE":"9194805489","NUM_GROUPS":"2","TOTAL_SUBJECTS":"24","NUM_MALES":"12","NUM_FEMALES":"12","PUBLICATIONS":"Nature Communications"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090","GENOTYPE_STRAIN":"C57BL/6","AGE_OR_AGE_RANGE":"7-8 week old","GENDER":"Male and female"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"serum_Pos_CN_30A1A_M",
"Factors":{"Experimental factor":"Conventionally-raised (CONV-R)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Male","RAW_FILE_NAME":"serum_Pos_CN_30A1A_M.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Pos_CN_30A1B_M",
"Factors":{"Experimental factor":"Conventionally-raised (CONV-R)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Male","RAW_FILE_NAME":"serum_Pos_CN_30A1B_M.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Pos_CN_30A1C_M",
"Factors":{"Experimental factor":"Conventionally-raised (CONV-R)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Male","RAW_FILE_NAME":"serum_Pos_CN_30A1C_M.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Pos_CN_30A2A_M",
"Factors":{"Experimental factor":"Conventionally-raised (CONV-R)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Male","RAW_FILE_NAME":"serum_Pos_CN_30A2A_M.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Pos_CN_30A2B_M",
"Factors":{"Experimental factor":"Conventionally-raised (CONV-R)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Male","RAW_FILE_NAME":"serum_Pos_CN_30A2B_M.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Pos_CN_30A2C_M",
"Factors":{"Experimental factor":"Conventionally-raised (CONV-R)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Male","RAW_FILE_NAME":"serum_Pos_CN_30A2C_M.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Pos_CN_9A1C_F",
"Factors":{"Experimental factor":"Conventionally-raised (CONV-R)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Female","RAW_FILE_NAME":"serum_Pos_CN_9A1C_F.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Pos_CN_9A2A_F",
"Factors":{"Experimental factor":"Conventionally-raised (CONV-R)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Female","RAW_FILE_NAME":"serum_Pos_CN_9A2A_F.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Pos_CN_9A2B_F",
"Factors":{"Experimental factor":"Conventionally-raised (CONV-R)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Female","RAW_FILE_NAME":"serum_Pos_CN_9A2B_F.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Pos_CN_9A2C_F",
"Factors":{"Experimental factor":"Conventionally-raised (CONV-R)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Female","RAW_FILE_NAME":"serum_Pos_CN_9A2C_F.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Pos_CN_9A2D_F",
"Factors":{"Experimental factor":"Conventionally-raised (CONV-R)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Female","RAW_FILE_NAME":"serum_Pos_CN_9A2D_F.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Pos_CN_9A2E_F",
"Factors":{"Experimental factor":"Conventionally-raised (CONV-R)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Female","RAW_FILE_NAME":"serum_Pos_CN_9A2E_F.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Pos_GF_27F2",
"Factors":{"Experimental factor":"Germ-free (GF)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Female","RAW_FILE_NAME":"serum_Pos_GF_27F2.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Pos_GF_27F3",
"Factors":{"Experimental factor":"Germ-free (GF)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Female","RAW_FILE_NAME":"serum_Pos_GF_27F3.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Pos_GF_27F4",
"Factors":{"Experimental factor":"Germ-free (GF)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Female","RAW_FILE_NAME":"serum_Pos_GF_27F4.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Pos_GF_27F5",
"Factors":{"Experimental factor":"Germ-free (GF)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Female","RAW_FILE_NAME":"serum_Pos_GF_27F5.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Pos_GF_27F6",
"Factors":{"Experimental factor":"Germ-free (GF)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Female","RAW_FILE_NAME":"serum_Pos_GF_27F6.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Pos_GF_27F7",
"Factors":{"Experimental factor":"Germ-free (GF)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Female","RAW_FILE_NAME":"serum_Pos_GF_27F7.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Pos_GF_27M1",
"Factors":{"Experimental factor":"Germ-free (GF)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Male","RAW_FILE_NAME":"serum_Pos_GF_27M1.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Pos_GF_27M2",
"Factors":{"Experimental factor":"Germ-free (GF)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Male","RAW_FILE_NAME":"serum_Pos_GF_27M2.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Pos_GF_27M5",
"Factors":{"Experimental factor":"Germ-free (GF)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Male","RAW_FILE_NAME":"serum_Pos_GF_27M5.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Pos_GF_27M7",
"Factors":{"Experimental factor":"Germ-free (GF)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Male","RAW_FILE_NAME":"serum_Pos_GF_27M7.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Pos_GF_27M8",
"Factors":{"Experimental factor":"Germ-free (GF)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Male","RAW_FILE_NAME":"serum_Pos_GF_27M8.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Pos_GF_27M9",
"Factors":{"Experimental factor":"Germ-free (GF)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Male","RAW_FILE_NAME":"serum_Pos_GF_27M9.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Neg_CN_30A1A_M",
"Factors":{"Experimental factor":"Conventionally-raised (CONV-R)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Male","RAW_FILE_NAME":"serum_Neg_CN_30A1A_M.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Neg_CN_30A1B_M",
"Factors":{"Experimental factor":"Conventionally-raised (CONV-R)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Male","RAW_FILE_NAME":"serum_Neg_CN_30A1B_M.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Neg_CN_30A1C_M",
"Factors":{"Experimental factor":"Conventionally-raised (CONV-R)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Male","RAW_FILE_NAME":"serum_Neg_CN_30A1C_M.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Neg_CN_30A2A_M",
"Factors":{"Experimental factor":"Conventionally-raised (CONV-R)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Male","RAW_FILE_NAME":"serum_Neg_CN_30A2A_M.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Neg_CN_30A2B_M",
"Factors":{"Experimental factor":"Conventionally-raised (CONV-R)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Male","RAW_FILE_NAME":"serum_Neg_CN_30A2B_M.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Neg_CN_30A2C_M",
"Factors":{"Experimental factor":"Conventionally-raised (CONV-R)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Male","RAW_FILE_NAME":"serum_Neg_CN_30A2C_M.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Neg_CN_9A1C_F",
"Factors":{"Experimental factor":"Conventionally-raised (CONV-R)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Female","RAW_FILE_NAME":"serum_Neg_CN_9A1C_F.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Neg_CN_9A2A_F",
"Factors":{"Experimental factor":"Conventionally-raised (CONV-R)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Female","RAW_FILE_NAME":"serum_Neg_CN_9A2A_F.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Neg_CN_9A2B_F",
"Factors":{"Experimental factor":"Conventionally-raised (CONV-R)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Female","RAW_FILE_NAME":"serum_Neg_CN_9A2B_F.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Neg_CN_9A2C_F",
"Factors":{"Experimental factor":"Conventionally-raised (CONV-R)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Female","RAW_FILE_NAME":"serum_Neg_CN_9A2C_F.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Neg_CN_9A2D_F",
"Factors":{"Experimental factor":"Conventionally-raised (CONV-R)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Female","RAW_FILE_NAME":"serum_Neg_CN_9A2D_F.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Neg_CN_9A2E_F",
"Factors":{"Experimental factor":"Conventionally-raised (CONV-R)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Female","RAW_FILE_NAME":"serum_Neg_CN_9A2E_F.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Neg_GF_27F2",
"Factors":{"Experimental factor":"Germ-free (GF)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Female","RAW_FILE_NAME":"serum_Neg_GF_27F2.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Neg_GF_27F3",
"Factors":{"Experimental factor":"Germ-free (GF)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Female","RAW_FILE_NAME":"serum_Neg_GF_27F3.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Neg_GF_27F4",
"Factors":{"Experimental factor":"Germ-free (GF)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Female","RAW_FILE_NAME":"serum_Neg_GF_27F4.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Neg_GF_27F5",
"Factors":{"Experimental factor":"Germ-free (GF)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Female","RAW_FILE_NAME":"serum_Neg_GF_27F5.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Neg_GF_27F6",
"Factors":{"Experimental factor":"Germ-free (GF)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Female","RAW_FILE_NAME":"serum_Neg_GF_27F6.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Neg_GF_27F7",
"Factors":{"Experimental factor":"Germ-free (GF)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Female","RAW_FILE_NAME":"serum_Neg_GF_27F7.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Neg_GF_27M1",
"Factors":{"Experimental factor":"Germ-free (GF)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Male","RAW_FILE_NAME":"serum_Neg_GF_27M1.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Neg_GF_27M2",
"Factors":{"Experimental factor":"Germ-free (GF)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Male","RAW_FILE_NAME":"serum_Neg_GF_27M2.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Neg_GF_27M5",
"Factors":{"Experimental factor":"Germ-free (GF)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Male","RAW_FILE_NAME":"serum_Neg_GF_27M5.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Neg_GF_27M7",
"Factors":{"Experimental factor":"Germ-free (GF)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Male","RAW_FILE_NAME":"serum_Neg_GF_27M7.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Neg_GF_27M8",
"Factors":{"Experimental factor":"Germ-free (GF)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Male","RAW_FILE_NAME":"serum_Neg_GF_27M8.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"serum_Neg_GF_27M9",
"Factors":{"Experimental factor":"Germ-free (GF)"},
"Additional sample data":{"Genotype":"C57BL/6","Gender":"Male","RAW_FILE_NAME":"serum_Neg_GF_27M9.mzXML"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Prior to sacrifice and sample harvest, all mice were observed under their original housing conditions for one week; animals were not considered if they exhibited significant signs of serious injury or morbidity (e.g. malocclusion or fight wounds). Upon euthanization in CO2 chambers, feces, bulk brain, and heart blood sera were harvested, snap-frozen, and stored in -80 ºC freezer before analysis.","SAMPLE_TYPE":"Blood (serum)","STORAGE_CONDITIONS":"-80℃"},

"TREATMENT":{"TREATMENT_SUMMARY":"Steady states only: C57BL/6 mouse littermates of ~7 weeks old raised under GF and conventional conditions were age-matched upon selection for sacrifice and analyses, resulting in a final total of 24 mice, including 12 GF mice and 12 SPF CONV-R mice with 6 males and 6 females included in each. The animals were raised under the following conditions: 22ºC, 40-70% humidity, and a daily 12:12 hour light-dark cycle. For dietary administration, we consistently fed all mice the same purified (and sterile) standard rodent diets and provided tap water ad libitum."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Fecal matter, blood sera, and brain tissues (of the cerebral cortical region) were aliquoted and extracted for metabolome analyses. To maximize coverage and throughput, extraction procedures were kept as simple and non-selective as can be.","SAMPLEPREP_PROTOCOL_FILENAME":"Protocol_sample_extraction.docx"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"UHPLC reverse phase C18 chromatography","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo Vanquish","COLUMN_NAME":"Waters Acquity BEH HSS T3 (100 x 2.1mm, 1.8um)","FLOW_GRADIENT":"2% B, 0-1 min; 2% to 15% B, 1-3 min; 15% to 50% B, 3-6 min; 50% to 98% B, 6-7.5 min; 98% B, 7.5-11.5 min; 98% to 2% B, 11.5-11.6 min; 2% B, 11.6-15 min","FLOW_RATE":"0.4 mL/min","COLUMN_TEMPERATURE":"40","SOLVENT_A":"0.1% formic acid in water","SOLVENT_B":"0.1% formic acid in acetonitrile"},

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

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"fullscan XCMS Online for data processing","MS_RESULTS_FILE":"ST001757_AN002862_Results.txt UNITS:Peak intensity (area) Has m/z:Yes Has RT:Yes RT units:Minutes"}

}