#METABOLOMICS WORKBENCH araskind_20191211_122141 DATATRACK_ID:1866 STUDY_ID:ST001287 ANALYSIS_ID:AN002147 PROJECT_ID:PR000869
VERSION             	1
CREATED_ON             	December 17, 2019, 12:59 pm
#PROJECT
PR:PROJECT_TITLE                 	Luminal succinate in UC-HMA (human microbiota-associated) mice.
PR:PROJECT_TYPE                  	MS analysis
PR:PROJECT_SUMMARY               	Luminal succinate level in UC-HMA (UC patient derived microbiota colonized HMA)
PR:PROJECT_SUMMARY               	mice, C. difficile infection susceptible mice. Patients with ulcerative colitis
PR:PROJECT_SUMMARY               	(UC) are known to be at higher risk for Clostridium difficile (C. difficile)
PR:PROJECT_SUMMARY               	infection (CDI), and CDI in UC patients is recognized as a major clinical
PR:PROJECT_SUMMARY               	problem because it worsens UC outcome. In order to assess the role of gut
PR:PROJECT_SUMMARY               	dysbiosis, seen in UC patients, we have established a human
PR:PROJECT_SUMMARY               	microbiota-associated mouse model in which germ-free mice are colonized with gut
PR:PROJECT_SUMMARY               	microbiota from UC patients. Utilizing this model, we found that UC microbiota
PR:PROJECT_SUMMARY               	colonized HMA mice (UC-HMA mice) were susceptible to CDI. To address the
PR:PROJECT_SUMMARY               	mechanism by which UC-HMA mice are unable to acquire the colonization resistance
PR:PROJECT_SUMMARY               	against C. difficile, we analyzed the luminal metabolites in UC-HMA mice,
PR:PROJECT_SUMMARY               	especially in succinate which is a crucial metabolite doe the growth of C.
PR:PROJECT_SUMMARY               	difficile.
PR:INSTITUTE                     	University of Michigan
PR:DEPARTMENT                    	Internal Medicine-Gastroenterology
PR:LABORATORY                    	Kamada Lab
PR:LAST_NAME                     	Kamada
PR:FIRST_NAME                    	Nobuhiko
PR:ADDRESS                       	Ann Arbor, MI
PR:EMAIL                         	nkamada@umich.edu
PR:PHONE                         	734-763-2142
#STUDY
ST:STUDY_TITLE                   	Luminal succinate in UC-HMA (human microbiota-associated) mice.
ST:STUDY_TYPE                    	MS analysis
ST:STUDY_SUMMARY                 	Patients with ulcerative colitis (UC) are known to be at higher risk for
ST:STUDY_SUMMARY                 	Clostridium difficile (C. difficile) infection (CDI), and CDI in UC patients is
ST:STUDY_SUMMARY                 	recognized as a major clinical problem because it worsens UC outcome. In order
ST:STUDY_SUMMARY                 	to assess the role of gut dysbiosis, seen in UC patients, we have established a
ST:STUDY_SUMMARY                 	human microbiota-associated mouse model in which germ-free mice are colonized
ST:STUDY_SUMMARY                 	with gut microbiota from UC patients. Utilizing this model, we found that UC
ST:STUDY_SUMMARY                 	microbiota colonized HMA mice (UC-HMA mice) were susceptible to CDI. To address
ST:STUDY_SUMMARY                 	the mechanism by which UC-HMA mice are unable to acquire the colonization
ST:STUDY_SUMMARY                 	resistance against C. difficile, we analyzed the luminal metabolites in UC-HMA
ST:STUDY_SUMMARY                 	mice, especially in succinate which is a crucial metabolite doe the growth of C.
ST:STUDY_SUMMARY                 	difficile.
ST:INSTITUTE                     	University of Michigan
ST:DEPARTMENT                    	Biomedical Research Core Facilities
ST:LABORATORY                    	Metabolomics core
ST:LAST_NAME                     	Kachman
ST:FIRST_NAME                    	Maureen
ST:ADDRESS                       	Ann Arbor, MI
ST:EMAIL                         	mkachman@med.umich.edu
ST:PHONE                         	734-232-0842
ST:NUM_GROUPS                    	63
ST:TOTAL_SUBJECTS                	3
#SUBJECT
SU:SUBJECT_TYPE                  	Mammal
SU:SUBJECT_SPECIES               	Mus musculus
SU:TAXONOMY_ID                   	10090
SU:GENOTYPE_STRAIN               	UC-hGB
#SUBJECT_SAMPLE_FACTORS:         	SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Raw file names and additional sample data
SUBJECT_SAMPLE_FACTORS           	SU0024964	S00034622	Replication:#1 | Treatment:Ctrl	RAW_FILE_NAME=2018-04-20_027.d
SUBJECT_SAMPLE_FACTORS           	SU0024965	S00034623	Replication:#1 | Treatment:Ctrl	RAW_FILE_NAME=2018-04-20_036.d
SUBJECT_SAMPLE_FACTORS           	SU0024966	S00034624	Replication:#1 | Treatment:Ctrl	RAW_FILE_NAME=2018-04-20_025.d
SUBJECT_SAMPLE_FACTORS           	SU0024967	S00034625	Replication:#1 | Treatment:SuccinateConsumingBacteria	RAW_FILE_NAME=2018-04-20_017.d
SUBJECT_SAMPLE_FACTORS           	SU0024968	S00034626	Replication:#1 | Treatment:SuccinateConsumingBacteria	RAW_FILE_NAME=2018-04-20_018.d
SUBJECT_SAMPLE_FACTORS           	SU0024969	S00034627	Replication:#2 | Treatment:Ctrl	RAW_FILE_NAME=2018-04-20_038.d
SUBJECT_SAMPLE_FACTORS           	SU0024970	S00034628	Replication:#2 | Treatment:Ctrl	RAW_FILE_NAME=2018-04-20_016.d
SUBJECT_SAMPLE_FACTORS           	SU0024971	S00034629	Replication:#2 | Treatment:Ctrl	RAW_FILE_NAME=2018-04-20_021.d
SUBJECT_SAMPLE_FACTORS           	SU0024972	S00034630	Replication:#2 | Treatment:Ctrl	RAW_FILE_NAME=2018-04-20_023.d
SUBJECT_SAMPLE_FACTORS           	SU0024973	S00034631	Replication:#2 | Treatment:Ctrl	RAW_FILE_NAME=2018-04-20_019.d
SUBJECT_SAMPLE_FACTORS           	SU0024974	S00034632	Replication:#2 | Treatment:SuccinateConsumingBacteria	RAW_FILE_NAME=2018-04-20_033.d
SUBJECT_SAMPLE_FACTORS           	SU0024975	S00034633	Replication:#2 | Treatment:SuccinateConsumingBacteria	RAW_FILE_NAME=2018-04-20_012.d
SUBJECT_SAMPLE_FACTORS           	SU0024976	S00034634	Replication:#2 | Treatment:SuccinateConsumingBacteria	RAW_FILE_NAME=2018-04-20_028.d
SUBJECT_SAMPLE_FACTORS           	SU0024977	S00034635	Replication:#2 | Treatment:SuccinateConsumingBacteria	RAW_FILE_NAME=2018-04-20_041.d
SUBJECT_SAMPLE_FACTORS           	SU0024978	S00034636	Replication:#2 | Treatment:SuccinateConsumingBacteria	RAW_FILE_NAME=2018-04-20_010.d
SUBJECT_SAMPLE_FACTORS           	SU0024979	S00034637	Replication:#3 | Treatment:Ctrl	RAW_FILE_NAME=2018-04-20_029.d
SUBJECT_SAMPLE_FACTORS           	SU0024980	S00034638	Replication:#3 | Treatment:Ctrl	RAW_FILE_NAME=2018-04-20_034.d
SUBJECT_SAMPLE_FACTORS           	SU0024981	S00034639	Replication:#3 | Treatment:Ctrl	RAW_FILE_NAME=2018-04-20_035.d
SUBJECT_SAMPLE_FACTORS           	SU0024982	S00034640	Replication:#3 | Treatment:Ctrl	RAW_FILE_NAME=2018-04-20_030.d
SUBJECT_SAMPLE_FACTORS           	SU0024983	S00034641	Replication:#3 | Treatment:Ctrl	RAW_FILE_NAME=2018-04-20_039.d
SUBJECT_SAMPLE_FACTORS           	SU0024984	S00034642	Replication:#3 | Treatment:Ctrl	RAW_FILE_NAME=2018-04-20_014.d
SUBJECT_SAMPLE_FACTORS           	SU0024985	S00034643	Replication:#3 | Treatment:Ctrl	RAW_FILE_NAME=2018-04-20_026.d
SUBJECT_SAMPLE_FACTORS           	SU0024986	S00034644	Replication:#3 | Treatment:SuccinateConsumingBacteria	RAW_FILE_NAME=2018-04-20_037.d
SUBJECT_SAMPLE_FACTORS           	SU0024987	S00034645	Replication:#3 | Treatment:SuccinateConsumingBacteria	RAW_FILE_NAME=2018-04-20_013.d
SUBJECT_SAMPLE_FACTORS           	SU0024988	S00034646	Replication:#3 | Treatment:SuccinateConsumingBacteria	RAW_FILE_NAME=2018-04-20_040.d
SUBJECT_SAMPLE_FACTORS           	SU0024989	S00034647	Replication:#3 | Treatment:SuccinateConsumingBacteria	RAW_FILE_NAME=2018-04-20_024.d
SUBJECT_SAMPLE_FACTORS           	SU0024990	S00034648	Replication:#3 | Treatment:SuccinateConsumingBacteria	RAW_FILE_NAME=2018-04-20_015.d
SUBJECT_SAMPLE_FACTORS           	SU0024991	S00034649	Replication:#3 | Treatment:SuccinateConsumingBacteria	RAW_FILE_NAME=2018-04-20_011.d
SUBJECT_SAMPLE_FACTORS           	SU0024992	S00034650	Replication:#3 | Treatment:SuccinateConsumingBacteria	RAW_FILE_NAME=2018-04-20_032.d
SUBJECT_SAMPLE_FACTORS           	SU0024993	S00034651	Replication:#3 | Treatment:SuccinateConsumingBacteria	RAW_FILE_NAME=2018-04-20_022.d
#COLLECTION
CO:COLLECTION_SUMMARY            	Mouse feces
CO:SAMPLE_TYPE                   	Feces
#TREATMENT
TR:TREATMENT_SUMMARY             	None
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	2018-4-20_Succinate_fecal_EX00837.docx
#CHROMATOGRAPHY
CH:CHROMATOGRAPHY_TYPE           	HILIC
CH:INSTRUMENT_NAME               	Agilent Q-TOF 6520
CH:COLUMN_NAME                   	Phenomenex Luna NH2, 1mm ID
CH:METHODS_FILENAME              	002-HILIC-27min-1mm-flatInsert_-_A2B2.m.zip
#ANALYSIS
AN:ANALYSIS_TYPE                 	MS
#MS
MS:INSTRUMENT_NAME               	Agilent 6520 QTOF
MS:INSTRUMENT_TYPE               	QTOF
MS:MS_TYPE                       	ESI
MS:ION_MODE                      	NEGATIVE
MS:MS_COMMENTS                   	Agilent Quant V8 was used for data analysis
#MS_METABOLITE_DATA
MS_METABOLITE_DATA:UNITS	pmol/mg
MS_METABOLITE_DATA_START
Samples	S00034622	S00034631	S00034632	S00034633	S00034634	S00034635	S00034636	S00034637	S00034638	S00034639	S00034640	S00034623	S00034641	S00034642	S00034643	S00034644	S00034645	S00034646	S00034647	S00034648	S00034649	S00034650	S00034624	S00034651	S00034625	S00034626	S00034627	S00034628	S00034629	S00034630
Factors	Replication:#1 | Treatment:Ctrl	Replication:#2 | Treatment:Ctrl	Replication:#2 | Treatment:SuccinateConsumingBacteria	Replication:#2 | Treatment:SuccinateConsumingBacteria	Replication:#2 | Treatment:SuccinateConsumingBacteria	Replication:#2 | Treatment:SuccinateConsumingBacteria	Replication:#2 | Treatment:SuccinateConsumingBacteria	Replication:#3 | Treatment:Ctrl	Replication:#3 | Treatment:Ctrl	Replication:#3 | Treatment:Ctrl	Replication:#3 | Treatment:Ctrl	Replication:#1 | Treatment:Ctrl	Replication:#3 | Treatment:Ctrl	Replication:#3 | Treatment:Ctrl	Replication:#3 | Treatment:Ctrl	Replication:#3 | Treatment:SuccinateConsumingBacteria	Replication:#3 | Treatment:SuccinateConsumingBacteria	Replication:#3 | Treatment:SuccinateConsumingBacteria	Replication:#3 | Treatment:SuccinateConsumingBacteria	Replication:#3 | Treatment:SuccinateConsumingBacteria	Replication:#3 | Treatment:SuccinateConsumingBacteria	Replication:#3 | Treatment:SuccinateConsumingBacteria	Replication:#1 | Treatment:Ctrl	Replication:#3 | Treatment:SuccinateConsumingBacteria	Replication:#1 | Treatment:SuccinateConsumingBacteria	Replication:#1 | Treatment:SuccinateConsumingBacteria	Replication:#2 | Treatment:Ctrl	Replication:#2 | Treatment:Ctrl	Replication:#2 | Treatment:Ctrl	Replication:#2 | Treatment:Ctrl
SUCCINIC ACID	343.63	605.50	352.73	229.49	250.39	306.44	197.47	404.17	422.75	229.54	307.26	294.50	430.40	340.53	327.97	121.54	242.78	132.50	296.97	205.91	283.22	268.98	389.46	545.91	128.83	150.09	380.83	395.79	589.89	458.74
MS_METABOLITE_DATA_END
#METABOLITES
METABOLITES_START
metabolite_name	quantified m/z	retention index	PubChem ID	KEGG ID	other_id	other_id_type	id_confidence	ri_type	inchi_key
SUCCINIC ACID	117.0188	14.46	1110		HMDB0000254	HMDB	1	Time, min	KDYFGRWQOYBRFD-UHFFFAOYSA-N
METABOLITES_END
#END