#METABOLOMICS WORKBENCH Hiroki_Murai_20230922_073218 DATATRACK_ID:4330 STUDY_ID:ST002879 ANALYSIS_ID:AN004718 PROJECT_ID:PR001800
VERSION             	1
CREATED_ON             	September 27, 2023, 11:23 am
#PROJECT
PR:PROJECT_TITLE                 	Metabolomic profiles in P. gingivalis cells treated with curcumin
PR:PROJECT_SUMMARY               	Metabolomics data for Porphyromonas gingivalis in the presence or absence of
PR:PROJECT_SUMMARY               	curcumin
PR:INSTITUTE                     	Osaka University
PR:DEPARTMENT                    	Graduate School of Dentistry
PR:LABORATORY                    	Joint Research Laboratory for Advanced Oral Environmental Science (SARAYA)
PR:LAST_NAME                     	Murai
PR:FIRST_NAME                    	Hiroki
PR:ADDRESS                       	1-8 Yamadaoka, Suita, Osaka, 565-0871, Japan
PR:EMAIL                         	murai-h@saraya.com
PR:PHONE                         	+81-6-6879-2922
#STUDY
ST:STUDY_TITLE                   	Metabolomic profiles in P. gingivalis treated with curcumin
ST:STUDY_SUMMARY                 	Curcumin, a major constituent of turmeric rhizomes (Curcuma-longa), has been
ST:STUDY_SUMMARY                 	reported to have various functions, including anti-oxidant, anti-inflammatory,
ST:STUDY_SUMMARY                 	anti-tumor, and anti-bacterial effects. Thus, curcumin is expected to effective
ST:STUDY_SUMMARY                 	for the prevention of periodontal disease. We previously showed that curcumin
ST:STUDY_SUMMARY                 	markedly inhibited the growth of P. gingivalis, and prevented biofilm formation
ST:STUDY_SUMMARY                 	as well as bacterial protease activity at a low concentration. Nevertheless,
ST:STUDY_SUMMARY                 	negligible bactericidal effects against some oral bacterial species such as
ST:STUDY_SUMMARY                 	Aggregatibacter actinomycetemcomitans and Streptococcus mitis, were found in
ST:STUDY_SUMMARY                 	order investigations. These reports suggest that curcumin exhibit
ST:STUDY_SUMMARY                 	species-specific antimicrobial activities, the molecular basis remains to be
ST:STUDY_SUMMARY                 	elucidated. This metabolomic analysis was conducted to investigate the mechanism
ST:STUDY_SUMMARY                 	of the antimicrobial action of curcumin toward P. gingivalis.
ST:INSTITUTE                     	Osaka University
ST:DEPARTMENT                    	Graduate School of Dentistry
ST:LABORATORY                    	Joint Research Laboratory for Advanced Oral Environmental Science (SARAYA)
ST:LAST_NAME                     	Murai
ST:FIRST_NAME                    	Hiroki
ST:ADDRESS                       	1-8 Yamadaoka, Suita, Osaka, 565-0871, Japan
ST:EMAIL                         	murai-h@saraya.com
ST:PHONE                         	+81-6-6879-2922
#SUBJECT
SU:SUBJECT_TYPE                  	Bacteria
SU:SUBJECT_SPECIES               	Porphyromonas gingivalis ATCC33277
SU:TAXONOMY_ID                   	431947
SU:SPECIES_GROUP                 	Microorganism
#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           	-	Control1	Factor:incubated in TSB	
SUBJECT_SAMPLE_FACTORS           	-	Control2	Factor:incubated in TSB	
SUBJECT_SAMPLE_FACTORS           	-	Control3	Factor:incubated in TSB	
SUBJECT_SAMPLE_FACTORS           	-	C1	Factor:incubated in TSB+Curcumin(10mg/L)	
SUBJECT_SAMPLE_FACTORS           	-	C2	Factor:incubated in TSB+Curcumin(10mg/L)	
SUBJECT_SAMPLE_FACTORS           	-	C3	Factor:incubated in TSB+Curcumin(10mg/L)	
#COLLECTION
CO:COLLECTION_SUMMARY            	Incubated cells were collected by centrifugation at 4℃. Collected cells were
CO:COLLECTION_SUMMARY            	washed with Milli-Q water and re-collected by centrifugation at 4℃. Bacterial
CO:COLLECTION_SUMMARY            	pellets (>5E+09 cells) were immediately fixed by methanol containing 5 µM
CO:COLLECTION_SUMMARY            	internal standard.
CO:SAMPLE_TYPE                   	Bacterial cells
CO:STORAGE_CONDITIONS            	-80℃
#TREATMENT
TR:TREATMENT_SUMMARY             	P. gingivalis cells were incubated anaerobically with TSB(DMSO0.1%) in the
TR:TREATMENT_SUMMARY             	presence or absence of 1mg/L of curcumin at 37℃ for 24h
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	Samples were stirred with 2000μL chloroform and 800 μL of Milli-Q water, and
SP:SAMPLEPREP_SUMMARY            	centrifuged at 4℃. After centrifugation, the aqueous layer is filtered by
SP:SAMPLEPREP_SUMMARY            	ultrafiltration tube. Filtrate samples were dried and dissolved in 25μL Milli-Q
SP:SAMPLEPREP_SUMMARY            	water.
#CHROMATOGRAPHY
CH:CHROMATOGRAPHY_TYPE           	CE
CH:INSTRUMENT_NAME               	Agilent CE
CH:COLUMN_NAME                   	Agilent Fused silica capillary (80cm x 50um)
CH:SOLVENT_A                     	none
CH:SOLVENT_B                     	none
CH:FLOW_GRADIENT                 	none
CH:FLOW_RATE                     	none
CH:COLUMN_TEMPERATURE            	none
#ANALYSIS
AN:ANALYSIS_TYPE                 	MS
#MS
MS:INSTRUMENT_NAME               	Agilent CE-TOFMS
MS:INSTRUMENT_TYPE               	TOF
MS:MS_TYPE                       	ESI
MS:ION_MODE                      	NEGATIVE
MS:MS_COMMENTS                   	Capillary : Fused silica capillary 50 μm × 80 cm Run buffer/Rinse buffer :
MS:MS_COMMENTS                   	Anion Buffer Solution (p/n : I3302-1023) Sample injection:Pressure injection
MS:MS_COMMENTS                   	50mbar, 10sec CE Voltage:Positive, 30kV MS scan range: m/z 50-1000
MS:CAPILLARY_VOLTAGE             	3500V
#MS_METABOLITE_DATA
MS_METABOLITE_DATA:UNITS	Relative area
MS_METABOLITE_DATA_START
Samples	Control1	Control2	Control3	C1	C2	C3
Factors	Factor:incubated in TSB	Factor:incubated in TSB	Factor:incubated in TSB	Factor:incubated in TSB+Curcumin(10mg/L)	Factor:incubated in TSB+Curcumin(10mg/L)	Factor:incubated in TSB+Curcumin(10mg/L)
10-Hydroxydecanoic acid	N.D.	N.D.	9.9E-05	N.D.	8.5E-05	9.0E-05
2-Hydroxypyridine	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
2-Phosphoglyceric acid	1.7E-03	1.4E-03	1.8E-03	1.1E-03	1.1E-03	1.3E-03
3-Hydroxybutyric acid	N.D.	9.2E-04	N.D.	N.D.	8.1E-04	7.9E-04
3-Hydroxyphenylacetic acid/4-Hydroxyphenylacetic acid/p-Anisic acid/Mandelic acid/o-Hydroxyphenylacetic acid	2.9E-03	2.5E-03	3.6E-03	7.7E-04	9.8E-04	6.4E-04
3-Phenylpropionic acid	6.7E-03	3.5E-03	3.7E-03	5.8E-03	1.2E-03	5.8E-03
3-Phosphoglyceric acid	3.2E-03	2.0E-03	2.9E-03	1.6E-03	3.0E-03	2.1E-03
4-Pyridoxic acid	N.D.	N.D.	N.D.	6.5E-05	1.1E-04	5.0E-05
5-Ketocaproic acid	1.4E-03	8.2E-04	1.0E-03	1.1E-03	1.1E-03	1.4E-03
Acetyl-CoA	1.3E-03	1.0E-03	2.1E-03	3.5E-04	8.5E-04	5.2E-04
Adenosine 3',5'-diphosphate	N.D.	N.D.	7.6E-05	N.D.	1.0E-04	9.7E-05
ADP	9.5E-03	8.5E-03	1.0E-02	7.9E-03	9.1E-03	8.3E-03
ADP-ribose	5.8E-03	6.0E-03	4.8E-03	2.8E-03	1.2E-03	1.4E-03
AMP	7.2E-03	6.6E-03	7.3E-03	4.5E-03	4.1E-03	3.7E-03
Ascorbate 2-phosphate	1.2E-04	1.3E-04	1.2E-04	1.7E-04	N.D.	6.3E-05
ATP	4.2E-03	3.5E-03	4.8E-03	2.0E-03	3.0E-03	2.4E-03
Butyric acid/Isobutyric acid	1.1E-02	7.7E-03	1.4E-02	3.6E-03	6.0E-03	4.1E-03
Capric acid	1.4E-03	1.3E-03	1.4E-03	1.1E-03	1.0E-03	1.2E-03
Caproic acid	2.7E-03	1.8E-03	2.3E-03	2.1E-03	2.6E-03	2.7E-03
Caprylic acid	9.1E-04	7.7E-04	8.1E-04	7.0E-04	7.9E-04	9.3E-04
CDP	1.1E-03	9.8E-04	1.4E-03	2.6E-04	4.1E-04	3.5E-04
Citric acid	N.D.	N.D.	1.7E-03	N.D.	1.5E-03	N.D.
CMP	1.4E-03	1.5E-03	1.7E-03	7.8E-04	6.6E-04	6.4E-04
Coenzyme A	2.6E-04	2.6E-04	3.9E-04	N.D.	1.5E-04	N.D.
Crotonic acid	1.1E-03	N.D.	7.9E-04	1.4E-03	1.3E-03	1.6E-03
CTP	2.0E-03	1.8E-03	2.6E-03	5.8E-04	1.2E-03	9.6E-04
Cysteine-S-sulfate	N.D.	N.D.	9.3E-05	N.D.	N.D.	N.D.
dADP	4.2E-04	3.0E-04	3.7E-04	2.5E-04	2.4E-04	2.0E-04
dAMP	2.9E-04	2.5E-04	3.3E-04	1.3E-04	1.2E-04	1.4E-04
dATP	6.3E-04	4.2E-04	7.0E-04	9.6E-05	2.4E-04	2.1E-04
dCMP	1.0E-04	6.1E-05	9.8E-05	N.D.	N.D.	N.D.
dGDP	1.0E-04	2.4E-04	2.2E-04	1.1E-04	1.8E-04	1.6E-04
dGTP	2.7E-04	2.0E-04	3.4E-04	1.4E-04	1.6E-04	1.4E-04
DL-O-Phosphoserine	8.2E-04	7.0E-04	9.1E-04	1.3E-04	2.4E-04	1.9E-04
dTDP	1.4E-03	1.2E-03	1.5E-03	6.0E-04	7.2E-04	6.5E-04
dTDP-glucose	1.1E-04	N.D.	1.6E-04	N.D.	1.7E-04	1.3E-04
dTMP	2.3E-03	2.2E-03	1.8E-03	3.6E-03	1.4E-03	1.4E-03
dTTP	2.8E-03	2.5E-03	2.9E-03	8.6E-04	1.3E-03	9.6E-04
Erythrose 4-phosphate	9.5E-04	7.0E-04	8.8E-04	4.3E-04	4.6E-04	4.2E-04
FAD	1.0E-02	8.9E-03	1.1E-02	5.0E-03	6.1E-03	5.4E-03
FMN	2.5E-03	2.3E-03	2.6E-03	1.3E-03	1.5E-03	1.3E-03
Formiminoglutamic acid	3.0E-03	2.6E-03	3.5E-03	1.9E-03	2.1E-03	2.4E-03
Fructose 1,6-diphosphate	1.9E-04	1.1E-04	2.1E-04	N.D.	N.D.	N.D.
Fructose 6-phosphate	2.1E-03	1.5E-03	2.0E-03	1.0E-03	1.1E-03	1.2E-03
GDP	3.4E-03	2.5E-03	3.8E-03	1.4E-03	1.8E-03	1.7E-03
GDP-L-fucose/ADP-glucose	3.1E-04	2.8E-04	3.4E-04	3.7E-04	3.6E-04	3.9E-04
Gluconic acid	2.1E-04	1.4E-04	2.5E-04	N.D.	2.8E-04	1.7E-04
Glucosamine 6-phosphate	2.0E-04	N.D.	1.8E-04	N.D.	N.D.	N.D.
Glucose 1-phosphate	4.5E-04	2.9E-04	4.9E-04	3.1E-04	2.6E-04	3.1E-04
Glucose 6-phosphate	6.0E-03	4.2E-03	6.2E-03	2.9E-03	2.9E-03	3.1E-03
Glucurone	N.D.	N.D.	N.D.	2.5E-04	N.D.	3.1E-04
Glyceric acid	3.1E-03	2.2E-03	2.6E-03	2.3E-03	2.9E-03	2.6E-03
GMP	1.2E-03	1.2E-03	1.4E-03	4.0E-04	5.2E-04	5.2E-04
GTP	4.9E-03	3.5E-03	5.2E-03	1.4E-03	2.3E-03	2.1E-03
Heptylic acid	1.4E-03	8.1E-04	1.3E-03	1.2E-03	1.5E-03	1.6E-03
IMP	3.3E-04	3.0E-04	3.6E-04	1.2E-04	1.7E-04	1.3E-04
Isobutyryl-CoA	1.4E-02	1.2E-02	2.1E-02	3.0E-03	5.5E-03	4.0E-03
Isovaleric acid/DL-2-Methylbutyric Acid/Valeric acid	1.6E-02	1.1E-02	1.9E-02	5.5E-03	1.0E-02	7.4E-03
Lactic acid	3.1E-03	2.4E-03	2.3E-03	2.2E-03	1.8E-03	2.8E-03
Lauric acid	1.1E-02	1.1E-02	1.3E-02	9.2E-03	9.0E-03	1.1E-02
Leucinic acid	N.D.	1.3E-04	N.D.	1.1E-04	N.D.	N.D.
Malic acid	1.1E-03	9.1E-04	1.1E-03	N.D.	N.D.	N.D.
Methyl sulfate	1.8E-04	N.D.	2.6E-04	N.D.	N.D.	N.D.
myo-Inositol 2-phosphate	N.D.	1.5E-04	2.9E-04	1.7E-04	2.2E-04	1.8E-04
Myristic acid	7.7E-03	6.0E-03	7.7E-03	4.0E-03	4.3E-03	6.1E-03
Myristoleic acid	3.4E-04	3.6E-04	3.3E-04	2.3E-04	1.1E-04	2.5E-04
N-Acetyl-D-glucosamine 1-phosphate	1.3E-03	1.1E-03	1.5E-03	7.9E-04	9.7E-04	9.8E-04
N-Acetyl-glucosamine 6-phosphate	4.6E-03	4.1E-03	5.0E-03	2.1E-03	2.7E-03	2.7E-03
N-Acetylmuramic acid	2.1E-04	2.0E-04	2.2E-04	1.4E-04	1.0E-04	1.3E-04
NAD+	1.2E-01	1.0E-01	1.2E-01	4.9E-02	6.2E-02	5.2E-02
NADP+	1.1E-02	9.0E-03	1.1E-02	3.7E-03	5.7E-03	5.2E-03
Pelargonic acid	2.6E-03	1.7E-03	2.5E-03	2.4E-03	2.3E-03	2.6E-03
Phosphoenolpyruvic acid	3.9E-03	3.1E-03	4.0E-03	2.4E-03	3.0E-03	2.6E-03
ppGpp	4.5E-03	1.7E-03	4.2E-03	6.8E-04	4.5E-03	1.8E-03
Propionic acid	3.3E-03	N.D.	4.2E-03	2.3E-03	3.0E-03	3.3E-03
Propionyl CoA	1.6E-03	1.5E-03	3.0E-03	5.3E-04	1.4E-03	1.0E-03
p-Toluic acid/o-Toluic acid/m-Toluic acid	1.8E-02	1.2E-02	1.8E-02	1.1E-02	1.4E-02	1.7E-02
Pyroglutamic acid	8.2E-03	7.2E-03	9.8E-03	4.6E-03	5.3E-03	4.2E-03
Quinic acid	5.5E-04	5.0E-04	3.7E-04	4.2E-04	3.6E-04	4.4E-04
Quinolinic acid	1.4E-04	1.2E-04	2.1E-04	N.D.	N.D.	N.D.
Retinoic acid	N.D.	N.D.	9.9E-05	N.D.	5.5E-05	7.4E-05
Ribose 5-phosphate	1.7E-04	N.D.	1.5E-04	N.D.	N.D.	9.4E-05
Ribulose 5-phosphate	1.1E-03	8.0E-04	8.2E-04	4.2E-04	4.3E-04	5.6E-04
Sedoheptulose 7-phosphate	4.3E-03	3.8E-03	4.7E-03	2.3E-03	2.2E-03	2.4E-03
sn-Glycero-3-phosphate	4.6E-04	3.7E-04	3.9E-04	2.6E-04	2.5E-04	2.3E-04
Succinic acid	3.7E-03	3.2E-03	3.8E-03	1.4E-03	N.D.	N.D.
Terephthalic acid	4.4E-04	3.1E-04	3.5E-04	3.4E-04	2.6E-04	3.4E-04
Thiamine diphosphate	7.4E-03	6.3E-03	1.3E-02	3.4E-03	1.0E-02	7.5E-03
Thiamine triphosphate	2.7E-04	2.1E-04	3.8E-04	1.1E-04	3.6E-04	2.3E-04
trans-Ferulic acid	N.D.	N.D.	N.D.	7.7E-04	4.9E-04	6.9E-04
trans-o-Coumaric acid/cis-p-Coumaric acid	N.D.	N.D.	N.D.	1.4E-04	1.1E-04	1.4E-04
Trehalose 6-phosphate	1.1E-04	9.5E-05	8.8E-05	N.D.	1.0E-04	9.2E-05
Tridecylic acid	1.1E-03	1.0E-03	1.1E-03	6.4E-04	6.7E-04	8.4E-04
UDP	4.1E-03	3.7E-03	4.7E-03	1.8E-03	3.0E-03	2.7E-03
UDP-glucuronic acid	2.7E-03	2.3E-03	3.4E-03	1.5E-03	1.7E-03	1.9E-03
UMP	4.5E-03	4.2E-03	5.1E-03	2.3E-03	2.7E-03	2.6E-03
Undecylic acid	1.1E-03	1.1E-03	1.1E-03	3.8E-04	3.1E-04	6.3E-04
UTP	3.5E-03	3.1E-03	4.3E-03	1.6E-03	2.8E-03	2.6E-03
Vanillic acid	2.4E-04	2.3E-04	2.2E-04	N.D.	4.8E-05	N.D.
XA0002	2.3E-03	2.3E-03	2.8E-03	8.6E-04	1.0E-03	6.7E-04
XA0017	N.D.	N.D.	N.D.	N.D.	N.D.	8.0E-05
XA0033	1.2E-04	1.5E-04	N.D.	N.D.	6.8E-05	N.D.
XA0080	1.6E-04	N.D.	1.3E-04	1.6E-04	N.D.	1.8E-04
Xanthosine	2.0E-04	1.9E-04	2.0E-04	1.6E-04	1.5E-04	1.4E-04
β-Hydro3-Hydroxyisovaleric acid	1.1E-03	4.0E-04	1.3E-03	1.3E-03	1.4E-03	1.5E-03
MS_METABOLITE_DATA_END
#METABOLITES
METABOLITES_START
metabolite_name	Pubchem ID	m/z
10-Hydroxydecanoic acid	74300	187.134
2-Hydroxypyridine	8871	94.029
2-Phosphoglyceric acid	439278	184.985
3-Hydroxybutyric acid	441	103.040
3-Hydroxyphenylacetic acid/4-Hydroxyphenylacetic acid/p-Anisic acid/Mandelic acid/o-Hydroxyphenylacetic acid	12122/127/7478/11914/11970	151.040
3-Phenylpropionic acid	107	149.061
3-Phosphoglyceric acid	439183	184.986
4-Pyridoxic acid	6723	182.046
5-Ketocaproic acid	18407	129.056
Acetyl-CoA	444493	403.554
Adenosine 3',5'-diphosphate	159296	426.021
ADP	6022	426.022
ADP-ribose	445794	558.064
AMP	6083	346.054
Ascorbate 2-phosphate	131711663	254.993
ATP	5957	505.989
Butyric acid/Isobutyric acid	264/6590	87.045
Capric acid	2969	171.139
Caproic acid	8892	115.076
Caprylic acid	379	143.108
CDP	6132	402.012
Citric acid	311	191.020
CMP	6131	322.047
Coenzyme A	87642	382.551
Crotonic acid	637090	85.029
CTP	6176	481.978
Cysteine-S-sulfate	115015	199.971
dADP	188966	410.028
dAMP	12599	330.061
dATP	15993	489.995
dCMP	13945	306.052
dGDP	439220	426.021
dGTP	65103	505.988
DL-O-Phosphoserine	68841	184.003
dTDP	164628	401.017
dTDP-glucose	443210	563.073
dTMP	9700	321.050
dTTP	64968	480.983
Erythrose 4-phosphate	122357	199.004
FAD	643975	391.571
FMN	643976	455.098
Formiminoglutamic acid	439233	173.057
Fructose 1,6-diphosphate	172313	338.988
Fructose 6-phosphate	603	259.022
GDP	8977	442.017
GDP-L-fucose/ADP-glucose	10918995/16500	588.078
Gluconic acid	10690	195.050
Glucosamine 6-phosphate	440997	258.036
Glucose 1-phosphate	65533	259.023
Glucose 6-phosphate	5958	259.023
Glucurone	92283	175.025
Glyceric acid	439194	105.019
GMP	6804	362.049
GTP	6830	521.987
Heptylic acid	8094	129.092
IMP	8582	347.038
Isobutyryl-CoA	3036931	417.571
Isovaleric acid/DL-2-Methylbutyric Acid/Valeric acid	10430/8314/7991	101.061
Lactic acid	612	89.024
Lauric acid	3893	199.171
Leucinic acid	439960	131.071
Malic acid	525	133.014
Methyl sulfate	6412	110.975
myo-Inositol 2-phosphate	160886	259.022
Myristic acid	11005	227.202
Myristoleic acid	5281119	225.187
N-Acetyl-D-glucosamine 1-phosphate	440272	300.049
N-Acetyl-glucosamine 6-phosphate	440996	300.048
N-Acetylmuramic acid	5462244	292.106
NAD+	5893	662.099
NADP+	5886	742.064
Pelargonic acid	8158	157.123
Phosphoenolpyruvic acid	1005	166.975
ppGpp	439450	300.470
Propionic acid	1032	73.029
Propionyl CoA	92753	410.564
p-Toluic acid/o-Toluic acid/m-Toluic acid	7470/8373/7418	135.046
Pyroglutamic acid	7405	128.035
Quinic acid	6508	191.056
Quinolinic acid	1066	166.014
Retinoic acid	444795	299.201
Ribose 5-phosphate	439167	229.012
Ribulose 5-phosphate	439184	229.012
Sedoheptulose 7-phosphate	165007	289.032
sn-Glycero-3-phosphate	439162	171.007
Succinic acid	1110	117.019
Terephthalic acid	7489	165.019
Thiamine diphosphate	1132	423.032
Thiamine triphosphate	511	502.993
trans-Ferulic acid	445858	193.051
trans-o-Coumaric acid/cis-p-Coumaric acid	637540/637542	163.040
Trehalose 6-phosphate	122336	421.075
Tridecylic acid	12530	213.186
UDP	6031	402.995
UDP-glucuronic acid	17473	579.025
UMP	6030	323.027
Undecylic acid	8180	185.155
UTP	6133	482.962
Vanillic acid	8468	167.035
XA0002	-	110.985
XA0017	-	186.113
XA0033	-	242.078
XA0080	440992	243.028
Xanthosine	64959	283.067
β-Hydro3-Hydroxyisovaleric acid	69362	117.056
METABOLITES_END
#END