Summary of Study ST000496

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000373. The data can be accessed directly via it's Project DOI: 10.21228/M8TW22 This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

Study ID	ST000496
Study Title	Distinct signatures of dental plaque metabolic byproducts dictated by periodontal inflammatory status
Study Summary	Onset of chronic periodontitis is associated with an aberrant polymicrobial community, termed dysbiosis. Findings of a recent model of its etiology suggested that dysbiosis holds a conserved metabolic signature as an emergent property. The purpose of this study was to identify robust biomarkers for periodontal inflammation severity. Furthermore, we investigated disease-associated metabolic signatures of periodontal microbiota using a salivary metabolomics approach. Collection of whole saliva samples was performed before and after removal of supragingival plaque (debridement). Periodontal inflamed surface area (PISA) was employed as an indicator of periodontal inflammatory status. Based on multivariate analyses using pre-debridement salivary metabolomics data, we found that the metabolites associated with higher PISA included cadaverine and hydrocinnamate, while uric acid and ethanolamine were associated with lower PISA. Next, we focused on dental plaque metabolic byproducts by selecting significantly decreased salivary metabolites following debridement. Metabolite set enrichment analysis revealed that polyamine metabolism, arginine and proline metabolism, butyric acid metabolism, and lysine degradation were distinctive metabolic signatures of dental plaque in the high PISA group, which may have relevance to the metabolic signatures of disease-associated communities. Collectively, our findings identified potential biomarkers of periodontal inflammatory status, while they also provide insight into metabolic signatures of dysbiotic communities.
Institute	Osaka University
Department	Graduate School of Dentistry
Last Name	Kuboniwa
First Name	Masae
Address	1-8 Yamadaoka, Suita, Osaka, 565-0871, Japan
Email	kuboniwa@dent.osaka-u.ac.jp
Phone	+81-6-6879-2922
Submit Date	2016-10-23
Raw Data File Type(s)	cdf
Analysis Type Detail	GC-MS
Release Date	2017-11-20
Release Version	1

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Project:

Project ID:	PR000373
Project DOI:	doi: 10.21228/M8TW22
Project Title:	Human salivary metabolomics studies
Project Summary:	Metabolic profiling studies on saliva samples from human subjects with varying levels of periodontal inflammation severity
Institute:	Osaka University
Department:	Preventive Dentistry
Last Name:	Kuboniwa
First Name:	Masae
Address:	1-8 Yamadaoka, Suita, Osaka, 565-0871, Japan
Email:	kuboniwa@dent.osaka-u.ac.jp
Phone:	+81-6-6879-2922

Subject:

Subject ID:	SU000517
Subject Type:	Human
Subject Species:	Homo sapiens
Taxonomy ID:	9606
Species Group:	Human

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id	local_sample_id	debridement
SA025699	Sa_pre_18	No
SA025700	Sa_pre_19	No
SA025701	Sa_pre_17	No
SA025702	Sa_pre_16	No
SA025703	Sa_pre_15	No
SA025704	Sa_pre_20	No
SA025705	Sa_pre_21	No
SA025706	Sa_pre_25	No
SA025707	Sa_pre_24	No
SA025708	Sa_pre_23	No
SA025709	Sa_pre_22	No
SA025710	Sa_pre_14	No
SA025711	Sa_pre_13	No
SA025712	Sa_pre_5	No
SA025713	Sa_pre_6	No
SA025714	Sa_pre_4	No
SA025715	Sa_pre_3	No
SA025716	Sa_pre_2	No
SA025717	Sa_pre_7	No
SA025718	Sa_pre_8	No
SA025719	Sa_pre_12	No
SA025720	Sa_pre_11	No
SA025721	Sa_pre_10	No
SA025722	Sa_pre_9	No
SA025723	Sa_pre_26	No
SA025724	Sa_pre_27	No
SA025725	Sa_pre_43	No
SA025726	Sa_pre_44	No
SA025727	Sa_pre_42	No
SA025728	Sa_pre_41	No
SA025729	Sa_pre_40	No
SA025730	Sa_pre_45	No
SA025731	Sa_pre_46	No
SA025732	Sa_pre_50	No
SA025733	Sa_pre_49	No
SA025734	Sa_pre_48	No
SA025735	Sa_pre_47	No
SA025736	Sa_pre_39	No
SA025737	Sa_pre_38	No
SA025738	Sa_pre_31	No
SA025739	Sa_pre_30	No
SA025740	Sa_pre_29	No
SA025741	Sa_pre_28	No
SA025742	Sa_pre_32	No
SA025743	Sa_pre_33	No
SA025744	Sa_pre_37	No
SA025745	Sa_pre_36	No
SA025746	Sa_pre_35	No
SA025747	Sa_pre_34	No
SA025748	Sa_pre_1	No
SA025649	Sa_pro_18	Yes
SA025650	Sa_pro_19	Yes
SA025651	Sa_pro_17	Yes
SA025652	Sa_pro_16	Yes
SA025653	Sa_pro_15	Yes
SA025654	Sa_pro_20	Yes
SA025655	Sa_pro_21	Yes
SA025656	Sa_pro_25	Yes
SA025657	Sa_pro_24	Yes
SA025658	Sa_pro_23	Yes
SA025659	Sa_pro_22	Yes
SA025660	Sa_pro_14	Yes
SA025661	Sa_pro_13	Yes
SA025662	Sa_pro_6	Yes
SA025663	Sa_pro_5	Yes
SA025664	Sa_pro_4	Yes
SA025665	Sa_pro_3	Yes
SA025666	Sa_pro_7	Yes
SA025667	Sa_pro_8	Yes
SA025668	Sa_pro_12	Yes
SA025669	Sa_pro_11	Yes
SA025670	Sa_pro_10	Yes
SA025671	Sa_pro_9	Yes
SA025672	Sa_pro_26	Yes
SA025673	Sa_pro_28	Yes
SA025674	Sa_pro_43	Yes
SA025675	Sa_pro_44	Yes
SA025676	Sa_pro_42	Yes
SA025677	Sa_pro_41	Yes
SA025678	Sa_pro_40	Yes
SA025679	Sa_pro_45	Yes
SA025680	Sa_pro_46	Yes
SA025681	Sa_pro_50	Yes
SA025682	Sa_pro_49	Yes
SA025683	Sa_pro_48	Yes
SA025684	Sa_pro_47	Yes
SA025685	Sa_pro_39	Yes
SA025686	Sa_pro_38	Yes
SA025687	Sa_pro_31	Yes
SA025688	Sa_pro_30	Yes
SA025689	Sa_pro_29	Yes
SA025690	Sa_pro_2	Yes
SA025691	Sa_pro_32	Yes
SA025692	Sa_pro_33	Yes
SA025693	Sa_pro_37	Yes
SA025694	Sa_pro_36	Yes
SA025695	Sa_pro_35	Yes
SA025696	Sa_pro_34	Yes
SA025697	Sa_pro_27	Yes
SA025698	Sa_pro_1	Yes

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Showing results 1 to 100 of 100

Collection:

Collection ID:	CO000511
Collection Summary:	The subjects were asked to refrain from brushing and using mouthwash for at least 1 hour prior to sample collection and periodontal examinations. We collected a minimum of 3 mL of unstimulated whole saliva between 1:00 and 3:00 p.m. Thereafter, saliva was sampled again at 15 minutes following removal of supragingival plaque and calculus with an ultrasonic scaler (debridement). Finally, 1 ml of each sample was immediately frozen with liquid nitrogen and stored at -80°C until analysis.
Sample Type:	Saliva

Treatment:

Treatment ID:	TR000531
Treatment Summary:	Debridement was performed with an ultrasonic scaler, as described in “Collection Summary”. To maintain the subgingival microbiota and avoid bleeding, we avoided insertion of the scalar tip into the gingival sulcus.

Sample Preparation:

Sampleprep ID:	SP000524
Sampleprep Summary:	Frozen saliva samples were freeze-dried overnight using a freeze-dryer (VD-800F; TAITEC, Saitama, Japan), and metabolites were extracted with 1 ml of MeOH/H2O/CHCl3 (5/2/2, v/v/v). As an internal standard, 60 µl of ribitol (0.2 mg/ml) was added to the mixture. The sample was centrifuged at 16,000 g for 3 min at 4 °C, and the supernatant (900 µl) was transferred to another microtube and mixed with 400µl of water. After centrifugation at 16,000 g for 3 min at 4 °C, 800µl of the supernatant was transferred to another microtube whose cap was pierced. The extract was evaporated using a vacuum centrifuge dryer for 2 h in order to remove methanol, then freeze-dried overnight. For derivatization, 100 µl of methoxyamine hydrochloride (20 mg/ml in pyrimidine) and 50 µl of N-methyl-N-(trimethylsilyl)trifluoroacetamide were employed. The sample was then used for GCMS analysis, and a 1 µL of sample was injected in split mode (25/1, v/v).

Sampleprep ID:

SP000524

Sampleprep Summary:

Frozen saliva samples were freeze-dried overnight using a freeze-dryer (VD-800F; TAITEC, Saitama, Japan), and metabolites were extracted with 1 ml of MeOH/H2O/CHCl3 (5/2/2, v/v/v). As an internal standard, 60 µl of ribitol (0.2 mg/ml) was added to the mixture. The sample was centrifuged at 16,000 g for 3 min at 4 °C, and the supernatant (900 µl) was transferred to another microtube and mixed with 400µl of water. After centrifugation at 16,000 g for 3 min at 4 °C, 800µl of the supernatant was transferred to another microtube whose cap was pierced. The extract was evaporated using a vacuum centrifuge dryer for 2 h in order to remove methanol, then freeze-dried overnight. For derivatization, 100 µl of methoxyamine hydrochloride (20 mg/ml in pyrimidine) and 50 µl of N-methyl-N-(trimethylsilyl)trifluoroacetamide were employed. The sample was then used for GCMS analysis, and a 1 µL of sample was injected in split mode (25/1, v/v).

Combined analysis:

Analysis ID	AN000762
Analysis type	MS
Chromatography type	GC
Chromatography system	Shimadzu GCMS-QP2010 ultra
Column	a 30 m × 0.25 mm i.d. fused silica capillary column coated with 0.25 µm CP-SIL 8 CB low bleed (Varian Inc., Palo Alto, CA)
MS Type	EI
MS instrument type	GC-TOF
MS instrument name	Shimadzu QP2010 Ultra
Ion Mode	POSITIVE
Units	Peak area

Chromatography:

Chromatography ID:	CH000548
Chromatography Summary:	The device used was GCMS-QP2010 ultra (Shimadzu Inc., Kyoto, Japan) equipped with a 30 m × 0.25 mm i.d. fused silica capillary column coated with 0.25 µm CP-SIL 8 CB low bleed (Varian Inc., Palo Alto, CA) and AOC-20i (Shimadzu) as an autosampler. The injection temperature was 230 °C. The helium gas flow rate through the column was 1.12 ml/min. The column temperature was held at 80 °C for 2 min and then raised by 15 °C /min to 330 °C and held for 6 min. The transfer line and the ion source temperatures were 250 °C and 200 °C, respectively. Ions were generated by a 70 kV electron impact (EI), and 20 scans/sec were recorded over the mass range 85-500. A standard alkane mixture (C8-C40) was injected at the beginning of the analysis for subsequent identification of metabolites.
Instrument Name:	Shimadzu GCMS-QP2010 ultra
Column Name:	a 30 m × 0.25 mm i.d. fused silica capillary column coated with 0.25 µm CP-SIL 8 CB low bleed (Varian Inc., Palo Alto, CA)
Column Temperature:	The column temperature was held at 80 °C for 2 min and then raised by 15 °C /min to 330 °C and held for 6 min.
Flow Rate:	The helium gas flow rate through the column was 1.12 ml/min.
Sample Injection:	1 µL
Chromatography Type:	GC

MS:

MS ID:	MS000674
Analysis ID:	AN000762
Instrument Name:	Shimadzu QP2010 Ultra
Instrument Type:	GC-TOF
MS Type:	EI
Ion Mode:	POSITIVE