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.

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Study IDST000496
Study TitleDistinct signatures of dental plaque metabolic byproducts dictated by periodontal inflammatory status
Study SummaryOnset 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
DepartmentGraduate School of Dentistry
Last NameKuboniwa
First NameMasae
Address1-8 Yamadaoka, Suita, Osaka, 565-0871, Japan
Emailkuboniwa@dent.osaka-u.ac.jp
Phone+81-6-6879-2922
Submit Date2016-10-23
Analysis Type DetailGC-MS
Release Date2017-11-20
Release Version1
Masae Kuboniwa Masae Kuboniwa
https://dx.doi.org/10.21228/M8TW22
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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
SA025699Sa_pre_18No
SA025700Sa_pre_19No
SA025701Sa_pre_17No
SA025702Sa_pre_16No
SA025703Sa_pre_15No
SA025704Sa_pre_20No
SA025705Sa_pre_21No
SA025706Sa_pre_25No
SA025707Sa_pre_24No
SA025708Sa_pre_23No
SA025709Sa_pre_22No
SA025710Sa_pre_14No
SA025711Sa_pre_13No
SA025712Sa_pre_5No
SA025713Sa_pre_6No
SA025714Sa_pre_4No
SA025715Sa_pre_3No
SA025716Sa_pre_2No
SA025717Sa_pre_7No
SA025718Sa_pre_8No
SA025719Sa_pre_12No
SA025720Sa_pre_11No
SA025721Sa_pre_10No
SA025722Sa_pre_9No
SA025723Sa_pre_26No
SA025724Sa_pre_27No
SA025725Sa_pre_43No
SA025726Sa_pre_44No
SA025727Sa_pre_42No
SA025728Sa_pre_41No
SA025729Sa_pre_40No
SA025730Sa_pre_45No
SA025731Sa_pre_46No
SA025732Sa_pre_50No
SA025733Sa_pre_49No
SA025734Sa_pre_48No
SA025735Sa_pre_47No
SA025736Sa_pre_39No
SA025737Sa_pre_38No
SA025738Sa_pre_31No
SA025739Sa_pre_30No
SA025740Sa_pre_29No
SA025741Sa_pre_28No
SA025742Sa_pre_32No
SA025743Sa_pre_33No
SA025744Sa_pre_37No
SA025745Sa_pre_36No
SA025746Sa_pre_35No
SA025747Sa_pre_34No
SA025748Sa_pre_1No
SA025649Sa_pro_18Yes
SA025650Sa_pro_19Yes
SA025651Sa_pro_17Yes
SA025652Sa_pro_16Yes
SA025653Sa_pro_15Yes
SA025654Sa_pro_20Yes
SA025655Sa_pro_21Yes
SA025656Sa_pro_25Yes
SA025657Sa_pro_24Yes
SA025658Sa_pro_23Yes
SA025659Sa_pro_22Yes
SA025660Sa_pro_14Yes
SA025661Sa_pro_13Yes
SA025662Sa_pro_6Yes
SA025663Sa_pro_5Yes
SA025664Sa_pro_4Yes
SA025665Sa_pro_3Yes
SA025666Sa_pro_7Yes
SA025667Sa_pro_8Yes
SA025668Sa_pro_12Yes
SA025669Sa_pro_11Yes
SA025670Sa_pro_10Yes
SA025671Sa_pro_9Yes
SA025672Sa_pro_26Yes
SA025673Sa_pro_28Yes
SA025674Sa_pro_43Yes
SA025675Sa_pro_44Yes
SA025676Sa_pro_42Yes
SA025677Sa_pro_41Yes
SA025678Sa_pro_40Yes
SA025679Sa_pro_45Yes
SA025680Sa_pro_46Yes
SA025681Sa_pro_50Yes
SA025682Sa_pro_49Yes
SA025683Sa_pro_48Yes
SA025684Sa_pro_47Yes
SA025685Sa_pro_39Yes
SA025686Sa_pro_38Yes
SA025687Sa_pro_31Yes
SA025688Sa_pro_30Yes
SA025689Sa_pro_29Yes
SA025690Sa_pro_2Yes
SA025691Sa_pro_32Yes
SA025692Sa_pro_33Yes
SA025693Sa_pro_37Yes
SA025694Sa_pro_36Yes
SA025695Sa_pro_35Yes
SA025696Sa_pro_34Yes
SA025697Sa_pro_27Yes
SA025698Sa_pro_1Yes
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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).

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
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