Summary of Study ST002265
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 PR001447. The data can be accessed directly via it's Project DOI: 10.21228/M8PH7X This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
| Study ID | ST002265 |
| Study Title | Multi-omic analysis reveals bacteria may have a role in dental erosion |
| Study Type | Research Study |
| Study Summary | NMR was performed on 11 saliva samples; 5 from participants classified as having dental erosion and 6 from healthy control participants with no dental erosion to assess the differences in metabolome between the two groups. NMR analysis alone revealed no significant differences between the dental erosion and healthy controls. However, bacterial mRNA sequencing of the oral microbiome from the same saliva samples was performed and the bacterial gene expression profiles was correlated to metabolite concentrations in the groups. The dental erosion group had strong correlations between metabolites associated with protein degradation and amino acid fermentation (formate, butyrate, propionate, 5-aminopentanoate, acetate, glycine, phenylalanine, dimethyl sulfone) and increased activity of species including 4 Prevotella species, Actinomyces graevenitzii, Tannerella species, and 2 Selenomas species, to name a few. Whereas in the healthy control group, the only positive correlations between metabolite concentrations and bacterial activity was for urea and 5-aminopentanoate; urea was positively correlated with Aggregatibacter actinomycetecomytans, Lysinibacillus fusiformis, and Veillonella tobetsuensis, and 5-aminopentanoate was positively correlated with 3 different Leptotrichia species, Streptococcus parasanguinis, and 2 Prevotella species. |
| Institute | King's College London |
| Last Name | Cleaver |
| First Name | Leanne |
| Address | Floor 17, Tower Wing, Guy's Hospital, King's College London, Great Maze Pond |
| leanne.cleaver@kcl.ac.uk | |
| Phone | 07464626438 |
| Submit Date | 2022-08-02 |
| Num Groups | 2 |
| Total Subjects | 11 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | fid |
| Analysis Type Detail | NMR |
| Release Date | 2022-09-05 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001447 |
| Project DOI: | doi: 10.21228/M8PH7X |
| Project Title: | Multi-omic analysis reveals bacteria may have a role in dental erosion |
| Project Type: | Research Study |
| Project Summary: | NMR was performed on 11 saliva samples; 5 from participants classified as having dental erosion and 6 from healthy control participants with no dental erosion to assess the differences in metabolome between the two groups. NMR analysis alone revealed no significant differences between the dental erosion and healthy controls. However, bacterial mRNA sequencing of the oral microbiome from the same saliva samples was performed and the bacterial gene expression profiles was correlated to metabolite concentrations in the groups. The dental erosion group had strong correlations between metabolites associated with protein degradation and amino acid fermentation (formate, butyrate, propionate, 5-aminopentanoate, acetate, glycine, phenylalanine, dimethyl sulfone) and increased activity of species including 4 Prevotella species, Actinomyces graevenitzii, Tannerella species, and 2 Selenomas species, to name a few. Whereas in the healthy control group, the only positive correlations between metabolite concentrations and bacterial activity was for urea and 5-aminopentanoate; urea was positively correlated with Aggregatibacter actinomycetecomytans, Lysinibacillus fusiformis, and Veillonella tobetsuensis, and 5-aminopentanoate was positively correlated with 3 different Leptotrichia species, Streptococcus parasanguinis, and 2 Prevotella species. |
| Institute: | King's College London |
| Department: | Centre for Host Microbiome Interactions |
| Last Name: | Cleaver |
| First Name: | Leanne |
| Address: | Floor 17, Tower Wing, Guy's Hospital, King's College London, Great Maze Pond |
| Email: | leanne.cleaver@kcl.ac.uk |
| Phone: | 07464626438 |
Subject:
| Subject ID: | SU002351 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample Type |
|---|---|---|
| SA217469 | SE1 2 | Erosion 1 |
| SA217470 | SE1 3 | Erosion 1 |
| SA217471 | SE1 1 | Erosion 1 |
| SA217472 | SE2 3 | Erosion 2 |
| SA217473 | SE2 2 | Erosion 2 |
| SA217474 | SE2 1 | Erosion 2 |
| SA217475 | SE3 3 | Erosion 3 |
| SA217476 | SE3 2 | Erosion 3 |
| SA217477 | SE3 1 | Erosion 3 |
| SA217478 | SE4 2 | Erosion 4 |
| SA217479 | SE4 3 | Erosion 4 |
| SA217480 | SE4 1 | Erosion 4 |
| SA217481 | SE5 3 | Erosion 5 |
| SA217482 | SE5 2 | Erosion 5 |
| SA217483 | SE5 1 | Erosion 5 |
| SA217484 | SH1 3 | Healthy 1 |
| SA217485 | SH1 2 | Healthy 1 |
| SA217486 | SH1 1 | Healthy 1 |
| SA217487 | SH2 2 | Healthy 2 |
| SA217488 | SH2 3 | Healthy 2 |
| SA217489 | SH2 1 | Healthy 2 |
| SA217490 | SH3 3 | Healthy 3 |
| SA217491 | SH3 2 | Healthy 3 |
| SA217492 | SH3 1 | Healthy 3 |
| SA217493 | SH4 3 | Healthy 4 |
| SA217494 | SH4 2 | Healthy 4 |
| SA217495 | SH4 1 | Healthy 4 |
| SA217496 | SH5 2 | Healthy 5 |
| SA217497 | SH5 3 | Healthy 5 |
| SA217498 | SH5 1 | Healthy 5 |
| SA217499 | SH6 3 | Healthy 6 |
| SA217500 | SH6 2 | Healthy 6 |
| SA217501 | SH6 1 | Healthy 6 |
| SA217502 | Sterile Saliva | Sterile Saliva |
| Showing results 1 to 34 of 34 |
Collection:
| Collection ID: | CO002344 |
| Collection Summary: | Participants were asked to chew on a piece of sterile parafilm and expectorate stimulated saliva into a sterile universal tube until approximately 6mls was collected. |
| Sample Type: | Saliva |
| Storage Conditions: | -20℃ |
Treatment:
| Treatment ID: | TR002363 |
| Treatment Summary: | No treatment |
Sample Preparation:
| Sampleprep ID: | SP002357 |
| Sampleprep Summary: | nuclear magnetic resonance (NMR) analysis on thawed saliva aliquots (500 l, n=3 per participant) was performed using a previously published method 11. Briefly, samples were centrifuged for 5 minutes at 13,000 RPM to remove cell debris. The supernatant was removed for NMR analysis and mixed at a ratio of 4:1 with sodium trimethylsilyl propionate (TSP) buffer and added to a 5mm NMR tube (Bruker, Coventry, UK). Spectra were acquired on a 600 MHz NMR spectrophotometer (Bruker). The spectra were processed on TopSpin (Bruker) to correct the phase and baseline, and to calibrate the TSP peak to 0 ppm. The identity of metabolites were assigned and the concentration (mM) obtained from spectra using Chenomx NMR Suite version 8.5 (Chenomix Ltd, Canada). |
| Processing Storage Conditions: | On ice |
Analysis:
| Analysis ID: | AN003700 |
| Laboratory Name: | NMR Centre, KCL |
| Analysis Type: | NMR |
| Num Factors: | 12 |
| Num Metabolites: | 16 |
| Units: | mM |
NMR:
| NMR ID: | NM000246 |
| Analysis ID: | AN003700 |
| Instrument Name: | Bruker AVANCE III HD 600 MHz NMR spectrometer |
| Instrument Type: | FT-NMR |
| NMR Experiment Type: | 1D-1H |
| Spectrometer Frequency: | 600MHz |
| NMR Probe: | TCI (1H/19F)/13C/15N Prodigy Cryoprobe |
| NMR Solvent: | TSP |
| NMR Tube Size: | 5mm |
| Pulse Sequence: | PROJECT |
| Temperature: | 298K |
| Number Of Scans: | 128 |
| Acquisition Time: | 2.62 s |
| Relaxation Delay: | 4 s |
| Spectral Width: | 20.8 ppm |
| Real Data Points: | 65536 points |
