#METABOLOMICS WORKBENCH LCleaver1_20220802_070316 DATATRACK_ID:3378 STUDY_ID:ST002265 ANALYSIS_ID:AN003700 PROJECT_ID:PR001447
VERSION             	1
CREATED_ON             	August 23, 2022, 10:06 am
#PROJECT
PR:PROJECT_TITLE                 	Multi-omic analysis reveals bacteria may have a role in dental erosion
PR:PROJECT_TYPE                  	Research Study
PR:PROJECT_SUMMARY               	NMR was performed on 11 saliva samples; 5 from participants classified as having
PR:PROJECT_SUMMARY               	dental erosion and 6 from healthy control participants with no dental erosion to
PR:PROJECT_SUMMARY               	assess the differences in metabolome between the two groups. NMR analysis alone
PR:PROJECT_SUMMARY               	revealed no significant differences between the dental erosion and healthy
PR:PROJECT_SUMMARY               	controls. However, bacterial mRNA sequencing of the oral microbiome from the
PR:PROJECT_SUMMARY               	same saliva samples was performed and the bacterial gene expression profiles was
PR:PROJECT_SUMMARY               	correlated to metabolite concentrations in the groups. The dental erosion group
PR:PROJECT_SUMMARY               	had strong correlations between metabolites associated with protein degradation
PR:PROJECT_SUMMARY               	and amino acid fermentation (formate, butyrate, propionate, 5-aminopentanoate,
PR:PROJECT_SUMMARY               	acetate, glycine, phenylalanine, dimethyl sulfone) and increased activity of
PR:PROJECT_SUMMARY               	species including 4 Prevotella species, Actinomyces graevenitzii, Tannerella
PR:PROJECT_SUMMARY               	species, and 2 Selenomas species, to name a few. Whereas in the healthy control
PR:PROJECT_SUMMARY               	group, the only positive correlations between metabolite concentrations and
PR:PROJECT_SUMMARY               	bacterial activity was for urea and 5-aminopentanoate; urea was positively
PR:PROJECT_SUMMARY               	correlated with Aggregatibacter actinomycetecomytans, Lysinibacillus fusiformis,
PR:PROJECT_SUMMARY               	and Veillonella tobetsuensis, and 5-aminopentanoate was positively correlated
PR:PROJECT_SUMMARY               	with 3 different Leptotrichia species, Streptococcus parasanguinis, and 2
PR:PROJECT_SUMMARY               	Prevotella species.
PR:INSTITUTE                     	King's College London
PR:DEPARTMENT                    	Centre for Host Microbiome Interactions
PR:LAST_NAME                     	Cleaver
PR:FIRST_NAME                    	Leanne
PR:ADDRESS                       	Floor 17, Tower Wing, Guy's Hospital, King's College London, Great Maze Pond
PR:EMAIL                         	leanne.cleaver@kcl.ac.uk
PR:PHONE                         	07464626438
#STUDY
ST:STUDY_TITLE                   	Multi-omic analysis reveals bacteria may have a role in dental erosion
ST:STUDY_TYPE                    	Research Study
ST:STUDY_SUMMARY                 	NMR was performed on 11 saliva samples; 5 from participants classified as having
ST:STUDY_SUMMARY                 	dental erosion and 6 from healthy control participants with no dental erosion to
ST:STUDY_SUMMARY                 	assess the differences in metabolome between the two groups. NMR analysis alone
ST:STUDY_SUMMARY                 	revealed no significant differences between the dental erosion and healthy
ST:STUDY_SUMMARY                 	controls. However, bacterial mRNA sequencing of the oral microbiome from the
ST:STUDY_SUMMARY                 	same saliva samples was performed and the bacterial gene expression profiles was
ST:STUDY_SUMMARY                 	correlated to metabolite concentrations in the groups. The dental erosion group
ST:STUDY_SUMMARY                 	had strong correlations between metabolites associated with protein degradation
ST:STUDY_SUMMARY                 	and amino acid fermentation (formate, butyrate, propionate, 5-aminopentanoate,
ST:STUDY_SUMMARY                 	acetate, glycine, phenylalanine, dimethyl sulfone) and increased activity of
ST:STUDY_SUMMARY                 	species including 4 Prevotella species, Actinomyces graevenitzii, Tannerella
ST:STUDY_SUMMARY                 	species, and 2 Selenomas species, to name a few. Whereas in the healthy control
ST:STUDY_SUMMARY                 	group, the only positive correlations between metabolite concentrations and
ST:STUDY_SUMMARY                 	bacterial activity was for urea and 5-aminopentanoate; urea was positively
ST:STUDY_SUMMARY                 	correlated with Aggregatibacter actinomycetecomytans, Lysinibacillus fusiformis,
ST:STUDY_SUMMARY                 	and Veillonella tobetsuensis, and 5-aminopentanoate was positively correlated
ST:STUDY_SUMMARY                 	with 3 different Leptotrichia species, Streptococcus parasanguinis, and 2
ST:STUDY_SUMMARY                 	Prevotella species.
ST:INSTITUTE                     	King's College London
ST:LAST_NAME                     	Cleaver
ST:FIRST_NAME                    	Leanne
ST:ADDRESS                       	Floor 17, Tower Wing, Guy's Hospital, King's College London, Great Maze Pond
ST:EMAIL                         	leanne.cleaver@kcl.ac.uk
ST:PHONE                         	07464626438
ST:NUM_GROUPS                    	2
ST:TOTAL_SUBJECTS                	11
#SUBJECT
SU:SUBJECT_TYPE                  	Human
SU:SUBJECT_SPECIES               	Homo sapiens
SU:TAXONOMY_ID                   	9606
#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           	-	Sterile Saliva	Sample Type:Sterile Saliva	RAW_FILE_NAME=10
SUBJECT_SAMPLE_FACTORS           	-	SE1 1	Sample Type:Erosion 1	RAW_FILE_NAME=20
SUBJECT_SAMPLE_FACTORS           	-	SE1 2	Sample Type:Erosion 1	RAW_FILE_NAME=30
SUBJECT_SAMPLE_FACTORS           	-	SE1 3	Sample Type:Erosion 1	RAW_FILE_NAME=40
SUBJECT_SAMPLE_FACTORS           	-	SE2 1	Sample Type:Erosion 2	RAW_FILE_NAME=50
SUBJECT_SAMPLE_FACTORS           	-	SE2 2	Sample Type:Erosion 2	RAW_FILE_NAME=60
SUBJECT_SAMPLE_FACTORS           	-	SE2 3	Sample Type:Erosion 2	RAW_FILE_NAME=70
SUBJECT_SAMPLE_FACTORS           	-	SE3 1	Sample Type:Erosion 3	RAW_FILE_NAME=80
SUBJECT_SAMPLE_FACTORS           	-	SE3 2	Sample Type:Erosion 3	RAW_FILE_NAME=90
SUBJECT_SAMPLE_FACTORS           	-	SE3 3	Sample Type:Erosion 3	RAW_FILE_NAME=100
SUBJECT_SAMPLE_FACTORS           	-	SE4 1	Sample Type:Erosion 4	RAW_FILE_NAME=110
SUBJECT_SAMPLE_FACTORS           	-	SE4 2	Sample Type:Erosion 4	RAW_FILE_NAME=120
SUBJECT_SAMPLE_FACTORS           	-	SE4 3	Sample Type:Erosion 4	RAW_FILE_NAME=130
SUBJECT_SAMPLE_FACTORS           	-	SE5 1	Sample Type:Erosion 5	RAW_FILE_NAME=140
SUBJECT_SAMPLE_FACTORS           	-	SE5 2	Sample Type:Erosion 5	RAW_FILE_NAME=150
SUBJECT_SAMPLE_FACTORS           	-	SE5 3	Sample Type:Erosion 5	RAW_FILE_NAME=160
SUBJECT_SAMPLE_FACTORS           	-	SH1 1	Sample Type:Healthy 1	RAW_FILE_NAME=170
SUBJECT_SAMPLE_FACTORS           	-	SH1 2	Sample Type:Healthy 1	RAW_FILE_NAME=180
SUBJECT_SAMPLE_FACTORS           	-	SH1 3	Sample Type:Healthy 1	RAW_FILE_NAME=190
SUBJECT_SAMPLE_FACTORS           	-	SH2 1	Sample Type:Healthy 2	RAW_FILE_NAME=200
SUBJECT_SAMPLE_FACTORS           	-	SH2 2	Sample Type:Healthy 2	RAW_FILE_NAME=210
SUBJECT_SAMPLE_FACTORS           	-	SH2 3	Sample Type:Healthy 2	RAW_FILE_NAME=220
SUBJECT_SAMPLE_FACTORS           	-	SH3 1	Sample Type:Healthy 3	RAW_FILE_NAME=230
SUBJECT_SAMPLE_FACTORS           	-	SH3 2	Sample Type:Healthy 3	RAW_FILE_NAME=240
SUBJECT_SAMPLE_FACTORS           	-	SH3 3	Sample Type:Healthy 3	RAW_FILE_NAME=250
SUBJECT_SAMPLE_FACTORS           	-	SH4 1	Sample Type:Healthy 4	RAW_FILE_NAME=260
SUBJECT_SAMPLE_FACTORS           	-	SH4 2	Sample Type:Healthy 4	RAW_FILE_NAME=270
SUBJECT_SAMPLE_FACTORS           	-	SH4 3	Sample Type:Healthy 4	RAW_FILE_NAME=280
SUBJECT_SAMPLE_FACTORS           	-	SH5 1	Sample Type:Healthy 5	RAW_FILE_NAME=290
SUBJECT_SAMPLE_FACTORS           	-	SH5 2	Sample Type:Healthy 5	RAW_FILE_NAME=300
SUBJECT_SAMPLE_FACTORS           	-	SH5 3	Sample Type:Healthy 5	RAW_FILE_NAME=310
SUBJECT_SAMPLE_FACTORS           	-	SH6 1	Sample Type:Healthy 6	RAW_FILE_NAME=320
SUBJECT_SAMPLE_FACTORS           	-	SH6 2	Sample Type:Healthy 6	RAW_FILE_NAME=330
SUBJECT_SAMPLE_FACTORS           	-	SH6 3	Sample Type:Healthy 6	RAW_FILE_NAME=340
#COLLECTION
CO:COLLECTION_SUMMARY            	Participants were asked to chew on a piece of sterile parafilm and expectorate
CO:COLLECTION_SUMMARY            	stimulated saliva into a sterile universal tube until approximately 6mls was
CO:COLLECTION_SUMMARY            	collected.
CO:SAMPLE_TYPE                   	Saliva
CO:STORAGE_CONDITIONS            	-20℃
#TREATMENT
TR:TREATMENT_SUMMARY             	No treatment
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	nuclear magnetic resonance (NMR) analysis on thawed saliva aliquots (500 l,
SP:SAMPLEPREP_SUMMARY            	n=3 per participant) was performed using a previously published method 11.
SP:SAMPLEPREP_SUMMARY            	Briefly, samples were centrifuged for 5 minutes at 13,000 RPM to remove cell
SP:SAMPLEPREP_SUMMARY            	debris. The supernatant was removed for NMR analysis and mixed at a ratio of 4:1
SP:SAMPLEPREP_SUMMARY            	with sodium trimethylsilyl propionate (TSP) buffer and added to a 5mm NMR tube
SP:SAMPLEPREP_SUMMARY            	(Bruker, Coventry, UK). Spectra were acquired on a 600 MHz NMR spectrophotometer
SP:SAMPLEPREP_SUMMARY            	(Bruker). The spectra were processed on TopSpin (Bruker) to correct the phase
SP:SAMPLEPREP_SUMMARY            	and baseline, and to calibrate the TSP peak to 0 ppm. The identity of
SP:SAMPLEPREP_SUMMARY            	metabolites were assigned and the concentration (mM) obtained from spectra using
SP:SAMPLEPREP_SUMMARY            	Chenomx NMR Suite version 8.5 (Chenomix Ltd, Canada).
SP:PROCESSING_STORAGE_CONDITIONS 	On ice
#ANALYSIS
AN:LABORATORY_NAME               	NMR Centre, KCL
#NMR
NM:INSTRUMENT_NAME               	Bruker AVANCE III HD 600 MHz NMR spectrometer
NM:INSTRUMENT_TYPE               	FT-NMR
NM:NMR_EXPERIMENT_TYPE           	1D-1H
NM:SPECTROMETER_FREQUENCY        	600MHz
NM:NMR_PROBE                     	TCI (1H/19F)/13C/15N Prodigy Cryoprobe
NM:NMR_SOLVENT                   	TSP
NM:NMR_TUBE_SIZE                 	5mm
NM:PULSE_SEQUENCE                	PROJECT
NM:TEMPERATURE                   	298K
NM:NUMBER_OF_SCANS               	128
NM:ACQUISITION_TIME              	2.62 s
NM:RELAXATION_DELAY              	4 s
NM:SPECTRAL_WIDTH                	20.8 ppm
NM:REAL_DATA_POINTS              	65536 points
#NMR_METABOLITE_DATA
NMR_METABOLITE_DATA:UNITS	mM
NMR_METABOLITE_DATA_START
Samples	Sterile Saliva	SE1 1	SE1 2	SE1 3	SE2 1	SE2 2	SE2 3	SE3 1	SE3 2	SE3 3	SE4 1	SE4 2	SE4 3	SE5 1	SE5 2	SE5 3	SH1 1	SH1 2	SH1 3	SH2 1	SH2 2	SH2 3	SH3 1	SH3 2	SH3 3	SH4 1	SH4 2	SH4 3	SH5 1	SH5 2	SH5 3	SH6 1	SH6 2	SH6 3
Factors	Sample Type:Sterile Saliva	Sample Type:Erosion 1	Sample Type:Erosion 1	Sample Type:Erosion 1	Sample Type:Erosion 2	Sample Type:Erosion 2	Sample Type:Erosion 2	Sample Type:Erosion 3	Sample Type:Erosion 3	Sample Type:Erosion 3	Sample Type:Erosion 4	Sample Type:Erosion 4	Sample Type:Erosion 4	Sample Type:Erosion 5	Sample Type:Erosion 5	Sample Type:Erosion 5	Sample Type:Healthy 1	Sample Type:Healthy 1	Sample Type:Healthy 1	Sample Type:Healthy 2	Sample Type:Healthy 2	Sample Type:Healthy 2	Sample Type:Healthy 3	Sample Type:Healthy 3	Sample Type:Healthy 3	Sample Type:Healthy 4	Sample Type:Healthy 4	Sample Type:Healthy 4	Sample Type:Healthy 5	Sample Type:Healthy 5	Sample Type:Healthy 5	Sample Type:Healthy 6	Sample Type:Healthy 6	Sample Type:Healthy 6
ALANINE	0	0.108	0.1513	0.132	0.0338	0.0297	0.0355	0.0662	0.0613	0.061	0.0605	0.0593	0.0594	0.0882	0.0976	0.0869	0.0612	0.0575	0.0625	0.0883	0.0811	0.0852	0.0857	0.0962	0.0888	0.0926	0.1045	0.1073	0.0587	0.0626	0.0714	0.0472	0.0568	0.0595
VALINE	0.005	0.0271	0.0327	0.0341	0.0112	0.0089	0.0106	0.0131	0.0125	0.0132	0.0202	0.0194	0.0186	0.0267	0.0286	0.0247	0.015	0.013	0.0147	0.0233	0.0217	0.0219	0.0277	0.0316	0.0281	0.0241	0.0274	0.0292	0.0117	0.0125	0.0146	0.0067	0	0
GLYCINE	0.1376	0.3226	0.3779	0.4126	0.0944	0.077	0.0969	0.1353	0.1088	0.1105	0.1428	0.1346	0.135	0.5089	0.5451	0.4802	0.1527	0.1275	0.1359	0.451	0.3982	0.4105	0.2724	0.2917	0.2771	0.4197	0.4695	0.4373	0.2338	0.232	0.2717	0.1229	0.1485	0.1559
PHENYLALANINE	0	0.04	0.0502	0.0372	0	0	0.0189	0.0215	0.0215	0.0234	0.0231	0.0226	0.0182	0.0503	0.0542	0.0495	0.0249	0.0225	0.0255	0.0298	0.0254	0.0247	0.0273	0.0318	0.0321	0.0294	0.0361	0.0389	0.0257	0.0265	0.0305	0.0146	0.0155	0.0177
PROLINE	0	0.3493	0.3648	0.3773	0	0	0	0	0	0	0.1744	0.1635	0.155	0.4837	0.5086	0.4576	0.1456	0.134	0	0.529	0.4589	0.4784	0.2684	0.3015	0.2909	0.452	0.5411	0.5539	0.232	0.2419	0.2725	0.0889	0.1031	0.1117
ACETATE	4.1287	4.8368	5.4604	5.599	3.1433	2.6603	3.052	2.2971	2.2424	2.3315	2.2192	2.0402	2.0158	8.994	9.7531	8.5943	0.871	0.8901	0.8969	3.4311	3.234	3.3115	8.5623	9.0406	8.6533	5.3442	5.6155	5.6862	3.5795	3.8498	4.1804	3.3061	3.7658	3.8674
ETHANOL	0	0.071	0.0763	0.0883	0.0558	0	0	0	0	0	0	0	0	0.0878	0.0868	0.0726	0	0	0	0	0	0	0.0957	0.1007	0.0957	0.1663	0.1903	0.1904	0.0938	0.0965	0.1108	0	0.1358	0
LACTATE	0.3051	0.5028	0.5399	0.5634	0.069	0.0641	0.0768	2.0941	2.0253	2.0187	0.1991	0.1812	0.192	0	0	0	0.4104	0.396	0.4104	0.093	0.0941	0.0925	0.0543	0.0573	0.0551	0.1432	0.1697	0.1674	0.2142	0.2242	0.2614	0.3186	0.3836	0.3797
URACIL	0	0.0324	0.0372	0.0406	0.0125	0.0094	0.0106	0	0	0	0.0142	0.0145	0.0151	0.0133	0.0202	0.0169	0.0174	0.016	0.0178	0.0153	0	0	0.0317	0.0343	0.0324	0.0208	0.0225	0.0238	0	0.0109	0.0129	0	0.0108	0
TYROSINE	0.0408	0.064	0.0693	0.0725	0.0293	0.0318	0.0286	0.0671	0.0436	0.0415	0.0652	0.0563	0.0376	0.1167	0.1242	0.1142	0.0316	0.0321	0.0364	0.0578	0.0579	0.0559	0.0527	0.0603	0.0467	0.0567	0.0668	0.0718	0.0499	0.0512	0.0608	0.0358	0.0491	0.0477
PROPIONATE	0.5641	0.4499	0.4982	0.5388	0.3079	0.2467	0.2895	0.2115	0.2009	0.1951	0.0497	0.0466	0.0469	0.9179	0.9874	0.8802	0.1399	0.1358	0.1461	0.2808	0.2797	0.2835	0.8899	0.9453	0.9195	0.7252	0.8011	0.8165	0.5464	0.5828	0.6578	0.4597	0.5527	0.5543
BUTYRATE	0	0	0	0	0	0	0	0	0	0	0	0	0	0.1406	0.114	0.1424	0	0	0	0	0	0	0	0	0	0	0.2262	0	0.1072	0.1194	0.1271	0	0	0
Formate	0.1783	0.1584	0.1206	0.1837	0.1885	0.122	0.1608	0.2871	0.2778	0.2864	0.1346	0.1334	0.1127	0.3889	0.4027	0.3422	0	0	0	0.0093	0	0	0.0512	0.0769	0.0598	0.4354	0.4929	0.4963	0.0731	0.0757	0.0962	0.7243	0.8827	0.8289
5-aminopentanoate	0	0	0	0	0	0	0	0	0	0	0	0	0	0.4288	0.4149	0.3967	0	0	0	0	0	0	0.3236	0.3818	0.3151	0.3742	0.4292	0.4463	0.2605	0.2385	0	0	0	0
Dimethyl sulfone	0.012	0.0145	0.0167	0.0164	0.4688	0.3974	0.4629	0.0309	0.0303	0.0288	0.0078	0.0072	0.0073	0	0	0	0.0164	0.0151	0.0163	0.0117	0.0122	0.0124	0.0095	0.01	0.0094	0.0135	0.0145	0.0146	0.0101	0.0106	0.0117	0.0115	0.0126	0.013
Urea	0.67	0.2833	0.2997	0.3328	0.4418	0.4252	0.4438	1.4956	1.4742	1.4389	2.671	2.634	2.5734	0.9761	1.0145	0.9415	1.1525	1.2848	1.2983	1.6435	1.6753	1.5438	0.3121	0.3431	0.3324	0.1712	0.2517	0.1972	0.8461	0.8855	0.9773	0.4658	0.5772	0.5843
NMR_METABOLITE_DATA_END
#METABOLITES
METABOLITES_START
metabolite_name	KEGG ID
ALANINE	C00041
VALINE	C00183
GLYCINE	C00037
PHENYLALANINE	C00079
PROLINE	C00148
ACETATE	C00033
ETHANOL	C00469
LACTATE	C00186
URACIL	C00106
TYROSINE	C00082
PROPIONATE	C00163
BUTYRATE	C00246
Formate	C00058
5-aminopentanoate
Dimethyl sulfone	C11142
Urea	C00086
METABOLITES_END
#END