Summary of Study ST002535

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 PR001631. The data can be accessed directly via it's Project DOI: 10.21228/M8W43G 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	ST002535
Study Title	Relationships between the gut microbiome and cognitive impairment in residents of long-term aged care.
Study Summary	Ageing-associated cognitive decline affects more than half of those in long-term residential aged care. Emerging evidence suggests that gut microbiome-host interactions influence the effects of modifiable risk factors. We investigated the relationship between gut microbiome characteristics and severity of cognitive impairment (CI) in 159 residents of long-term aged care. Severe CI was associated with a significantly increased abundance of proinflammatory bacterial species, including Methanobrevibacter smithii and Alistipes finegoldii, and decreased relative abundance of beneficial bacterial clades. Severe CI was associated with increased microbial capacity for methanogenesis, and reduced capacity for synthesis of short-chain fatty acids, neurotransmitters glutamate and gamma-aminobutyric acid, and amino acids required for neuro-protective lysosomal activity. These relationships were independent of age, sex, antibiotic exposure, and diet. Our findings implicate multiple gut microbiome-brain pathways in ageing-associated cognitive decline, including inflammation, neurotransmission, and autophagy, and highlight the potential to predict and prevent cognitive decline through microbiome-targeted strategies.
Institute	South Australian Health and Medical Research Institute
Last Name	Shoubridge
First Name	Andrew
Address	North Terrace, Adelaide, South Australia, 5000, Australia
Email	andrew.shoubridge@sahmri.com
Phone	+61405041977
Submit Date	2023-03-26
Raw Data Available	Yes
Raw Data File Type(s)	mzML
Analysis Type Detail	LC-MS
Release Date	2023-04-04
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001631
Project DOI:	doi: 10.21228/M8W43G
Project Title:	Metabolomic Profiling of Human Faecal Samples
Project Summary:	Targeted analysis of SCFAs and polar metabolites in samples from human faeces.
Institute:	South Australian Health and Medical Research Institute
Department:	Lifelong Health
Laboratory:	Microbiome and Host Health Programme
Last Name:	Shoubridge
First Name:	Andrew
Address:	North Terrace, Adelaide, South Australia, 5000, Australia
Email:	andrew.shoubridge@sahmri.com
Phone:	+61405041977

Subject:

Subject ID:	SU002635
Subject Type:	Human
Subject Species:	Homo sapiens
Taxonomy ID:	9606
Gender:	Male and female

Factors:

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

mb_sample_id	local_sample_id	CI_group
SA254947	PBQC_001	-
SA254948	PBQC_007	-
SA254949	PBQC_008	-
SA254950	PBQC_005	-
SA254951	PBQC_003	-
SA254952	AS_36	-
SA254953	PBQC_002	-
SA254954	PBQC_009	-
SA254955	PBQC_004	-
SA254956	PBQC_006	-
SA254957	R_Blank_01	-
SA254958	R_Blank_02	-
SA254959	AS_05	2
SA254960	AS_28	2
SA254961	AS_33	2
SA254962	AS_34	2
SA254963	AS_03	2
SA254964	AS_35	2
SA254965	AS_26	2
SA254966	AS_06	2
SA254967	AS_20	2
SA254968	AS_08	2
SA254969	AS_13	2
SA254970	AS_21	2
SA254971	AS_32	3
SA254972	AS_17	3
SA254973	AS_16	3
SA254974	AS_31	3
SA254975	AS_19	3
SA254976	AS_12	3
SA254977	AS_23	3
SA254978	AS_10	3
SA254979	AS_27	3
SA254980	AS_22	3
SA254981	AS_04	3
SA254982	AS_24	4
SA254983	AS_11	4
SA254984	AS_09	4
SA254985	AS_07	4
SA254986	AS_02	4
SA254987	AS_14	4
SA254988	AS_15	4
SA254989	AS_29	4
SA254990	AS_25	4
SA254991	AS_01	4
SA254992	AS_18	4
SA254993	AS_30	4

Showing results 1 to 47 of 47

Showing results 1 to 47 of 47

Collection:

Collection ID:	CO002628
Collection Summary:	Stool was collected and stored using Norgen Stool Nucleic Acid Collection and Preservation Tubes (Norgen Biotek, ON, Canada).
Sample Type:	Feces
Storage Conditions:	-80℃

Treatment:

Treatment ID:	TR002647
Treatment Summary:	Stool samples containing buffer were vortexed vigorously and 1 ml was transferred to a clean 2 ml tube. Samples were centrifuged for 20 min at 13,000 xg at 4°C and the supernatant was transferred to a clean 2 ml screw-cap tube for storage.

Sample Preparation:

Sampleprep ID:	SP002641
Sampleprep Summary:	SCFA analysis was performed using an Agilent 6490 series triple quadrupole mass spectrometer (Agilent Technologies) with chromatographic separation on an Agilent 1200 series high-performance liquid chromatography system (HPLC) (Agilent Technologies). SCFAs were extracted by adding 360μL of 50% acetonitrile with 10μM 4-methylvaleric acid internal standard to 40μL of biological sample supernatant. Samples were then vortexed for 30 seconds, incubated at 10oC for 30 minutes at 950RPM, centrifuged at 14,000RPM for five minutes at 4oC, followed by supernatant collection. Derivatisation for SCFA analysis was performed by first adding 20μL of 20μM 13C6-nitrophenylhydrazine as internal standard to 40μL of the extracted supernatant, followed by 20μL each of 200mM nitrophenylhydrazine and 120mM 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC), incubated at 40oC for 30 minutes at 950RPM, quenched with 20μL of 200mM quinic acid, and incubated at 40oC for a further 30 minutes at 950RPM. Lastly, the samples were reconstituted with 1.9mL of 15% acetonitrile and 1μL was injected onto the column. Pooled biological quality controls (PBQCs) were created by pooling extracts (20μL) from individual biological samples and injected onto the column in five sample intervals. A reagent and procedural blank of the original sample preservation buffer was included for analysis to perform background correction. Polar metabolite analysis was performed using an Agilent 6545 series quadrupole time-of-flight mass spectrometer (Agilent Technologies) with chromatographic separation on an Agilent 1200 series HPLC system (Agilent Technologies). Metabolite extraction was performed by first adding a solvent mixture of acetonitrile, methanol and water to 20μL of biological sample, followed by vortexing, sonication and agitation. Samples were then centrifuged and supernatant collected and mixed with an internal standard mixture containing 13C5, 15N-valine, 13C6-leucine, and 13C6-sorbitol, and 14μL of sample was injected onto the column. Samples were injected in a randomised order and PBQCs were injected onto the column in five sample intervals. Data matrices were imported to the web-based platform MetaboAnalyst (v5.0) for quality control checks by multivariate statistics. SCFA data were normalised to internal standards, and polar metabolite data were log-transformed and median-normalised.

Sampleprep ID:

SP002641

Sampleprep Summary:

SCFA analysis was performed using an Agilent 6490 series triple quadrupole mass spectrometer (Agilent Technologies) with chromatographic separation on an Agilent 1200 series high-performance liquid chromatography system (HPLC) (Agilent Technologies). SCFAs were extracted by adding 360μL of 50% acetonitrile with 10μM 4-methylvaleric acid internal standard to 40μL of biological sample supernatant. Samples were then vortexed for 30 seconds, incubated at 10oC for 30 minutes at 950RPM, centrifuged at 14,000RPM for five minutes at 4oC, followed by supernatant collection. Derivatisation for SCFA analysis was performed by first adding 20μL of 20μM 13C6-nitrophenylhydrazine as internal standard to 40μL of the extracted supernatant, followed by 20μL each of 200mM nitrophenylhydrazine and 120mM 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC), incubated at 40oC for 30 minutes at 950RPM, quenched with 20μL of 200mM quinic acid, and incubated at 40oC for a further 30 minutes at 950RPM. Lastly, the samples were reconstituted with 1.9mL of 15% acetonitrile and 1μL was injected onto the column. Pooled biological quality controls (PBQCs) were created by pooling extracts (20μL) from individual biological samples and injected onto the column in five sample intervals. A reagent and procedural blank of the original sample preservation buffer was included for analysis to perform background correction. Polar metabolite analysis was performed using an Agilent 6545 series quadrupole time-of-flight mass spectrometer (Agilent Technologies) with chromatographic separation on an Agilent 1200 series HPLC system (Agilent Technologies). Metabolite extraction was performed by first adding a solvent mixture of acetonitrile, methanol and water to 20μL of biological sample, followed by vortexing, sonication and agitation. Samples were then centrifuged and supernatant collected and mixed with an internal standard mixture containing 13C5, 15N-valine, 13C6-leucine, and 13C6-sorbitol, and 14μL of sample was injected onto the column. Samples were injected in a randomised order and PBQCs were injected onto the column in five sample intervals. Data matrices were imported to the web-based platform MetaboAnalyst (v5.0) for quality control checks by multivariate statistics. SCFA data were normalised to internal standards, and polar metabolite data were log-transformed and median-normalised.

Combined analysis:

Analysis ID	AN004170
Analysis type	MS
Chromatography type	HILIC
Chromatography system	Agilent 1200
Column	Merck SeQuant ZIC-HILIC (150 x 2.1mm,5um)
MS Type	ESI
MS instrument type	QTOF
MS instrument name	Agilent 6545 QTOF
Ion Mode	NEGATIVE
Units	ng/ml

Chromatography:

Chromatography ID:	CH003088
Instrument Name:	Agilent 1200
Column Name:	Merck SeQuant ZIC-HILIC (150 x 2.1mm,5um)
Column Temperature:	40
Flow Gradient:	time = 0 min, 90% B; t = 0.5 min, 90% B; t = 12 min, 40% B; t = 14 min, 40% B; t = 15 min, 5%; t = 18 min, 5% B; and t = 19 min, 90%.
Flow Rate:	250 ul/min
Solvent A:	100% water; 20 mM ammonium carbonate (pH 9.0)
Solvent B:	100% acetonitrile
Chromatography Type:	HILIC

MS:

MS ID:	MS003917
Analysis ID:	AN004170
Instrument Name:	Agilent 6545 QTOF
Instrument Type:	QTOF
MS Type:	ESI
MS Comments:	Negative mode LC-MS data were collected in centroid mode with a scan range of 50 to 1700 mass-to-charge ratio (m/z) and an acquisition rate of 1.2 spectra/s. Samples were analyzed in the same analytical batch and randomized with a quality control every five samples. Authentic standards were also run to generate the library for targeted analysis. Level 1 metabolite identification [according to the Metabolite Standard Initiative] was based on matching accurate mass, retention time, and tandem MS (MS/MS) spectra to the 550 authentic standards in the MA in-house library. Metabolite abundance based on area under the curve (AUC) was obtained using Agilent Masshunter Quantitative Analysis B 0.7.00. Statistical analysis was performed applying the web-based platform MetaboAnalyst applying no missing value imputation, normalization to median peak area, and no scaling or transformation. RAW_FILE_NAME=AS_01.mzML to AS_35.mzML refer to metabolite detection of short-chain fatty acids, and RAW_FILE_NAME=AS_001.mzML to AS_035.mzML refer the polar metabolites.
Ion Mode:	NEGATIVE