Summary of study ST000150

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 PR000131. The data can be accessed directly via it's Project DOI: 10.21228/M8WW2P This work is supported by NIH grant, U2C- DK119886.

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Study IDST000150
Study TitleAssociation of Metabolic Profile and Microbiome in Chronic Pressure Ulcer Wounds
Study SummaryChronic, non-healing wounds contribute significantly to the suffering of patients with co-morbidities in the clinical population with mild to severely compromised immune systems. Normal wound healing proceeds through a well-described process. However, in chronic wounds this process seems to become dysregulated at the transition between resolution of inflammation and re-epithelialization. Bioburden in the form of colonizing bacteria is a major contributor to the delayed headlining in chronic wounds such as pressure ulcers. However how the microbiome influences the wound metabolic landscape is unknown. Here, we have used a Systems Biology approach to determine the association between the taxonomic and metabolomic profile of wounds colonized by bacteria. Pressure ulcer biopsies were harvested from primary chronic wounds and bisected into top and bottom sections prior to analysis of microbiome by pyrosequencing and analysis of metabolome using 1H nuclear magnetic resonance (NMR) spectroscopy. Bacterial taxonomy revealed that wounds were colonized predominantly by three main phyla, but differed significantly at the genus level. While taxonomic profiles demonstrated significant variability between wounds, metabolic profiles shared significant similarity based on the depth of the wound biopsy. Association between taxonomy and metabolic landscape indicated significant wound-to-wound similarity in metabolite enrichment sets and metabolic pathway impacts, especially with regard to amino acid metabolism. To our knowledge, this is the first demonstration of a statistically robust correlation between bacterial colonization and metabolic landscape within the chronic wound environment.
Institute
Montana State University
DepartmentChemistry and Biochemistry
LaboratoryAmmons
Last NameAmmons
First NameMary Cloud
Address103 CBB, Montana State University, Bozeman, MT 59717
Emailmcammons@chemistry.montana.edu
Phone406-600-0301
Submit Date2015-03-10
Num GroupsNA
Total Subjects4 patients/8 samples
Raw Data AvailableNo
Analysis Type DetailNMR
Release Date2015-04-20
Release Version1
Mary Cloud Ammons Mary Cloud Ammons
https://dx.doi.org/10.21228/M8WW2P
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000131
Project DOI:doi: 10.21228/M8WW2P
Project Title:Association of Metabolic Profile and Microbiome in Chronic Pressure Ulcer Wounds
Project Type:NMR metabolomic and 16S rRNA taxonomic profiling in chronic pressure ulcer wounds
Project Summary:Chronic, non-healing wounds contribute significantly to the suffering of patients with co-morbidities in the clinical population with mild to severely compromised immune systems. Normal wound healing proceeds through a well-described process. However, in chronic wounds this process seems to become dysregulated at the transition between resolution of inflammation and re-epithelialization. Bioburden in the form of colonizing bacteria is a major contributor to the delayed headlining in chronic wounds such as pressure ulcers. However how the microbiome influences the wound metabolic landscape is unknown. Here, we have used a Systems Biology approach to determine the association between the taxonomic and metabolomic profile of wounds colonized by bacteria. Pressure ulcer biopsies were harvested from primary chronic wounds and bisected into top and bottom sections prior to analysis of microbiome by pyrosequencing and analysis of metabolome using 1H nuclear magnetic resonance (NMR) spectroscopy. Bacterial taxonomy revealed that wounds were colonized predominantly by three main phyla, but differed significantly at the genus level. While taxonomic profiles demonstrated significant variability between wounds, metabolic profiles shared significant similarity based on the depth of the wound biopsy. Association between taxonomy and metabolic landscape indicated significant wound-to-wound similarity in metabolite enrichment sets and metabolic pathway impacts, especially with regard to amino acid metabolism. To our knowledge, this is the first demonstration of a statistically robust correlation between bacterial colonization and metabolic landscape within the chronic wound environment.
Institute:Montana State University
Department:Chemistry and Biochemistry
Laboratory:Ammons and Copie
Last Name:Ammons
First Name:Mary Cloud
Address:103 CBB, Montana State University, Bozeman, MT 59717
Email:mcammons@chemistry.montana.edu
Phone:406-600-0301
Funding Source:NIH 1KO1GM103821-01 and 1RO3AR060995-01A1

Subject:

Subject ID:SU000169
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:63|27|23|43
Gender:Male|Female|Female|Male
Human Race:African American|African American|White, non-hispanic|African American
Human Ethnicity:Cerebral palsy, mental retardation, scoliosis, seizure disorder|Deep vein thrombosis, anemia, bipolar, herpes simplex virus|Urinary tract infection, anxiety, depression
Human Lifestyle Factors:None|Cerebral palsy, mental retardation, scoliosis, seizure disorder|Deep vein thrombosis, anemia, bipolar, herpes simplex virus|Urinary tract infection, anxiety, depression
Human Medications:Systemic:Bactrim Topical:None|None|Systemic:Vancomycin|Systemic:Doxycycline Topical:Mesalt
Human Nutrition:Well nourished|G-tube fed, liquid only, malnourished|Well nourished|Inadequate protein intake
Species Group:Human

Factors:

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

mb_sample_id local_sample_id Patient
SA008210P1BPatient 1
SA008211P1TPatient 1
SA008212P2BPatient 2
SA008213P2TPatient 2
SA008214P3TPatient 3
SA008215P3BPatient 3
SA008216P4BPatient 4
SA008217P4TPatient 4
Showing results 1 to 8 of 8

Collection:

Collection ID:CO000155
Collection Summary:Samples were collected via punch biopsy from wound edge and sectioned into top and bottom
Collection Protocol Comments:Chronicity is defined as wounds lasting more than 30 days
Sample Type:Tissue
Collection Method:Punch biopsy
Collection Location:Wound Edge
Collection Frequency:Single Collection
Volumeoramount Collected:9-32 mg
Storage Conditions:Flash frozen in liquid nitrogen, shipped on dry ice, stored at -80C
Tissue Cell Identification:T=Top section B=Bottom section
Tissue Cell Quantity Taken:9-32mg

Treatment:

Treatment ID:TR000174

Sample Preparation:

Sampleprep ID:SP000169
Sampleprep Summary:Cold methanol/chloroform extraction
Processing Method:Biopsy samples were resuspended in ice-cold 60% aqueous methanol and homogenized using a tissue homogenizer (Tissue Tearor™ Model 985370-395, Biospec Products Inc., Bartlesville, OK) set to 2-minute intervals of 10 seconds on and 5 seconds off
Processing Storage Conditions:On ice
Extraction Method:1:1 aqueous chloroform
Extract Cleanup:Aqueous layers collected and lyophilized
Extract Storage:Lyophilized samples were stored at -80C
Sample Resuspension:Resuspended in 10mM NaH2PO4/Na2HPO4
Organ:Skin
Organ Specification:Chronic wound biopsy

Chromatography:

Chromatography ID:CH000166

Analysis:

Analysis ID:AN000237
Laboratory Name:Copie Lab
Analysis Type:NMR
Software Version:Topspin version 3
Operator Name:Brian Tripet
Detector Type:cryoprobeTM
Chromatography ID:CH000166
Num Factors:4
Num Metabolites:121

NMR:

NMR ID:NM000052
Analysis ID:AN000237
Instrument Name:Bruker Avance III
Instrument Type:FT-NMR
NMR Experiment Type:1D 1H
Spectrometer Frequency:600 MHz
Offset Frequency:600 mHz
Presaturation Power Level:cryoprobeTM
Chemical Shift Ref Cpd:10mM NaH2PO4/ Na2HPO4
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