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.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000150 |
| Study Title | Association of Metabolic Profile and Microbiome in Chronic Pressure Ulcer Wounds |
| Study 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 |
| Last Name | Ammons |
| First Name | Mary Cloud |
| Address | 103 CBB, Montana State University, Bozeman, MT 59717 |
| mcammons@chemistry.montana.edu | |
| Phone | 406-600-0301 |
| Submit Date | 2015-03-10 |
| Num Groups | NA |
| Total Subjects | 4 patients/8 samples |
| Raw Data Available | No |
| Analysis Type Detail | NMR |
| Release Date | 2015-04-20 |
| Release Version | 1 |
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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 |
|---|---|---|
| SA008210 | P1B | Patient 1 |
| SA008211 | P1T | Patient 1 |
| SA008212 | P2B | Patient 2 |
| SA008213 | P2T | Patient 2 |
| SA008214 | P3T | Patient 3 |
| SA008215 | P3B | Patient 3 |
| SA008216 | P4B | Patient 4 |
| SA008217 | P4T | Patient 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 |
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 |
