Summary of Study ST003183

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 PR001982. The data can be accessed directly via it's Project DOI: 10.21228/M8J14Q 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.

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Study IDST003183
Study TitleCampylobacter infection of young children in Colombia and its impact on the gastrointestinal metabolome
Study SummaryCampylobacter infections are a leading cause of bacterial-derived gastroenteritis worldwide with particularly profound impacts on pediatric patients in low-and-middle income countries. It remains unclear how Campylobacter impacts these hosts, though it is becoming increasingly evident that it is a multifactorial process that depends on the host immune response, the gastrointestinal microbiota, various bacterial factors, and host nutritional status. Since these factors likely vary between adult and pediatric patients in different regions of the world, it is important that studies define these attributes in well characterized clinical cohorts in diverse settings. In this study, we analyzed the metabolomic profiles of asymptomatic and symptomatic pediatric patients in Colombia that were either infected or uninfected with Campylobacter during a case-controlled study on acute diarrheal disease. Using computational models, we identified fecal metabolites that were associated with Campylobacter infection and found that glucose-6-phosphate and homovanillic acid were the strongest predictors of infection in these pediatric patients, which suggest that colonocyte metabolism are impacted during infection.
Institute
University of Tennessee
Last NameJohnson
First NameJeremiah
Address1311 Cumberland Avenue, Knoxville, TN, 37996, USA
Emailjjohn358@utk.edu
Phone8659746229
Submit Date2024-04-18
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2024-09-19
Release Version1
Jeremiah Johnson Jeremiah Johnson
https://dx.doi.org/10.21228/M8J14Q
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001982
Project DOI:doi: 10.21228/M8J14Q
Project Title:Campylobacter infection of young children in Colombia and its impact on the gastrointestinal metabolome
Project Type:MS quantitative analysis
Project Summary:Campylobacter infections are a leading cause of bacterial-derived gastroenteritis worldwide with particularly profound impacts on pediatric patients in low-and-middle income countries. It remains unclear how Campylobacter impacts these hosts, though it is becoming increasingly evident that it is a multifactorial process that depends on the host immune response, the gastrointestinal microbiota, various bacterial factors, and host nutritional status. Since these factors likely vary between adult and pediatric patients in different regions of the world, it is important that studies define these attributes in well characterized clinical cohorts in diverse settings. In this study, we analyzed the metabolomic profiles of asymptomatic and symptomatic pediatric patients in Colombia that were either infected or uninfected with Campylobacter during a case-controlled study on acute diarrheal disease. Using computational models, we identified fecal metabolites that were associated with Campylobacter infection and found that glucose-6-phosphate and homovanillic acid were the strongest predictors of infection in these pediatric patients, which suggest that colonocyte metabolism are impacted during infection.
Institute:University of Tennessee
Department:Microbiology
Laboratory:Johnson
Last Name:Johnson
First Name:Jeremiah
Address:1311 Cumberland Avenue, Knoxville, TN, 37996, USA
Email:jjohn358@utk.edu
Phone:8659746229

Subject:

Subject ID:SU003302
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 source PCR positive Diarrhea
SA346728CCN6Feces No No
SA346729CCN5Feces No No
SA346730CCN3Feces No No
SA346731CCN7Feces No No
SA346732CCN4Feces No No
SA346733CCN9Feces No No
SA346734CCN19Feces No No
SA346735CCN13Feces No No
SA346736CCN10Feces No No
SA346737CCN2Feces No No
SA346738CCN8Feces No No
SA346739CCN1Feces No No
SA346740CCN17Feces No Yes
SA346741CCN18Feces No Yes
SA346742CCN16Feces No Yes
SA346743CCN15Feces No Yes
SA346744CCN12Feces No Yes
SA346745CCN14Feces No Yes
SA346746CCN11Feces No Yes
SA346747CCN20Feces No Yes
SA346748CCP17Feces Yes No
SA346749CCP4Feces Yes No
SA346750CCP16Feces Yes No
SA346751CCP18Feces Yes No
SA346752CCP19Feces Yes No
SA346753CCP20Feces Yes No
SA346754CCP2Feces Yes Yes
SA346755CCP3Feces Yes Yes
SA346756CCP7Feces Yes Yes
SA346757CCP12Feces Yes Yes
SA346758CCP13Feces Yes Yes
SA346759CCP14Feces Yes Yes
SA346760CCP1Feces Yes Yes
SA346761CCP10Feces Yes Yes
SA346762CCP9Feces Yes Yes
SA346763CCP6Feces Yes Yes
SA346764CCP15Feces Yes Yes
SA346765CCP8Feces Yes Yes
SA346766CCP5Feces Yes Yes
Showing results 1 to 39 of 39

Collection:

Collection ID:CO003295
Collection Summary:Stool samples were collected from children aged two weeks to 59 months on either the day of enrollment or up to one-week post-enrollment from August to December 2014. Samples were collected in disposable plastic containers and transported to the Laboratoriode Investigaciones Biomédicas y Biotecnológicas (LIBB) at the Universidad de Santander, Bucaramanga, Colombia within four hours. Once samples were examined for color, consistency, presence of blood and/or mucus, aliquots were made and stored at -80°C. The samples were tested for viral, parasitic, and bacterial infections, including adenovirus, astrovirus, norovirus, rotavirus, sapovirus, Entamoeba histolytica, Giardia lamblia, Cryptosporidium spp., Campylobacter spp., Salmonella spp., Shigella spp., Yersinia spp., enteroaggregative Escherichia coli, diffuse-adhering E. coli, enteropathogenic E. coli, enteroinvasive E. coli, and enterotoxigenic E. coli. Campylobacter was detected by isolating on Campylosel agar (Biomerieux) and confirmed using API CAMPY (Biomerieux) and quantitative PCR (qPCR) as previously described. Briefly, human stool samples were diluted 1:10 in DEPC-treated water (Life Technologies), vortexed, and centrifuged. DNA was extracted using a QIAamp DNA stool mini kit (Qiagen) and stored at −20°C. A qPCR assay for C. jejuni and C. coli were conducted on a CFX96 Touch™ Real-Time PCR System as previously described (Bio-Rad). Each well included a 25 µl reaction mixture with 1 µl of DNA, 12.5 µl of TaqMan® environmental master mix, 9 µl of nuclease free water, 1 µl of each primer: cadF-Forward (5’-CTGCTAAACCATAGAAATAAAATTTCTCAC-3’) and cadF-Reverse (5’-CTTTGAAGGTAATTTAGATATGGATAATCG-3’) at a final concentration of 0.4 µM, and 0.5 µl of cadF-Probe (5’-[HEX]-CATTTTGACGATTTTTGGCTTGA-[BHQ2]-3’) at a final concentration of 0.2 µM. The cycling conditions were as follows: 95°C for 10 min, followed by 45 cycles of 95°C for 15 s and 55°C for 1 min.
Sample Type:Feces

Treatment:

Treatment ID:TR003311
Treatment Summary:None

Sample Preparation:

Sampleprep ID:SP003309
Sampleprep Summary:Metabolites were extracted from participant fecal samples by adding 0.650 mL of Metabolic Extraction Solvent (MES) (20:40:40 H2O:ACN:MeOH + 0.1 M Formic acid) to 0.1 gram of sample and mixing thoroughly before adding another 0.650 mL of MES and chilling at -20°C for 20 minutes. Samples were centrifuged (4°C at 13,500 rpm) and the supernatant was transferred to a fresh microcentrifuge tube and stored at 4°C. The resulting pellet was resuspended in 0.2 mL of MES and chilled at -20°C for 20 minutes before centrifugation and transfer of the supernatant to a fresh microcentrifuge tube. The samples were put on ice and transported to the Biological and Small Molecule Mass Spectrometry Core (BSMMSC) of the University of Tennessee where the supernatants were dried under nitrogen and the resulting pellets resuspended in 0.300 mL of milliQ H2O before being transferred to autosampler vials.

Combined analysis:

Analysis ID AN005227
Analysis type MS
Chromatography type Reversed phase
Chromatography system Dionex UltiMate 3000 UHPLC
Column Phenomonex Synergi Hydro RP (100 x 2.0 mm, 2.5 um)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive Plus Orbitrap
Ion Mode NEGATIVE
Units relative abundance

Chromatography:

Chromatography ID:CH003954
Instrument Name:Dionex UltiMate 3000 UHPLC
Column Name:Phenomonex Synergi Hydro RP (100 x 2.0 mm, 2.5 um)
Column Temperature:25
Flow Gradient:mobile phase A during the 25-minute method was 100% at minute zero, 80% at minute 5, 45% at minute 13, 5% at minute 15.5, and 100% at minute 19 and 25, while the mobile phase B gradient equalized the percentage
Flow Rate:0.2 mL/minute
Solvent A:97% methanol/3% water; 11 mM tributylamine; 15 mM acetic acid
Solvent B:100% methanol
Chromatography Type:Reversed phase

MS:

MS ID:MS004960
Analysis ID:AN005227
Instrument Name:Thermo Q Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:scan range of 72-1000 m/z
Ion Mode:NEGATIVE
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