Summary of Study ST004091

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 PR002570. The data can be accessed directly via it's Project DOI: 10.21228/M8FN9W 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.

Show all samples  
Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data files (Contains raw data)
Study IDST004091
Study TitleThe Chromobacterium Volatilome is Strongly Influenced by Growth on Liquid versus Solid Media
Study TypeUntargeted metabolomics
Study SummaryThe study of microbial volatile organic compounds (mVOCs) is a growing area of research, with applications ranging from agriculture to human health. The majority of the mVOC data are from in vitro liquid cultures, while few analyses of bacterial and fungal volatilomes on solid media cultures exist. Studies comparing liquid versus solid cultures of bacteria and fungi show significant changes to the soluble metabolites that are produced, suggesting that large differences would be observed for mVOCs based on the culture conditions. To test this idea, we characterized the volatilomes of two species of Chromobacterium, C. violaceum (strain ATCC12472) and C. vaccinii (strain MWU328), and those of their isogenic cviR− quorum-sensing mutants cultured on solid versus liquid King’s Medium B media. VOCs were sampled using thin-film solid-phase microextraction (TF-SPME) and analyzed by two-dimensional gas chromatography–time-of-flight mass spectrometry (GC×GC-TOFMS). Of the three variables examined – Chromobacterium species, media type, and quorum sensing ability – growth on liquid versus solid media caused the most significant differences in the volatilomes. Bacterial species and strain were also influential, but to a lesser degree. Our findings indicate the importance of growth conditions in microbial volatilomics, and therefore, more consideration should be given to how microorganisms are cultured for volatilome analyses and how those conditions are reported.
Institute
Arizona State University
Last NameBean
First NameHeather
AddressPO Box 874501, Tempe, AZ, 85287, USA
EmailHeather.D.Bean@asu.edu
Phone480-727-3395
Submit Date2025-07-29
Raw Data AvailableYes
Raw Data File Type(s)smp
Analysis Type DetailGC-MS
Release Date2025-08-25
Release Version1
Heather Bean Heather Bean
https://dx.doi.org/10.21228/M8FN9W
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR002570
Project DOI:doi: 10.21228/M8FN9W
Project Title:The Chromobacterium Volatilome is Strongly Influenced by Growth on Liquid versus Solid Media
Project Type:Untargeted metabolomics
Project Summary:The study of microbial volatile organic compounds (mVOCs) is a growing area of research, with applications ranging from agriculture to human health. The majority of the mVOC data are from in vitro liquid cultures, while few analyses of bacterial and fungal volatilomes on solid media cultures exist. Studies comparing liquid versus solid cultures of bacteria and fungi show significant changes to the soluble metabolites that are produced, suggesting that large differences would be observed for mVOCs based on the culture conditions. In this study, we conducted an untargeted analysis of the volatile profiles of two species of Chromobacterium, C. violaceum (strain ATCC12472) and C. vaccinii (strain MWU328), and those of their isogenic cviR− quorum-sensing mutants cultured on solid and liquid King’s Medium B media.
Institute:Arizona State University
Department:School of Life Sciences
Laboratory:Bean Laboratory
Last Name:Bean
First Name:Heather
Address:PO Box 874501, Tempe AZ, 85287, USA
Email:Heather.D.Bean@asu.edu
Phone:480-727-3395

Subject:

Subject ID:SU004244
Subject Type:Bacteria
Subject Species:Chromobacterium violaceum; Chromobacterium vaccinii
Taxonomy ID:536;1108595
Cell Biosource Or Supplier:ATCC; Midwestern University

Factors:

Subject type: Bacteria; Subject species: Chromobacterium violaceum; Chromobacterium vaccinii (Factor headings shown in green)

mb_sample_id local_sample_id Sample source Strain Culture medium
SA474371CV12472w_solid_3B_1Bacteria cviR- KMB_agar
SA474372CV328w_solid_2A_1Bacteria cviR- KMB_agar
SA474373CV328w_solid_3C_1Bacteria cviR- KMB_agar
SA474374CV328w_solid_1A_1Bacteria cviR- KMB_agar
SA474375CV12472w_solid_2B_1Bacteria cviR- KMB_agar
SA474376CV12472w_solid_6C_1Bacteria cviR- KMB_agar
SA474377CV12472w_solid_1C_1Bacteria cviR- KMB_agar
SA474378CV328w_solid_2B_1Bacteria cviR- KMB_agar
SA474379CV12472w_solid_5A_1Bacteria cviR- KMB_agar
SA474380CV12472w_solid_5B_1Bacteria cviR- KMB_agar
SA474381CV328w_solid_6A_1Bacteria cviR- KMB_agar
SA474382CV328w_solid_1B_1Bacteria cviR- KMB_agar
SA474383CV328w_solid_3A_1Bacteria cviR- KMB_agar
SA474384CV328w_solid_1C_1Bacteria cviR- KMB_agar
SA474385CV328w_solid_5C_1Bacteria cviR- KMB_agar
SA474386CV328w_solid_6C_1Bacteria cviR- KMB_agar
SA474387CV12472w_solid_4B_1Bacteria cviR- KMB_agar
SA474388CV12472w_solid_3C_1Bacteria cviR- KMB_agar
SA474389CV12472w_solid_2C_1Bacteria cviR- KMB_agar
SA474390CV12472w_solid_5C_1Bacteria cviR- KMB_agar
SA474391CV12472w_solid_2A_1Bacteria cviR- KMB_agar
SA474392CV12472w_solid_1B_1Bacteria cviR- KMB_agar
SA474393CV328w_solid_5B_1Bacteria cviR- KMB_agar
SA474394CV12472w_solid_6A_1Bacteria cviR- KMB_agar
SA474395CV12472w_solid_6B_1Bacteria cviR- KMB_agar
SA474396CV328w_solid_6B_1Bacteria cviR- KMB_agar
SA474397CV328w_solid_3B_1Bacteria cviR- KMB_agar
SA474398CV12472w_solid_3A_1Bacteria cviR- KMB_agar
SA474399CV12472w_solid_4C_1Bacteria cviR- KMB_agar
SA474400CV12472w_solid_1A_1Bacteria cviR- KMB_agar
SA474401CV328w_solid_5A_1Bacteria cviR- KMB_agar
SA474402CV328w_solid_2C_1Bacteria cviR- KMB_agar
SA474403CV328w_solid_4C_1Bacteria cviR- KMB_agar
SA474404CV12472w_solid_4A_1Bacteria cviR- KMB_agar
SA474405CV328w_solid_4A_1Bacteria cviR- KMB_agar
SA474406CV328w_solid_4B_1Bacteria cviR- KMB_agar
SA474407CV328w_liquid_4A_1Bacteria cviR- KMB_broth
SA474408CV12472w_liquid_1C_1Bacteria cviR- KMB_broth
SA474409CV328w_liquid_4C_1Bacteria cviR- KMB_broth
SA474410CV12472w_liquid_5C_1Bacteria cviR- KMB_broth
SA474411CV12472w_liquid_6B_1Bacteria cviR- KMB_broth
SA474412CV12472w_liquid_3C_1Bacteria cviR- KMB_broth
SA474413CV328w_liquid_6C_1Bacteria cviR- KMB_broth
SA474414CV328w_liquid_2C_1Bacteria cviR- KMB_broth
SA474415CV328w_liquid_3B_1Bacteria cviR- KMB_broth
SA474416CV12472w_liquid_1A_1Bacteria cviR- KMB_broth
SA474417CV12472w_liquid_4A_1Bacteria cviR- KMB_broth
SA474418CV12472w_liquid_3B_1Bacteria cviR- KMB_broth
SA474419CV12472w_liquid_5B_1Bacteria cviR- KMB_broth
SA474420CV328w_liquid_4B_1Bacteria cviR- KMB_broth
SA474421CV12472w_liquid_4C_1Bacteria cviR- KMB_broth
SA474422CV12472w_liquid_2C_1Bacteria cviR- KMB_broth
SA474423CV12472w_liquid_5A_1Bacteria cviR- KMB_broth
SA474424CV328w_liquid_5B_1Bacteria cviR- KMB_broth
SA474425CV12472w_liquid_3A_1Bacteria cviR- KMB_broth
SA474426CV12472w_liquid_1B_1Bacteria cviR- KMB_broth
SA474427CV12472w_liquid_6C_1Bacteria cviR- KMB_broth
SA474428CV12472w_liquid_4B_1Bacteria cviR- KMB_broth
SA474429CV328w_liquid_3A_1Bacteria cviR- KMB_broth
SA474430CV328w_liquid_1A_1Bacteria cviR- KMB_broth
SA474431CV328w_liquid_6B_1Bacteria cviR- KMB_broth
SA474432CV328w_liquid_2A_1Bacteria cviR- KMB_broth
SA474433CV328w_liquid_2B_1Bacteria cviR- KMB_broth
SA474434CV328w_liquid_5C_1Bacteria cviR- KMB_broth
SA474435CV12472w_liquid_2B_1Bacteria cviR- KMB_broth
SA474436CV328w_liquid_5A_1Bacteria cviR- KMB_broth
SA474437CV328w_liquid_1B_1Bacteria cviR- KMB_broth
SA474438CV12472w_liquid_6A_1Bacteria cviR- KMB_broth
SA474439CV328w_liquid_6A_1Bacteria cviR- KMB_broth
SA474440CV12472w_liquid_2A_1Bacteria cviR- KMB_broth
SA474299KMB_liquid_1C_1Bacteria NA KMB_broth
SA474300CV12472_solid_6A_1Bacteria QS+ KMB_agar
SA474301CV328_solid_5B_1Bacteria QS+ KMB_agar
SA474302CV328_solid_3C_1Bacteria QS+ KMB_agar
SA474303CV328_solid_1C_1Bacteria QS+ KMB_agar
SA474304CV12472_solid_1A_1Bacteria QS+ KMB_agar
SA474305CV328_solid_1A_1Bacteria QS+ KMB_agar
SA474306CV12472_solid_1C_1Bacteria QS+ KMB_agar
SA474307CV12472_solid_2C_1Bacteria QS+ KMB_agar
SA474308CV12472_solid_6B_1Bacteria QS+ KMB_agar
SA474309CV328_solid_6B_1Bacteria QS+ KMB_agar
SA474310CV12472_solid_5A_1Bacteria QS+ KMB_agar
SA474311CV12472_solid_6C_1Bacteria QS+ KMB_agar
SA474312CV328_solid_6C_1Bacteria QS+ KMB_agar
SA474313CV328_solid_2C_1Bacteria QS+ KMB_agar
SA474314CV328_solid_1B_1Bacteria QS+ KMB_agar
SA474315CV328_solid_4A_1Bacteria QS+ KMB_agar
SA474316CV328_solid_2A_1Bacteria QS+ KMB_agar
SA474317CV328_solid_5A_1Bacteria QS+ KMB_agar
SA474318CV12472_solid_4B_1Bacteria QS+ KMB_agar
SA474319CV328_solid_2B_1Bacteria QS+ KMB_agar
SA474320CV12472_solid_3C_1Bacteria QS+ KMB_agar
SA474321CV12472_solid_2A_1Bacteria QS+ KMB_agar
SA474322CV12472_solid_1B_1Bacteria QS+ KMB_agar
SA474323CV328_solid_3B_1Bacteria QS+ KMB_agar
SA474324CV12472_solid_3A_1Bacteria QS+ KMB_agar
SA474325CV328_solid_4C_1Bacteria QS+ KMB_agar
SA474326CV328_solid_6A_1Bacteria QS+ KMB_agar
SA474327CV328_solid_5C_1Bacteria QS+ KMB_agar
SA474328CV328_solid_4B_1Bacteria QS+ KMB_agar
Showing page 1 of 2     Results:    1  2  Next     Showing results 1 to 100 of 164

Collection:

Collection ID:CO004237
Collection Summary:Quorum sensing sufficient (QS+) Chromobacterium violaceum (ATCC 12472), Chromobacterium vaccinii (MWU 328), and their respective isogenic quorum sensing mutants (cviR-), 12472w and 328w, were cultured in King’s Medium B (KMB). Six biological replicates of each strain were prepared for each media type (i.e., broth or agar). Uninoculated medium controls were prepared in triplicates for KMB broth and KMB agar, respectively.
Sample Type:Bacterial cells

Treatment:

Treatment ID:TR004253
Treatment Summary:Four different strains of Chromobacterium (ATCC 12472, 12472w, MWU 328, 328w) were inoculated in King’s Medium B (KMB) broth and incubated overnight at 25ºC. Sub-cultures of each strain were transferred into replicates of KMB broth (liquid) and KMB agar (solid). Culture replicates were incubated at 25ºC for 7 h and 15.5 h for broth and agar, respectively.

Sample Preparation:

Sampleprep ID:SP004250
Sampleprep Summary:The volatile metabolites were captured using headspace thin-film solid-phase microextraction (HS-TF-SPME). For volatile collection, thin-films composed of divinylbenzene and polydimethylsiloxane (DVB/PDMS) on a carbon mesh were placed in technical triplicates in each biological culture or media-only control. For broth cultures, thin-films were suspended in the flask headspace. For agar cultures, thin-films were placed on the inverted lid of the petri dish. Cultures were incubated at 25ºC for an additional 1 h for volatile collection. After VOC collection, thin-films were removed from cultures and place in thermal desorption tubes and stored at 4ºC prior to analysis. Volatile metabolite analysis was performed using a Gerstel® MPS Robotic Pro MultiPurpose autosampler directed by Maestro® software (Gerstel®, Inc., Linthicum, MD) and two-dimensional gas chromatography−time-of-flight mass spectrometry (GC×GC–TOFMS) using a LECO® Pegasus® 4D and Agilent® 7890B GC (LECO® Corp., St. Joseph, MI).
Extraction Method:Headspace thin-film microextraction (HS-TFME)

Chromatography:

Chromatography ID:CH005161
Chromatography Summary:Column 1: Rxi-624Sil MS,(60m × 0.25mm × 1.4um); Column 2: Stabilwax,(1m × 0.25mm × 0.5um)
Methods Filename:ST_GCxGC_methods.pdf
Instrument Name:Agilent 7890B
Column Name:Rxi-624Sil MS (60m × 0.25mm, 1.4um) and Stabilwax (1m × 0.25mm, 0.5um)
Column Temperature:NA
Flow Gradient:NA
Flow Rate:2 mL∙min-1 (constant)
Solvent A:NA
Solvent B:NA
Chromatography Type:GC

Analysis:

Analysis ID:AN006793
Analysis Type:MS
Analysis Protocol File:ST_MS_methods.pdf
Chromatography ID:CH005161
Has Rt:1
Rt Units:Seconds
Results File:ST004091_AN006793_Results.txt
Units:Peak areas
  logo