Summary of Study ST001659

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, where it has been assigned Project ID PR001064. The data can be accessed directly via it's Project DOI: 10.21228/M85H6W This work is supported by NIH grant, U2C- DK119886.


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 IDST001659
Study TitleIdentify putative volatile biomarkers of Coccidioides spp. grown in vitro
Study TypeUntargeted metabolomics
Study SummaryValley fever (coccidioidomycosis) is an endemic fungal pneumonia of the North and South American deserts. The causative agents of Valley fever are the dimorphic fungi Coccidioides immitis and C. posadasii, which grow as mycelia in the environment and spherules within the lungs of vulnerable hosts. The current diagnostics for Valley fever are severely lacking due to poor sensitivity and invasiveness, contributing to a 23-day median time-to-diagnosis, and therefore new diagnostic tools are needed. We are working toward the development of a breath-based diagnostic for coccidioidomycosis, and in this initial study we characterized the volatile metabolomes (or volatilomes) of in vitro cultures of Coccidioides. Using solid-phase microextraction and comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry (GC×GC–TOFMS), we characterized the VOCs produced by six strains of each species during mycelial or spherule growth. We detected a total of 353 VOCs that were at least two-fold more abundant in a Coccidioides culture versus medium controls and found the volatile metabolome of Coccidioides is more dependent on growth phase (spherule versus mycelia) than on the species. The volatile profiles of C. immitis and C. posadasii have strong similarities, indicating that a single suite of Valley fever breath biomarkers can be developed to detect both species.
Arizona State University
DepartmentSchool of Life Sciences
LaboratoryBean Laboratory
Last NameBean
First NameHeather
AddressPO Box 874501 Tempe, AZ 85287
Submit Date2021-01-22
PublicationsLifecycle dominates the volatilome character of the dimorphic fungus Coccidioides spp Emily A. Higgins Keppler, Heather L. Mead, Bridget M. Barker, Heather D. Bean bioRxiv 2021.01.15.426916; doi:
Raw Data AvailableYes
Raw Data File Type(s)smp
Analysis Type DetailGC-MS
Release Date2021-03-15
Release Version1
Heather Bean Heather Bean application/zip

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Project ID:PR001064
Project DOI:doi: 10.21228/M85H6W
Project Title:Volatile Biomarkers for a Valley Fever Breath Test
Project Type:GCxGC-TOFMS metabolomics
Project Summary:Coccidioidomycosis, or valley fever, is prevalent in AZ, with more than 12,000 new human infections diagnosed every year. In highly endemic areas, e.g., Phoenix and Tucson, up to 30% of community-acquired pneumonia may be caused by Valley fever, and cases are on the rise. The current diagnostics for Valley fever are severely lacking due to invasiveness (biopsy) and poor sensitivity (serology), strongly contributing to an unacceptable 23-day median time-to-diagnosis. There is a critical need for sensitive and non-invasive diagnostics for identifying Valley fever lung infections. Our long-term goal is to substantially shorten the time-to-diagnosis for Valley fever through the development of sensitive and specific breath-based diagnostics for coccidioidomycosis lung infections. The overall objective of this application is to identify and validate putative volatile biomarkers of Coccidioides infections via metabolomics analyses of in vitro cultures, mouse model lung infections, and lung specimens from humans with Valley fever. At the completion of the proposed study, we expect to have identified and validated a panel of 10-15 volatile biomarkers for the sensitive and specific detection of valley fever in lung specimens.
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
Funding Source:Arizona Biomedical Research Centre New Investigator Award to HDB


Subject ID:SU001736
Subject Type:Fungi
Subject Species:Coccidioides posadasii;Coccidioides immitis
Taxonomy ID:199306;5501


Subject type: Fungi; Subject species: Coccidioides posadasii;Coccidioides immitis (Factor headings shown in green)

mb_sample_id local_sample_id Culture tempurature Culture conditions
SA151948RMSCC2010 Mycelia_230°C normoxia
SA151949RMSCC3506 Mycelia_230°C normoxia
SA151950RMSCC2010 Mycelia_330°C normoxia
SA151951RMSCC2010 Mycelia_430°C normoxia
SA151952RMSCC3506 Mycelia_330°C normoxia
SA151953RMSCC2009 Mycelia_330°C normoxia
SA151954RMSCC2006 Mycelia_330°C normoxia
SA151955RS Mycelia_130°C normoxia
SA151956RMSCC2009 Mycelia_230°C normoxia
SA151957B3221 Mycelia_230°C normoxia
SA151958RMSCC2009 Mycelia_430°C normoxia
SA151959RMSCC3506 Mycelia_130°C normoxia
SA151960RMSCC2395 Mycelia_330°C normoxia
SA151961RMSCC2395 Mycelia_430°C normoxia
SA151962RMSCC3505 Mycelia_330°C normoxia
SA151963RMSCC3505 Mycelia_230°C normoxia
SA151964RMSCC2395 Mycelia_130°C normoxia
SA151965RMSCC3505 Mycelia_430°C normoxia
SA151966RMSCC2343 Mycelia_130°C normoxia
SA151967RMSCC2343 Mycelia_330°C normoxia
SA151968RMSCC2343 Mycelia_430°C normoxia
SA151969RMSCC2006 Mycelia_230°C normoxia
SA151970RMSCC2006 Mycelia_430°C normoxia
SA151971Silveira Mycelia_230°C normoxia
SA151972Control Mycelia_230°C normoxia
SA151973RS Mycelia_330°C normoxia
SA151974Control Mycelia_430°C normoxia
SA151975Silveira Mycelia_330°C normoxia
SA151976B3222 Mycelia_430°C normoxia
SA151977B3221 Mycelia_330°C normoxia
SA151978B3221 Mycelia_430°C normoxia
SA151979B3222 Mycelia_230°C normoxia
SA151980B3222 Mycelia_330°C normoxia
SA151981Silveira Mycelia_130°C normoxia
SA151982Control Mycelia_330°C normoxia
SA151983GT-166 Mycelia_430°C normoxia
SA151984GT-166 Mycelia_230°C normoxia
SA151985GT-166 Mycelia_330°C normoxia
SA151986RS Mycelia_430°C normoxia
SA151987RS Spherule_139°C 10% CO2
SA151988RMSCC3506 Spherule_339°C 10% CO2
SA151989Silveira Spherule_239°C 10% CO2
SA151990RMSCC2395 Spherule_239°C 10% CO2
SA151991Silveira Spherule_339°C 10% CO2
SA151992RMSCC3505 Spherule_139°C 10% CO2
SA151993RMSCC3506 Spherule_239°C 10% CO2
SA151994RMSCC3506 Spherule_139°C 10% CO2
SA151995RS Spherule_239°C 10% CO2
SA151996RMSCC3505 Spherule_339°C 10% CO2
SA151997Silveira Spherule_139°C 10% CO2
SA151998RS Spherule_339°C 10% CO2
SA151999RMSCC3505 Spherule_239°C 10% CO2
SA152000RMSCC2010 Spherule_139°C 10% CO2
SA152001Control Spherule_239°C 10% CO2
SA152002Control Spherule_139°C 10% CO2
SA152003Control Spherule_339°C 10% CO2
SA152004GT-166 Spherule_139°C 10% CO2
SA152005GT-166 Spherule_239°C 10% CO2
SA152006B3222 Spherule_339°C 10% CO2
SA152007B3222 Spherule_239°C 10% CO2
SA152008B3221 Spherule_139°C 10% CO2
SA152009B3221 Spherule_239°C 10% CO2
SA152010B3221 Spherule_339°C 10% CO2
SA152011B3222 Spherule_139°C 10% CO2
SA152012GT-166 Spherule_339°C 10% CO2
SA152013RMSCC2006 Spherule_139°C 10% CO2
SA152014RMSCC2343 Spherule_139°C 10% CO2
SA152015RMSCC2010 Spherule_339°C 10% CO2
SA152016RMSCC2343 Spherule_239°C 10% CO2
SA152017RMSCC2343 Spherule_339°C 10% CO2
SA152018RMSCC2395 Spherule _139°C 10% CO2
SA152019RMSCC2010 Spherule_239°C 10% CO2
SA152020RMSCC2009 Spherule_339°C 10% CO2
SA152021RMSCC2006 Spherule_239°C 10% CO2
SA152022RMSCC2006 Spherule_339°C 10% CO2
SA152023RMSCC2009 Spherule_139°C 10% CO2
SA152024RMSCC2009 Spherule_239°C 10% CO2
SA152025RMSCC2395 Spherule_139°C 10% CO2
Showing results 1 to 78 of 78


Collection ID:CO001729
Collection Summary:All Coccidioides isolates were grown under BSL-3 containment, using conditions that induce mycelial or spherule growth. For mycelial growth, a 50 ml vented falcon tube containing 10 ml of RPMI media (filter sterilized RPMI 1640, 10% fetal bovine serum) was inoculated with a 1 cm x 1 cm 2xGYE agar plug for each strain. These plates were inoculated using 100 µl of glycerol stock, spread across the plate, and cultured for 30°C for two weeks. Control RPMI media was inoculated with a plug from sterile 2xGYE agar media. Each sample, including media control, was prepared in triplicate. Cultures were grown on a shaking incubator at 150 rpm, 30°C for 96 h. For spherule cultures, a 50 ml vented falcon tube containing 10 ml of RPMI media was inoculated to a final concentration of 1.0 x 10^5 arthroconidia/ml in 1xPBS. Arthroconidia were grown and harvested. Strains RMSCC2343 and RMSCC3505 did not produce enough conidia to achieve 1.0 x 10^5 arthroconidia/ml, and were inoculated at 7.0 x 10^4 and 4.0 x 10^4 arthroconidia/ml, respectively. Control media was inoculated with 1 ml of sterile 1xPBS. Cultures were grown on a shaking incubator at 150 rpm, at 39°C in 10% CO2 for 96 h. Mycelial and spherule cultures were spun at 12,000 x g at 4°C for 10 min to pellet the cells. The supernatant was removed and place in a Nanosep MF Centrifugal Devices with Bio-Inert® Membrane 0.2 µm spin filter and centrifuged at 3,200 x g for 4 min. The filtrate was stored at −80°C until volatile metabolomics analysis. The Coccidioides spp. culture filtrates and media blanks were allowed to thaw at 4°C overnight, and then 2 ml were transferred and sealed into sterilized 10 ml GC headspace vials with PTFE/silicone septum screw caps. All samples were stored for up to 12 d at 4°C until analyzed.
Sample Type:Fungi cells


Treatment ID:TR001749
Treatment Summary:All Coccidioides isolates were grown under BSL-3 containment, using conditions that induce mycelial or spherule growth. See Collection Protocol for details

Sample Preparation:

Sampleprep ID:SP001742
Sampleprep Summary:Filtrate samples were heated to 50 degrees Celsius with agitation, and volatiles were sampled for 10 minutes using solid-phase microextraction (SPME) and analyzed using comprehensive gas chromatography coupled to time-of-flight mass spectrometry.
Sampleprep Protocol Filename:ehiggins_invitro_GCxGC_methods.docx
Extraction Method:Solid-phase microextraction (SPME)

Combined analysis:

Analysis ID AN002710
Analysis type MS
Chromatography type GC
Chromatography system Agilent 7890B
Column Multidimensional configuration
MS Type EI
MS instrument type GC x GC-TOF
MS instrument name Leco Pegasus 4D GCxGC TOF
Units Peak areas


Chromatography ID:CH001999
Chromatography Summary:Samples analyzed using comprehensive two-dimensional gas chromatography (GCxGC). See attached method file.
Instrument Name:Agilent 7890B
Column Name:Multidimensional configuration
Chromatography Type:GC


MS ID:MS002507
Analysis ID:AN002710
Instrument Name:Leco Pegasus 4D GCxGC TOF
Instrument Type:GC x GC-TOF
MS Type:EI
MS Comments:see attached MS methods