Summary of Study ST002523

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 PR001625. The data can be accessed directly via it's Project DOI: 10.21228/M8NM7N 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 IDST002523
Study TitleCandida expansion in the human gut is associated with an ecological signature that supports growth under dysbiotic conditions
Study SummaryThe overgrowth of Candida species in the human gut is considered a prerequisite for invasive candidiasis. However, our understanding of how gut bacteria promote or restrict overgrowth of Candida species in the human gut is still limited. By integrating mycobiome and shotgun metagenomics data from stool of 75 patients at risk but with no systemic candidiasis, we revealed that bacterial communities from high Candida samples had greater metabolic potential whereas communities from low Candida had greater functional redundancy. In addition, we developed machine learning models that used only bacterial taxa or functional relative abundances to predict the levels of Candida genus and species in an external validation cohort with an area under the curve of 78.6-81.1%. Last, we proposed an intriguing mechanism for Candida species overgrowth based on a decrease in short-chain fatty acid producing-bacteria resulting in increased oxygen levels. These conditions create a metabolic niche for Candida species to use lactate as a carbon source and overtake their fungal competitors in the human gut.
Institute
Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute (Leibniz-HKI)
DepartmentMicrobiome Dynamics
Last NameBastian
First NameSeelbinder
AddressBeutenbergstraße 11a, Jena, Thuringia, 07745, Germany
Emailbastian.seelbinder@leibniz-hki.de
Phone+4936415321360
Submit Date2023-03-23
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2023-04-12
Release Version1
Seelbinder Bastian Seelbinder Bastian
https://dx.doi.org/10.21228/M8NM7N
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001625
Project DOI:doi: 10.21228/M8NM7N
Project Title:Metabolomics of human urine
Project Type:MS quantitative analysis
Project Summary:Metabolomics of human urine to support the findings in Candida expansion in the gut of lung cancer patients associates with an ecological signature that supports growth under dysbiotic conditions
Institute:Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute (Leibniz-HKI)
Department:Microbiome Dynamics
Last Name:Seelbinder
First Name:Bastian
Address:Beutenbergstraße 11a, Jena, Thuringia, 07745, Germany
Email:bastian.seelbinder@leibniz-hki.de
Phone:+4936415321360

Subject:

Subject ID:SU002623
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:68 (63, 73)
Weight Or Weight Range:77 (62, 87)
Height Or Height Range:170 (160, 176)
Gender:Male and female
Human Ethnicity:White
Human Medications:anti-PD-1 immune checkpoint inhibitors (nivolumab or pembrolizumab)
Human Inclusion Criteria:consecutive advanced cancer patients

Factors:

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

mb_sample_id local_sample_id Candida Gender Immunotherapy
SA254492MT239High Female Pembrolizumab
SA254493MK175High Female Pembrolizumab
SA254494MK329High Male Nivolumab
SA254495MK304High Male Nivolumab
SA254496MK311High Male Nivolumab
SA254497MK209High Male Nivolumab
SA254498MT241High Male Pembrolizumab
SA254499MK324High Male Pembrolizumab
SA254500MT196High Male Pembrolizumab
SA254501MK300High Male Pembrolizumab
SA254502MT242Low Female Nivolumab
SA254503MK115Low Female Nivolumab
SA254504MK227Low Female Nivolumab
SA254505MK287Low Female Pembrolizumab
SA254506MK251Low Male Nivolumab
SA254507MT252Low Male Nivolumab
SA254508MT245Low Male Nivolumab
SA254509MT238Low Male Nivolumab
SA254510MK279Low Male Pembrolizumab
Showing results 1 to 19 of 19

Collection:

Collection ID:CO002616
Collection Summary:Human urine samples were collected by from lung cancer patients and frozen at -80 °C. Samples were shipped to MS-OMICS for metabolomic analysis.
Sample Type:Urine
Storage Conditions:-80℃

Treatment:

Treatment ID:TR002635
Treatment Summary:To unfreeze samples at MS-OMICS, samples were assigned to their SpinX filters and centrifugated at 15,000 RPM for 5 minutes at 4 °C. Urine samples were then diluted 11 times in mobile phase eluent A and fortified with stable isotope labelled standards before analysis.
Treatment Compound:mobile phase eluent A

Sample Preparation:

Sampleprep ID:SP002629
Sampleprep Summary:Urine samples were then diluted 11 times in mobile phase eluent A and fortified with stable isotope labelled standards before analysis.

Combined analysis:

Analysis ID AN004157
Analysis type MS
Chromatography type Reversed phase
Chromatography system Thermo Vanquish
Column Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.8um)
MS Type ESI
MS instrument type QTRAP
MS instrument name Thermo Orbitrap Exploris 240
Ion Mode UNSPECIFIED
Units Peak area

Chromatography:

Chromatography ID:CH003076
Chromatography Summary:The samples were analysed with our semi-polar metabolites method, which is a slightly modified version of the protocol described by Catalin et al. (UPLC/MS Monitoring of Water-Soluble Vitamin Bs in Cell Culture Media in Minutes, Water Application note 2011, 720004042en). The analysis was carried out in a randomised order using a UPLC system (Vanquish, Thermo Fisher Scientific) coupled with a high-resolution quadrupole-orbitrap mass spectrometer Orbitrap Exploris 240 MS, Thermo Fisher Scientific.
Instrument Name:Thermo Vanquish
Column Name:Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.8um)
Column Temperature:30
Flow Gradient:300 μL/min: 0-2 min: 0% B, 2-12 min: 35% B, 12-13 min: 90% B, 13-14 min: 90% B, 14-15 min: 0% B
Flow Rate:300 μL/min
Solvent A:100% water; 10 mM ammonium formate; 0.1% formic acid (pH 3.1)
Solvent B:100% methanol; 10 mM ammonium formate; 0.1% formic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS003904
Analysis ID:AN004157
Instrument Name:Thermo Orbitrap Exploris 240
Instrument Type:QTRAP
MS Type:ESI
MS Comments:The ionization was achieved with an electrospray ionization interface operated in positive and negative ionization mode under polarity switching. Data were processed using Compound Discoverer 3.3 (Thermo Fisher Scientific) and Skyline 21.2.
Ion Mode:UNSPECIFIED
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