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.
| Study ID | ST002523 |
| Study Title | Candida expansion in the human gut is associated with an ecological signature that supports growth under dysbiotic conditions |
| Study Summary | The 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) |
| Department | Microbiome Dynamics |
| Last Name | Bastian |
| First Name | Seelbinder |
| Address | Beutenbergstraße 11a, Jena, Thuringia, 07745, Germany |
| bastian.seelbinder@leibniz-hki.de | |
| Phone | +4936415321360 |
| Submit Date | 2023-03-23 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-04-12 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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 |
