Summary of Study ST002779

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 PR001734. The data can be accessed directly via it's Project DOI: 10.21228/M8K72B 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 IDST002779
Study TitleContribution of sugar transporters to spatial microbiota colonization along the longitudinal root axis of Arabidopsis
Study SummaryLongitudinal gut-axes of animals show spatial heterogeneity of microbiota related to physiological differentiation. Plant roots show functional heterogeneity in cellular architecture, transcriptome, metabolic states, and immunity. We hypothesized that axial differentiation impacts spatial colonization by rhizobiota along the root axis. We developed two growth systems, ArtSoil and CD-Rhizotrons, to dissect Arabidopsis thaliana roots into three segments. We identified distinct rhizobiota communities in the segments, supporting spatial microbiota differentiation along the axis. Root metabolite profiling revealed differential enrichment and specificity. Correlation analyses point to strong reliance of rhizobiota on carbohydrate supply from the host. Bioinformatic analyses and GUS histochemistry indicate sugar and/or microbe-induced accumulation of SWEET2, 4, and 12 sugar uniporters. Profiling of root-segments in sweet mutants showed impaired spatial rhizobiota arrangement. Correlation analysis revealed complex interconnected metabolite-rhizobiota networks. This work uncovers interdependency between root physiology and microbiota colonization and a contribution of SWEETs to shaping local adaptation of root microbiota.
Heinrich Heine University Düsseldorf
Last NameWesthoff
First NamePhilipp
AddressUniversitätsstr. 1 40225 Düsseldorf
Phone+49 211-8110926
Submit Date2023-06-26
Raw Data AvailableYes
Raw Data File Type(s)cdf
Analysis Type DetailGC-MS
Release Date2024-02-08
Release Version1
Philipp Westhoff Philipp Westhoff application/zip

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Sample Preparation:

Sampleprep ID:SP002892
Sampleprep Summary:For metabolite extraction, 0.5 mL of chilled extraction buffer (2:5:2 ratio of ddH2O: methanol: chloroform containing 5µM ribitol as internal standard) was added into each root sample and vortex for 20 secs. Metal beads in the tubes were removed. Sample tubes were shaken on a rotary shaker for 30 mins at 4°C. The samples were then centrifuged at 20, 000g for 5 mins at 4°C. After centrifugation, 0.5 ml of supernatant was carefully aspirated and transferred to a clean 1.5 ml microcentrifuge tube. Samples were stored at-80°C. For GC-MS analysis 30µl of sample were dried by vacuum centrifugation in glass inlet tubes. Dried samples were derivatized according to (Gu et al. 2012 DOI:10.1039/c2ib00109h) and measured as described (Shim et al. 2019 DOI:10.3389/fpls.2019.01726)