MassIVE MSV000095476

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EcoFAB 2.0 Root Microbiome Ring Trial

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Description

The experiment aimed to demonstrate the reproducibility of microbiome formation, metabolite production, and plant growth across multiple laboratories using the EcoFAB 2.0 system. To achieve this, five laboratories (A-E) conducted the identical experiment. In each laboratory, Brachypodium distachyon Bd21-3 was grown in the EcoFAB 2.0 system and subjected to the following treatments: an axenic (mock-inoculated) plant control, two synthetic communities SynCom16 or SynCom17 (+/-Burkholderia sp. OAS925, a strong root colonizer), or a plant-free medium control. Each treatment was replicated seven times (n=7). After 22 days, the spent hydroponic growth medium was collected and analyzed using polar HILIC metabolomics to determine the exometabolite composition. [doi:10.25345/C5Q23RB6B] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Ring trial ; Brachypodium ; SynCom ; microbiome ; reproducibility ; exudates

Contact

Principal Investigators:
(in alphabetical order) 		Trent Northen, Lawrence Berkeley National Laboratory, USA
Submitting User: vnovak

Publications

Novak V, Andeer PF, King E, Calabria J, Fitzpatrick C, Kelm JM, Wippel K, Kosina SM, Bowen BP, Daum C, Zane M, Yadav A, Chen M, Russ D, Adams CA, Owens TK, Lee B, Ding Y, Sordo Z, Chakraborty R, Roux S, Deutschbauer AM, Ushizima D, Zengler K, Arsova B, Dangl JL, Schulze-Lefert P, Watt M, Vogel JP, Northen TR.
Breaking the reproducibility barrier with standardized protocols for plant-microbiome research.
PLoS Biol. 2025 Sep;23(9):e3003358. Epub 2025 Sep 8.

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Number of distinct conditions across all analyses (original submission and reanalyses) associated with this dataset.

Distinct condition labels are counted across all files submitted in the "Metadata" category having a "Condition" column in this dataset.

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Number of distinct biological replicates across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct technical replicates across all analyses (original submission and reanalyses) associated with this dataset.

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Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

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Number of distinct protein accessions reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct proteins quantified across all analyses (original submission and reanalyses) associated with this dataset.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

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Number of distinct proteins found to be differentially abundant in at least one comparison across all analyses (original submission and reanalyses) associated with this dataset.

A protein is differentially abundant if its change in abundance across conditions is found to be statistically significant with an adjusted p-value <= 0.05 and lists no issues associated with statistical tests for differential abundance.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
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