TY  - JOUR
AU  - Novak, Vlastimil
AU  - Andeer, Peter F.
AU  - King, Eoghan
AU  - Calabria, Jacob
AU  - Fitzpatrick, Connor
AU  - Kelm, Jana M.
AU  - Wippel, Kathrin
AU  - Kosina, Suzanne M.
AU  - Bowen, Benjamin P.
AU  - Daum, Chris
AU  - Zane, Matthew
AU  - Yadav, Archana
AU  - Chen, Mingfei
AU  - Russ, Dor
AU  - Adams, Catharine A.
AU  - Owens, Trenton K.
AU  - Lee, Bradie
AU  - Ding, Yezhang
AU  - Sordo, Zineb
AU  - Chakraborty, Romy
AU  - Roux, Simon
AU  - Deutschbauer, Adam M.
AU  - Ushizima, Daniela
AU  - Zengler, Karsten
AU  - Arsova, Borjana
AU  - Dangl, Jeffery L.
AU  - Schulze-Lefert, Paul
AU  - Watt, Michelle
AU  - Vogel, John P.
AU  - Northen, Trent R.
TI  - Breaking the reproducibility barrier with standardized protocols for plant–microbiome research
JO  - PLoS biology
VL  - 23
IS  - 9
SN  - 1544-9173
CY  - Lawrence, KS
PB  - PLoS
M1  - FZJ-2026-00384
SP  - e3003358 -
PY  - 2025
AB  - Inter-laboratory replicability is crucial yet challenging in microbiome research. Leveraging microbiomes to promote soil health and plant growth requires understanding underlying molecular mechanisms using reproducible experimental systems. In a global collaborative effort involving five laboratories, we aimed to help advance reproducibility in microbiome studies by testing our ability to replicate synthetic community assembly experiments. Our study compared fabricated ecosystems constructed using two different synthetic bacterial communities, the model grass Brachypodium distachyon, and sterile EcoFAB 2.0 devices. All participating laboratories observed consistent inoculum-dependent changes in plant phenotype, root exudate composition, and final bacterial community structure, where Paraburkholderia sp. OAS925 could dramatically shift microbiome composition. Comparative genomics and exudate utilization linked the pH-dependent colonization ability of Paraburkholderia, which was further confirmed with motility assays. The study provides detailed protocols, benchmarking datasets, and best practices to help advance replicable science and inform future multi-laboratory reproducibility studies.
LB  - PUB:(DE-HGF)16
DO  - DOI:10.1371/journal.pbio.3003358
UR  - https://juser.fz-juelich.de/record/1050632
ER  -