MZMine 3 settings.

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.

微生物组研究领域中，实验室间可重复性至关重要却极具挑战。利用微生物组促进土壤健康与植物生长，需借助可复现的实验体系解析其背后的分子机制。本研究依托涵盖5家实验室的全球协作网络，通过验证我们重复合成群落组装实验的能力，旨在推动微生物组研究的可重复性提升。本研究针对两种不同合成细菌群落构建的人工生态系统、模式草本植物二穗短柄草（Brachypodium distachyon）以及无菌EcoFAB 2.0装置开展对照实验。所有参与实验室均观察到一致的接种量依赖性变化：植物表型、根系分泌物组成与最终细菌群落结构均发生显著改变，其中帕拉伯克霍尔德氏菌属菌株OAS925（Paraburkholderia sp. OAS925）可大幅重塑微生物组组成。比较基因组学与分泌物利用分析揭示了帕拉伯克霍尔德氏菌属菌株的pH依赖性定殖能力，该结论通过运动性实验得到进一步验证。本研究提供了详细的实验方案、基准数据集与最佳实践指南，以期推动可复现科学研究的发展，并为未来多实验室可重复性研究提供参考。