Community standards and future opportunities for synthetic communities in plant–microbiota research

Northen, Trent R.; Kleiner, Manuel; Torres, Marta; Kovács, Ákos T.; Nicolaisen, Mette Haubjerg; Krzyżanowska, Dorota M.; Sharma, Shilpi; Lund, George; Jelsbak, Lars; Baars, Oliver; Kindtler, Nikolaj Lunding; Wippel, Kathrin; Dinesen, Caja; Ferrarezi, Jessica A.; Marian, Malek; Pioppi, Adele; Xu, Xinming; Andersen, Tonni; Geldner, Niko; Schulze-Lefert, Paul; Vorholt, Julia A.; Garrido-Oter, Ruben

doi:10.1038/s41564-024-01833-4

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2024

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Cited by 2 publications

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A cross-systems primer for synthetic microbial communities

Mehlferber,

Arnault,

Joshi

et al. 2024

Nat Microbiol

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A cross-systems primer for synthetic microbial communities

Mehlferber,

Arnault,

Joshi

et al. 2024

Nat Microbiol

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Multi-laboratory Study Establishes Reproducible Methods for Plant-Microbiome Research in Fabricated Ecosystems

Novak,

Andeer,

King

et al. 2024

Preprint

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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 grassBrachypodium 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 whereParaburkholderiasp. OAS925 could dramatically shift microbiome composition. Comparative genomics and exudate utilization linked the pH-dependent colonization ability ofParaburkholderia, 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.

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Community standards and future opportunities for synthetic communities in plant–microbiota research

Cited by 2 publications

References 114 publications

A cross-systems primer for synthetic microbial communities

A cross-systems primer for synthetic microbial communities

Multi-laboratory Study Establishes Reproducible Methods for Plant-Microbiome Research in Fabricated Ecosystems

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