Amping up reproducibility of microbiome studies through standardized protocols and fabricated ecosystems

There is ample evidence for the impacts of plant microbiomes to plant growth and metabolism, but there are also challenges to obtaining reproducible data. In a first of its kind multi-laboratory microbiome reproducibility study, researchers from five groups across three continents used prefabricated single-plant sterile incubation chambers (see https://www.protocols.io/view/use-of-ecofab-2-0-for-reproducible-plant-microbe-i-kxygxyydkl8j/v1) to study microbiome of the model grass, Brachyopodium distachyon. The authors applied synthetic bacterial communities (SymCom) to Brachypodium distachyon in sterile chambers, and then they examined plant phenotype, microbiome assembly and exo-metabolite profiles. The authors tested two synthetic communities. SynCom16 and SynCom17. SymCom17 has 17 bacterial isolates including the dominant root colonizer Paraburkholderia sp. OAS925, whereas SynCom16 lacks this dominant species. After 22 days, plant biomass was quantified. Plants inoculated with either SynCom showed smaller biomass than those grown sterilely, although the decrease in biomass with SynCom17 was greater, possibly due to Paraburkholderia sp. Importantly, there was minimal variation  between labs of the plant phenotypes, exuded metabolites, and final microbiome composition. The findings show that through standardized protocols and conditions, plant-microbiome research can be highly reproducible.  (Summary by Indrani Kakati @indranik333 @indranik18.bsky.social) PLOSBio 10.1371/journal.pbio.3003358