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@ARTICLE{Novak:1050632,
      author       = {Novak, Vlastimil and Andeer, Peter F. and King, Eoghan and
                      Calabria, Jacob and Fitzpatrick, Connor and Kelm, Jana M.
                      and Wippel, Kathrin and Kosina, Suzanne M. and Bowen,
                      Benjamin P. and Daum, Chris and Zane, Matthew and Yadav,
                      Archana and Chen, Mingfei and Russ, Dor and Adams, Catharine
                      A. and Owens, Trenton K. and Lee, Bradie and Ding, Yezhang
                      and Sordo, Zineb and Chakraborty, Romy and Roux, Simon and
                      Deutschbauer, Adam M. and Ushizima, Daniela and Zengler,
                      Karsten and Arsova, Borjana and Dangl, Jeffery L. and
                      Schulze-Lefert, Paul and Watt, Michelle and Vogel, John P.
                      and Northen, Trent R.},
      title        = {{B}reaking the reproducibility barrier with standardized
                      protocols for plant–microbiome research},
      journal      = {PLoS biology},
      volume       = {23},
      number       = {9},
      issn         = {1544-9173},
      address      = {Lawrence, KS},
      publisher    = {PLoS},
      reportid     = {FZJ-2026-00384},
      pages        = {e3003358 -},
      year         = {2025},
      abstract     = {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.},
      cin          = {IBG-2},
      ddc          = {610},
      cid          = {I:(DE-Juel1)IBG-2-20101118},
      pnm          = {2171 - Biological and environmental resources for
                      sustainable use (POF4-217)},
      pid          = {G:(DE-HGF)POF4-2171},
      typ          = {PUB:(DE-HGF)16},
      doi          = {10.1371/journal.pbio.3003358},
      url          = {https://juser.fz-juelich.de/record/1050632},
}