Plant-associated bacterial culture collections database

The link to the culture colleciton database can be found here. If you have specific questions or requests, please contact Dr. Shingo Miyauchi.

Arabidopsis thaliana root and leaf culture collections

Healthy plants host in their above and belowground organs taxonomically structured bacterial assemblies, and members of these communities contribute to plant growth and health. We established Arabidopsis leaf- and root-derived microbiota culture collections representing the majority of bacterial species that are reproducibly detectable by culture-independent community profiling.

Here we provide access to the library of sequenced genomes from the At-SPHERE culture collections from Arabidopsis leaves and roots.

Lotus japonicus root and nodule culture collections

Roots of different plant species are colonised by bacterial communities, that are distinct even when hosts share the same habitat. It remains unclear to what extent the host actively selects these communities and whether commensals are adapted to a specific plant species. To address this question, we assembled a sequence-indexed bacterial culture collection from roots and nodules of Lotus japonicus that contains representatives of most species previously identified using metagenomics.

Here we provide access to the library of sequenced genomes from the Lj-SPHERE culture collections from Lotus roots and nodules.


If you use the data available in this website, please, include the following citation(s):

Bai, Y.*, Müller, D. B.*, Srinivas, G.*, Garrido-Oter, R.*, Potthoff, E., Rott, M., Dombrowski, N., Münch, P. C., Spaepen, S., Remus-Emsermann, M., Hüttel, B., McHardy, A. C., Vorholt, J. A., and Schulze-Lefert, P. Functional overlap of the Arabidopsis leaf and root microbiota. Nature, 2015.

Wippel, K.*, Tao, K.*, Niu, Y., Zgadzaj, R., Guan, R., Dahms, E., Zhang, P., Jensen, D. B., Logemann, E., Radutoiu, S., Schulze-Lefert, P.+, Garrido-Oter, R.+. Host preference and invasiveness of commensals in the Lotus and Arabidopsis root microbiota. bioRxiv, 2021.


Requests for strains of the At-RSPHERE and soil collection can be addressed to Prof. Paul Shulze-Lefert.
Requests for isolates of the At-LSPHERE collection can be addressed to Prof. Julia Vorholt.

Requests for isolates of the Lj-LSPHERE collection can be addressed to Prof. Paul Schulze-Lefert, Prof. Simona Radutoiu. or Ruben Garrido-Oter.

Questions regarding the culture collection database can be directed to Ruben Garrido-Oter.