Dataset index
Title: Genome sequencing underlying Schäfer et al., 2022
Description: Reads obtained from genome resequencing of Aeromicrobium sp. Leaf245 ethyl-methansulfonate (EMS) mutagenized clones to map mutations manifesting in loss of inhibition of Nocardioides sp. Leaf374.
Year: 2022
Permanent identifier: PRJEB47688
Responsible PI: J. Vorholt (ETHZ)
Research article: Mapping phyllosphere microbiota interactions in planta to establish genotype–phenotype relationships
Title: Amplicon sequencing reads underlying Schäfer et al., 2022
Description: 16S rRNA gene amplicon sequencing reads
Year: 2022
Permanent identifier: PRJEB50894
Responsible PI: J. Vorholt (ETHZ)
Research article: Mapping phyllosphere microbiota interactions in planta to establish genotype–phenotype relationships
Title: Proteomics data underlying Hemmerle et al., 2022
Description: MS-based proteomics data
Year: 2022
Permanent identifier: 10.6019/PXD026619
Responsible PI: J. Vorholt (ETHZ)
Research article: Dynamic character displacement among a pair of bacterial phyllosphere commensals in situ
Title: amplicon sequencing data underlying Causevic et al., 2022
Description: NatCom and SynCom 16S rRNA gene amplicon sequencing data – raw sequence reads
Year: 2022
Permanent identifier: PRJNA767350
Responsible PI: J. R. van der Meer (UNIL)
Research article: Reproducible Propagation of Species-Rich Soil Bacterial Communities Suggests Robust Underlying Deterministic Principles of Community Formation
Title: Pivotal role of O-antigenic polysaccharide display in the sensitivity against phage tail-like particles in environmental Pseudomonas kin competition
Description: Tn-Seq raw data
Year: 2022
Permanent identifier: 10.5061/dryad.1zcrjdft6
Responsible PI: C. Keel (UNIL)
Research article: Pivotal role of O-antigenic polysaccharide display in the sensitivity against phage tail-like particles in environmental Pseudomonas kin competition
Title: Meta-omics-aided isolation of elusive anaerobic arsenic-methylating soil bacteria
Description: Metagenomic, metatranscriptomics, metaproteomics analyses
Year: 2022
Permanent identifier: 10.5281/zenodo.4605527
Responsible PI: R. Bernier-Latmani (EPFL)
Research article: Meta-omics-aided isolation of an elusive anaerobic arsenic-methylating soil bacterium
Title: Genome sequencing of Arabidopsis phyllosphere isolates underlying Vogel et al., 2021
Description: Bacterial genomic data for seventeen bacterial leaf isolates belonging to the At-LSPHERE strain collection
Year: 2021
Permanent identifier: PRJEB47672
Responsible PI: J. Vorholt (ETH Zurich)
Research article: Protective role of the Arabidopsis leaf microbiota against a bacterial pathogen
Title: Raw reads of demultiplexed 16S rDNA amplicon samples underlying Pfeilmeier et al., 2021
Description: 16S rRNA amplicon sequencing raw data
Year: 2021
Permanent identifier: European Nucleotide Archive (ENA) – identifier: PRJEB44158
Responsible PI: J. Vorholt (ETHZ)
Research article: The plant NADPH oxidase RBOHD is required for microbiota homeostasis in leaves
Title: Metabolomics raw data (together with relevant metadata) underlying Maier et al., 2021
Description: Metabolomics raw data
Year: 2021
Permanent identifier: MetaboLights (EMBL-EBI) – identifier: MTBLS2522
Responsible PI: J. Vorholt (ETHZ)
Research article: A General Non-Self Response as Part of Plant Immunity
Title: Transcriptomics raw data underlying Maier et al., 2021
Description: Transcriptomics raw data
Year: 2021
Permanent identifier: European Nucleotide Archive (ENA) – identifier: PRJEB40488
Responsible PI: J. Vorholt (ETHZ)
Research article: A General Non-Self Response as Part of Plant Immunity
Title: mOTUs v2 database
Description: Database for the marker gene-based OTU (mOTU) profiler. The mOTUs profiler is a computational tool that estimates relative abundance of known and currently unknown microbial community members using metagenomic shotgun sequencing data.
Year: 2021
Responsible PI: S. Sunagawa (ETHZ)
Research article: Microbial abundance, activity and population genomic profiling with mOTUs2
Title: Soil Community Growth and Diversity Simulations under Low and High Connectivity Conditions (version MATLAB 2016a)
Description: MATLAB community simulations, MATLAB imaging script, and MATLAB dataset
Year: 2021
Responsible PI: J. R. van der Meer (UNIL)
Research article: Environmental Connectivity Controls Diversity in Soil Microbial Communities.”
Title: 16S rRNA amplicon sequencing raw data underlying Dubey et al., 2021
Description: 16S rRNA amplicon sequencing raw data
Year: 2021
Permanent identifier: NCBI Short Read Archive – PRJNA661487
Responsible PI: J. R. van der Meer (UNIL)
Research article: Environmental Connectivity Controls Diversity in Soil Microbial Communities
Title: CellCognize: a neural network pipeline for cell type classification from flow cytometry data
Description: Flow cytometry data; neural network data; 16S sequencing data
Year: 2020
Responsible PI: J. R. van der Meer (UNIL)
Research article: Rapid detection of microbiota cell type diversity using machine-learned classification of flow cytometry data