Dataset index
Title: VorholtLab/i-At-LSPHERE: v1.0
Description: v1.0 public release for the publication “Metabolic interaction models recapitulate leaf microbiota ecology” by Schäfer, Pacheco, et al.
Year: 2023
Permanent identifier: 10.5281/zenodo.7915629.
Responsible PI: J. Vorholt (ETHZ)
Research article: Modelling of metabolic interactions predicts ecological outcomes for leaf microbiota members in situ
Title: MicrobiologyETHZ/platescan: v1.0
Description: v1.0 public release for the publication, “Modelling of metabolic interactions predicts ecological outcomes for leaf microbiota members in situ”
Year: 2023
Permanent identifier: 10.5281/zenodo.7898735.
Responsible PI: J. Vorholt (ETHZ)
Research article: Modelling of metabolic interactions predicts ecological outcomes for leaf microbiota members in situ
Title: EPFL-LCSB/open: First release for OpEn framework
Description: The code was released before pubilcation Tha paper titled: “Optimal enzyme utilization suggests that concentrations and thermodynamics determine binding mechanisms and enzyme saturations” by A. Sahin. D.R. Weilandt and V. Hatzimanikatis
Year: 2023
Permanent identifier: 10.5281/zenodo.7829275.
Responsible PI: V. Hatzimanikatis (EPFL)
Research article: Optimal enzyme utilization suggests that concentrations and thermodynamics determine binding mechanisms and enzyme saturations
Title: Data Collection for the article 'Controlled motility in the cyanobacterium Trichodesmium regulates aggregate architecture'
Description: Data that support the findings of the publication ‘Controlled motility in the cyanobacterium Trichodesmium regulates aggregate architecture’ by U. Pfreundt, J. Slomka, G. Schneider, A. Sengupta, F. Carrara, V. Fernandez, M. Ackermann, R. Stocker
Year: 2023
Permanent identifier: 10.3929/ethz-b-000596515
Responsible PI: R. Stocker (ETHZ)
Research article: Controlled motility in the cyanobacterium Trichodesmium regulates aggregate architecture
Title: Integration host factor regulates colonization factors in the bee gut symbiont Frischella perrara
Description: Code, scripts and numeric data files of experimental data underlying Schmidt, Santos Matos, et al., 2023
Year: 2023
Permanent identifier: 10.5281/zenodo.7778751
Responsible PI: P. Engel (UNIL)
Research article: Integration host factor regulates colonization factors in the bee gut symbiont Frischella perrara
Title: STrack: A tool to Simply Track bacterial cells in microscopy time-lapse images
Description: The datasets consist of time-lapse images underlying the research article “STrack: A tool to Simply Track bacterial cells in microscopy time-lapse images”. Please visit the STrack github page for instructions on how to install and use STrack to track cells in images containing segmented cell masks: https://github.com/Helena-todd/STrack
Year: 2023
Permanent identifier: 10.5281/zenodo.7670637
Responsible PI: J. R. van der Meer (UNIL)
Research article: STrack: A Tool to Simply Track Bacterial Cells in Microscopy Time-Lapse Images
Title: ClostriTof microflex Biotyper library plugin and associated raw Maldi spectra version 2.0
Description: This dataset contains the ClostriTof microflex Biotyper library plugin, an installation guide as well as the raw spectral data for all library and validation strains used to construct the ClostriTof library plugin.
Year: 2023
Permanent identifier: 10.5281/zenodo.7773644
Responsible PI: P. Vonaesch (UNIL)
Research article: A MALDI-TOF MS library for rapid identification of human commensal gut bacteria from the class Clostridia
Title: code lukasmalfi/E_Coli: Version 1.0
Description: Customized code used to produce the results presented in the study Laganenka et al. 2023. Original workflow as used in https://doi.org/10.1038/s41564-022-01286-7
Year: 2023
Permanent identifier: 10.5281/zenodo.7829005
Responsible PI: C. Von Mering (UZH) and W.-D. Hardt (ETHZ)
Research article: Chemotaxis and autoinducer-2 signalling mediate colonization and contribute to co-existence of Escherichia coli strains in the murine gut
Title: The gut microbiota affects the social network of honey bees
Description: This dataset contains input files needed to reproduce the automated behavioral tracking data analyses of the research article “The gut microbiota affects the social network of honey bees”. Codes using these data and additional datasets are available at: https://github.com/JoanitoLiberti/The-gut-microbiota-affects-the-social-network-of-honey-bees/
Year: 2022
Permanent identifier: 10.5281/zenodo.5797980
Responsible PI: P. Engel (UNIL)
Research article: The gut microbiota affects the social network of honeybees
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: RNA sequencing of Frischella perrara
Description: RNA sequencing of Frischella perrara PEB0191 during in vitro growth and gut colonization. Expression profiling by high throughput sequencing (Illumina HiSeq and MiniSeq).
Year: 2021
Permanent identifier: GSE189728
Responsible PI: P. Engel (UNIL)
Research article: Integration host factor regulates colonization factors in the bee gut symbiont Frischella perrara
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