Dataset index

mBARq 1.0.0
Software for performing statistical analysis, visualization, and contextualization of data generated from studies using transposon-insertion sequencing or barcoded isogenic strains.
2024-08-23
A. Sintsova
10.5281/zenodo.13364628
Sintsova, A., et al. (2024). "mBARq: a versatile and user-friendly framework for the analysis of DNA barcodes from transposon insertion libraries, knockout mutants, and isogenic strain populations." Bioinformatics 40(2). DOI: 10.1093/bioinformatics/btae078
S. Sunagawa (ETHZ)
Computation
Code
Source data for the manuscript titled “An engineered bacterial symbiont allows noninvasive biosensing of the honey bee gut environment”
Tests to measure performance of Snodgrassella alvi bacteria, engineered with plasmids, to serve as biosensors in the bee gut.
2024-08-16
A. Chhun
10.1371/journal.pbio.3002523
Chhun, A., et al. (2024). "An engineered bacterial symbiont allows noninvasive biosensing of the honey bee gut environment." PLoS biology 22(3): e3002523. DOI: 10.1371/journal.pbio.3002523
The plasmids developed in this study have been deposited in Addgene and are available via the following accession numbers: pAC04 (#197400), pAC06 (#197401), pAC08 (#197402), pAC09 (#197403), pAC10 (#197404), pAC11 (#197405), pAC12 (#197406), pAC13 (#197407), pAC14 (#197408), pAC23 (#197409), pAC24 (#197410), pAC25 (#197411), pAC26 (#197412), pAC17V5a (#197413) and pAC17V5b (#197414).
Y. Schaerli (UNIL)
Animal, Synthetic
Bee gut, Engineered systems
Culture, Flow cytometry, Imaging, qPCR
Dataset Expanding the Pseudomonas diversity of the wheat rhizosphere: four novel species antagonizing fungal phytopathogens and with plant-beneficial properties
Growth of wheat plants inoculated with newly-identified species of Pseudomonas bacteria. Observation, from experiments in culture, of antagonistic interaction between the novel Pseudomonas species and fungal pathogens.
2024-05-27
N. Poli, C. Keel and D. Garrido-Sanz
10.5281/zenodo.11354667
Poli, N., et al. (2024). "Expanding the Pseudomonas diversity of the wheat rhizosphere: four novel species antagonizing fungal phytopathogens and with plant-beneficial properties." Frontiers in Microbiology 15: 1440341. DOI: 10.3389/fmicb.2024.1440341
Poli, N., et al. (2024). "Complete genome of four novel Pseudomonas species." NCBI. Permanent Identifier: PRJNA1095474
C. Keel (UNIL)
Plants, soil and environment
Plants, Soil
Culture
Dataset Natural plant disease suppressiveness in soils extends to insect pest control
Certain Swiss soils naturally suppress fungal pathogens. This study explored the extent to which growing in these soils also protects plants from insects that feed on their leaves. Researchers measured physical leaf damage, survival of insect pest larvae, hormones related to the plant stress response, and compounds related to plant defense.
2024-05-21
N. Harmsen, P. Vesga, G. Glauser, F. Klötzli, C. M. Heiman, A. Altenried, J. Vacheron, D. Muller, Y. Moënne-Loccoz, T. Steinger, C. Keel and D. Garrido-Sanz
10.5281/zenodo.11232061
Harmsen, N., et al. (2024). "Natural plant disease suppressiveness in soils extends to insect pest control." Microbiome 12(1): 127. DOI: 10.1186/s40168-024-01841-w
Harmsen, N., et al. (2024). "Role of soil suppressiveness against Oulema melanopus: microbiome responses." NCBI. Permanent Identifier: PRJNA1075215., Soil suppressiveness in insect pest control - raw data tables and R code.
C. Keel (UNIL)
Plants, soil and environment
Plants
Complete genome of four novel Pseudomonas species
Whole-genome sequencing of four novel Pseudomonas species which demonstrate beneficial effects in wheat growth.
2024-04-02
N. Poli, C. J. Keel and D. Garrido-Sanz
NCBI PRJNA1095474
Poli, N., et al. (2024). "Expanding the Pseudomonas diversity of the wheat rhizosphere: four novel species antagonizing fungal phytopathogens and with plant-beneficial properties." Frontiers in Microbiology 15: 1440341. DOI: 10.3389/fmicb.2024.1440341
Poli, N., et al. (2024). "Dataset Expanding the Pseudomonas diversity of the wheat rhizosphere: four novel species antagonizing fungal phytopathogens and with plant-beneficial properties." Zenodo. Permanent Identifier: 10.5281/zenodo.11354667
C. Keel (UNIL)
Plants, soil and environment
Plants, Soil
Whole-genome sequencing
Metagenomics Dataset of Aerobic Granular Sludge
Aerobic granular sludge from a wastewater treatment process was grown in a reactor with different nutrients. The metagenomic assemblies, MAGs and associated metadata are provided in this dataset.
2024-03-27
J. S. Saini, A. Adler, L. Cardona, P. N. Rodilla Ramírez, R. Pei and C. Holliger
10.5281/zenodo.10229272
Saini, J. S., et al. (2024). "Microbial genome collection of aerobic granular sludge cultivated in sequencing batch reactors using different carbon source mixtures." Microbiology Resource Announcements 13(5): e00102-00124. DOI: 10.1128/mra.00102-24
C. Holliger (EPFL)
Plants, soil and environment
Water
Metagenomics
S1_Flow_Cytometry_Data
These data measure the induction state of type III secretion system (T3SS) proteins of Salmonella bacteria grown in vitro.
2024-03-18
C. Ernst
10.5281/zenodo.10829181
Ernst, C., et al. (2024). "Direct Salmonella injection into enteroid cells allows the study of host–pathogen interactions in the cytosol with high spatiotemporal resolution." PLoS biology 22(4): e3002597. DOI: 10.1371/journal.pbio.3002597
J. Vorholt (ETHZ), W.-D. Hardt (ETHZ)
Animal
Gut, Mouse gut
Flow cytometry
Mitri-lab/community_evolution_experiment: v1.0.0
Code used for analyzing whole-genome and RNA sequencing data.
2024-02-22
E. Ulrich
10.5281/zenodo.10694150
Piccardi, P., et al. (2024). "The evolution of reduced facilitation in a four-species bacterial community." Evolution Letters: qrae036. DOI: 10.1093/evlett/qrae036
Piccardi, P., et al. (2023). "Species isolated from Metal Working Fluids Genome sequencing and assembly." NCBI BioProject. Permanent Identifier: PRJNA991498, Piccardi, P., et al. (2024). "Data accompanying "The evolution of reduced facilitation in a four-species bacterial community"." Zenodo. Permanent Identifier: 10.5281/zenodo.10694070
S. Mitri (UNIL)
Synthetic
Engineered systems
Code
Data accompanying “The evolution of reduced facilitation in a four-species bacterial community”
Starting with a community of four bacteria that positively interact to degrade a pollutant, this study measured changes in their interactions and their degradation efficiency over 44 weeks.
2024-02-22
P. Piccardi, E. Ulrich, M. Garcia-Garcerà, R. Di Martino, S. E. Testa and S. Mitri
10.5281/zenodo.10694070
Piccardi, P., et al. (2024). "The evolution of reduced facilitation in a four-species bacterial community." Evolution Letters: qrae036. DOI: 10.1093/evlett/qrae036
Piccardi, P., et al. (2023). "Species isolated from Metal Working Fluids Genome sequencing and assembly." NCBI BioProject. Permanent Identifier: PRJNA991498, Ulrich, E. (2024). "Mitri-lab/community_evolution_experiment: v1.0.0." Zenodo. Permanent Identifier: 10.5281/zenodo.10694150
S. Mitri (UNIL)
Synthetic
Engineered systems
Culture
Assessing microbiome population dynamics using wild-type isogenic standardized hybrid (WISH)-tags
Differentiating and quantifying populations of microbial strains
2024-01-11
B. B. J. Daniel, Y. Steiger, A. Sintsova, C. Field, B. D. Nguyen, C. Schubert, Y. Cherrak, S. Sunagawa, W.-D. Hardt and J. A. Vorholt
10.5281/zenodo.8369611
Daniel, B. B. J., et al. (2024). "Assessing microbiome population dynamics using wild-type isogenic standardized hybrid (WISH)-tags." Nature Microbiology 9(4): 1103-1116. DOI: 10.1038/s41564-024-01634-9
Daniel, B., et al. (2024). "Amplicon sequencing reads for WISH-tag barcoded bacterial strains " ENA. Permanent Identifier: PRJEB66333
J. Vorholt (ETHZ)
Animal, Plants, soil and environment
Mouse gut, Plants
Culture
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