Dataset index

Description: Software for performing statistical analysis, visualization, and contextualization of data generated from studies using transposon-insertion sequencing or barcoded isogenic strains.

Description: Tests to measure performance of Snodgrassella alvi bacteria, engineered with plasmids, to serve as biosensors in the bee gut.

Description: 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.

Description: 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.

Description: Whole-genome sequencing of four novel Pseudomonas species which demonstrate beneficial effects in wheat growth.

Description: 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.

Description: These data measure the induction state of type III secretion system (T3SS) proteins of Salmonella bacteria grown in vitro.

Description: 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.

Description: Code used for analyzing whole-genome and RNA sequencing data.

Description: Differentiating and quantifying populations of microbial strains

Description: Bacteria that are barcoded to differentiate members of the same strain during microbiome assembly (early vs. latecomers)

Description: Mathematical model of the interaction between bacteria in co-culture depending on the chemistry of their environment.

Description: A tab-delimited file listing genomes used in mOTUs3 with metadata that map each genome to a mOTU and provide additional information such as the data source, quality metrics and download links.

Description: Microbial community composition of the bee gut and bee feces, including samples of bees that received fecal transplants.

Description: Scripts for data analysis

Description: Here, we test whether phenotypic plasticity leads to a shift in proteome allocation during co-occurrence of two bacterial species from the abundant, leaf-colonizing families Sphingomonadaceae and Rhizobiaceae in their natural habitat.

Description: The repository includes data and R code necessary to reproduce all figures and analyses presented in the study titled "Identifying microbiota community patterns important for plant protection using machine learning in synthetic community experiments."

Description: Raw CFU count, qPCR, metabolomics, NanoSIMS and GC-MS data, as well as codes for data analysis.

Description: Time-lapse microscopy images showing the spatial arrangement of individual members of a microbial community growing in a microfluidic device.

Description: Development of soil microbial communities in microcosms over time, with and without the addition of inoculated Pseudomonas bacteria.

Description: Data to investigate the cell surface features of Pseudomonas protegens CHA0 that make it vulnerable to the bacteriophage ΦGP100. Processed data from transposon sequencing, as well as culture data of wild type and mutant P. protegens exposed to phages.

Description: Pictures of plants at harvest timepoint (14 days post infection) of all experiments and data shown in publication.

Description: Code for generation of WISH tags (intrastrain bacterial barcodes)

Description:

Description: Scripts for analysis of bacterial surface growth data.

Description: Database of genomes of the bacterial strains that naturally inhabit the honeybee gut.

Description: R script for microbial community analysis

Description: Growth of wheat plants inoculating with beneficial Pseudomonas bacteria. Also, measurements of competition among different Pseudomonas strains grown in bulk soil or in the rhizosphere.

Description: We investigated how Bacillus colonies evolve on surfaces. This study includes both gDNA data to identify the mutations in Bacillus as well as RNA-seq data to quantify the gene expression changes that result from the genomic mutations.

Description: We studied the evolution of surface expansion in Bacillus subtilis and Bacillus cereus and used flow cytometry to determine the cell state composition at both the colony edge and in the center.

Description: Plate counts of Salmonella strains to quantify the transfer of plasmids from bacteria already colonizing the mouse gut (donors) to bacteria newly introduced to the mouse gut (recipients)

Description: Epithelial cell loss and pathogen loads during Salmonella infection

Description: Microbially-mediated methylation of arsenic (As) plays an important role in the As biogeochemical cycle, particularly in rice paddy soils where methylated As, generated microbially, is translocated into rice grains. The presence of the arsenite (As(III)) methyltransferase gene (arsM) in soil microbes has been used as an indication of their capacity for As methylation. Here, we evaluate the ability of seven microorganisms encoding active ArsM enzymes to methylate As.

Description: Microbially-mediated methylation of arsenic (As) plays an important role in the As biogeochemical cycle, particularly in rice paddy soils where methylated As, generated microbially, is translocated into rice grains. The presence of the arsenite (As(III)) methyltransferase gene (arsM) in soil microbes has been used as an indication of their capacity for As methylation. Here, we evaluate the ability of seven microorganisms encoding active ArsM enzymes to methylate As.

Description: Sequencing data to distinguish pathogenic Salmonella bacteria from non-virulent Salmonella mutants

Description: Changes in genomes and gene expression in a bacterial community that evolves over 44 weeks. The community was initially characterized by positive interactions, but the interactions weaken over time.

Description: These are data from spent medium assays to decipher the metabolic interactions among four bacterial species: Agrobacterium tumefaciens, Comamonas testosteroni, Microbacterium saperdae, and Ochrobactrum anthropi. These assays help determine whether metabolites secreted by one organism are consumed by, and/or affect the growth of a different organism.

Description: Data obtained from insect experiments and plant-pathogen inhibition assays.

Description: We assessed the microbiota composition in an agropastoral community with a pre-industrial, yet nutritionally distinct lifestyle.

Description: A mathematical model of a simplified gut composed of two connected patches where species and metabolites can flow from an upstream patch, allowing upstream species to affect downstream species’ growth.

Description: These are Jupyter notebooks that record a mathematical model of meta-community dynamics in a chain network. The model analyzes how upstream species affect downstream stability in gut microbiota.

Description: Images, bacterial strain collection

Description: This repository contains all data necessary to score colony growth on agar plates using the software tool 'platescan' (github.com/MicrobiologyETHZ/platescan) for the strains presented in Schäfer, Pacheco, et al.

Description: Software tool for image analysis.

Description: Transposon sequencing to investigate the genetic features that allow the ΦGP100 phage to gain entry to Pseudomonas protegens CHA0 cells.

Description: We aimed to study the impact of COVID-19 and the severity on the gut microbiota of a longitudinal cohort. We collected 100 fecal samples from COVID-19 and non-COVID patients. Gut microbiota were characterized with 16S rRNA gene (V3V4) sequencing.

Description: We performed a prospective, observational cohort study in the intensive care unit (ICU) at Lausanne university hospital. A total of 73 endotracheal aspirates and 93 rectal-swabs were obtained from 38 critically ill adults who required mechanical ventilation. Lung and gut microbiota were characterized using bacterial 16S ribosomal RNA sequencing.

Description: The nitrogen-fixing cyanobacterium Trichodesmium forms filamentous aggregates in response to stress. In this study, analysis of images and videos of individuals and pairs of filaments revealed how the motion of filaments exposed to stress affects overall colony architecture. This data set includes raw microscopy images and code for image analysis, statistical computation, and mathematical modeling of filament motion.

Description: Workflow for the OpEn framework, which explores the optimal modes of operation for enzymes, based on catalytic efficiency.

Description: A bioinformatic approach to understand how E. coli uses chemotaxis when it colonizes a host gut.

Description: Data analysis script, bacterial growth.

Description: Vaccine, veterinary.

Description: Mass spectrometry, library plugin

Description: Changes in a natural soil microbial community with contrasting nutrient availability upon establishment of a plant-beneficial bacterial inoculant in the wheat rhizosphere, compared to bulk soil

Description: Technical advances in microscopy have led to higher-quality images that capture larger areas of growth, containing a great number of cells. STrack is an automated computational tool that efficiently tracks cells in time-lapse images.

Description: Input files needed to reproduce the automated social 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 on Github. Associated code: https://github.com/JoanitoLiberti/The-gut-microbiota-affects-the-social-network-of-honeybees Associated RNA sequencing dataset: Liberti, J. and T. Kay (2023). "The gut microbiota affects the social network of honey bees." NCBI Gene Expression Omnibus. Permanent Identifier: GSE192784

Description: Mouse model, population dynamics, bacterial growth.

Description: Pseudomonas veronii 1YdBTEX2 can break down monoaromatic compounds, making it a good candidate for bioaugmentation in polluted soils. This work aimed to characterize the genes that this strain needs to grow and establish in a polluted soil where a microbial community is already present.

Description: Sequencing of bacterial isolates from six stingless bee species from Brazil. Evolution of the social bee gut microbiota.

Description: Computational workflow to investigate cellular function by identifying metabolic gaps at the reaction and enzyme level, and proposing known and hypothetical reactions and computational enzyme annotation methods.

Description: We studied 2778 bacterial genomes and 188 metagenomes from cheese-associated microbial communities, which are dominated by a few bacterial taxa and occur in relatively stable environments.

Description: This dataset contains the (700k) genomes (reference genomes, sags, mags) that were used to build the mOTUs 3 database. The genomes are stored in a hierarchical structure and all genomes that belong to one mOTU are added to a tar file. Associated database: Milanese, A., et al. (2023). "mOTUs database." Zenodo. Permanent Identifier: 10.5281/zenodo.5140350 Associated metadata: Ruscheweyh, H.-J., et al. (2022). "mOTUs3 - genome metadata." Zenodo. Permanent Identifier: 10.5281/zenodo.6975138 Tool for downloading genomes: https://github.com/motu-tool/motus_v3_genomes

Description: Mouse model, population dynamics, bacterial growth.

Description: In gnotobiotic mice, we investigated food intake, digestion efficiency, energy expenditure and respiratory quotient using a novel isolator-housed metabolic cage system.

Description: We measured the food intake, digestion efficiency, energy expenditure, and respiratory quotient of mice with a simplified gut microbiome, to see how the microbiota contribute to obesity.

Description: Volatilome, mass spectrometry, metabolism, colonization.

Description: Enterobacteriaceae isolates from healthy humans and from Salmonellosis patients in remission.

Description: Toolbox to implement large-scale kinetic models for various biological domains such as signaling, gene expression and metabolism.

Description: Computational resource consisting of a comprehensive biochemical reaction network centered around aromatic amino acid biosynthesis and a computational toolbox for navigating this network.

Description: We extracted an isolate capable of methylating arsenic under anoxic conditions from a complex soil microbiome. Based on the metagenome-assembled genomes of microorganisms producing the ArsM enzyme, we isolated Paraclostridium sp. strain EML, which was confirmed to actively methylate As anaerobically.

Description: Mutations that attenuate Salmonella Typhimurium can emerge and destabilize cooperative virulence during infection. We asked if horizontal gene transfer of alleles encoding virulence could restore and maintain virulence. This sequencing bioproject investigates the genetic basis for loss of virulence in isolates in which virulence has been restored, but then subsequently lost once again.

Description: Synthetic community

Description: In this work, we use 489 generalized enzymatic reaction rules to map both known and unknown metabolic processes around a biochemical database of 1.5 million biological compounds. We predict over 5 million reactions and integrate nearly 2 million naturally and synthetically-derived compounds into the global network of biochemical knowledge, named ATLASx.

Description: Identifying the lipopolysaccharides on the surface of certain strains of Pseudomonas bacteria that make them vulnerable to attack by weaponry produced by other strains of the same species.

Description: Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the community to assess methods on realistic and complex datasets with long and short- read sequences, created computationally from ∼1,700 novel and known genomes, as well as ∼600 novel plasmids and viruses. Raw data for otherwise unpublished novel genomes of the strain madness data set are stored here.

Description: Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the community to assess methods on realistic and complex datasets with long and short- read sequences, created computationally from ∼1,700 novel and known genomes, as well as ∼600 novel plasmids and viruses. Raw data for otherwise unpublished novel genomes of the marine data set are stored here.

Description: Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the community to assess methods on realistic and complex datasets with long and short- read sequences, created computationally from ∼1,700 novel and known genomes, as well as ∼600 novel plasmids and viruses. Raw data for otherwise unpublished novel genomes of the plant-associated data set are stored here.

Description: Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the community to assess methods on realistic and complex datasets with long and short- read sequences, created computationally from ∼1,700 novel and known genomes, as well as ∼600 novel plasmids and viruses. Raw data for otherwise unpublished novel genomes of the plasmid data are stored here.

Description: Bacterial interactions in a synthetic plant leaf microbial community.

Description: RNA-sequencing of gut and different brain regions of gnotobiotic honeybees.

Description: Here we use honeybees to probe the effect of the gut microbiota on host social behavior. We found that the microbiota increased the rate of interaction between bees and the complexity of the emergent colony social network. Microbiota colonization was associated with higher abundances of one third of the metabolites detected in the brain, including amino acids with roles in synaptic transmission and brain energetic function. A subset of these metabolites were significant predictors of the number of social interactions of bees. Microbiota colonization also affected brain transcriptional processes related to amino acid metabolism and epigenetic modifications, particularly in areas of the brain implicated in sensory perception. These results demonstrate considerable effects of the gut microbiota on honeybee social organization and highlight the associated changes in individual neurophysiology.

Description: RNA sequencing of Frischella perrara PEB0191 during in vitro growth and gut colonization.

Description: Single-cell transcriptomics, gene expression.

Description: Bacterial genomic data for seventeen bacterial leaf isolates belonging to the At-LSPHERE strain collection (Bai et al 2015, 10.1038/nature16192).

Description: Soil microbiomes reach high densities and complexity globally. Here we designed and studied the development of two representative soil synthetic communities in soil and liquid microcosms. Using multispecies sequencing, we contrast community growth under conditions of cycling and long batch incubation regimes.

Description: Metabolomics

Description: We investigated the effects of antibiotics in the environment on the growth of microbial communities. We tested microbial communities from freshwater, activated sludge and soil, to see if they can degrade antibiotics at low concentrations without being overcome by the antibiotics' toxicity.

Description: This dataset contains video microscopy movies showing the degradation of organic particles by marine microorganisms under flow conditions. This study represents carbon flux in the ocean's biological pump.

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.

Description: Microbes are phylogenetically and metabolically diverse. Yet capturing this diversity, assigning functions to host organisms and exploring the biosynthetic potential in natural environments remains challenging. We reconstructed >25,000 draft genomes, including from >2,500 uncharacterized species, from globally-distributed ocean microbial communities, and combined them with ∼10,000 genomes from cultivated and single cells. Mining this resource revealed ∼40,000 putative biosynthetic gene clusters (BGCs), many from unknown phylogenetic groups.

Description: Growth of microbial communities in freshwater, activated sludge and soil in the presence of low concentrations of antibiotics

Description: Here we used massive transposon sequencing to identify and characterize genes in the monoaromatic-compound degrading bacterium Pseudomonas veronii 1YdBTEX2 of importance for its growth and survival. Bacterial inoculants, bioremediation.

Description: Assembly submissions, including participants' submissions, of the CAMI 2 challenge data sets

Description: The metabolic capabilities of the species and the local environment shape the microbial interactions in a community either through the exchange of metabolic products or the competition for the resources. Cells are often arranged in close proximity to each other, creating a crowded environment that unevenly reduce the diffusion of nutrients. Herein, we investigated how the crowding conditions and metabolic variability among cells shape the dynamics of microbial communities.

Description: Simulated data of crowding conditions in microbial communities.

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Description: Here, we characterize the microbiota of the model alga Chlamydomonas reinhardtii and reveal extensive taxonomic and functional overlap with the root microbiota of land plants.

Description: A rationally induced IgA response blocking all of escape trajectories selected for Salmonella mutants carrying deletions of the O-antigen polymerase wzyB. Due to their short O-antigen, evolved mutants were susceptible to environmental stressors (detergents, complement), to predation (bacteriophages), and were impaired in gut colonization and virulence.

Description: Mouse gut, pathogen, virulence

Description: This data repository contains the latest version of the "honey bee gut microbiota genomic database", and two example data-sets, which can be used to run the pipelines: Community_profiling (Github) Species_validation (Github) For previous publications using these pipelines, see 10.1038/s41467-019-08303-0, 10.1016/j.cub.2020.04.070 The genomic database contains data from a total of 198 bacterial genomes, as detailed in the database metafile (see file descriptions here below). It has been tested on the Western and Eastern honey bee (Apis mellifera, Apis cerana), for which it has been shown to recruit about 90% of all the reads in most metagenomic samples (excluding host-derived reads). The database also contains genomes derived from other bee species, such as bumble bees, but it has not been tested with metagenomic data for these bee species yet.

Description: In order to deepen in our understanding of the effects of pesticide exposure on bee health, we aimed to elucidate the impact of chronic exposure to sublethal doses of glyphosate on the honey bee gut microbiota, immune response, and survival, and its potential interaction with the widespread pathogens N. ceranae and DWV.

Description: Assemble Streptococcus thermophilus metagenome assembled genome from the starter culture rmk202.

Description: Lactobacillus delbrueckii subsp. lactis metagenome assembled genome from the starter culture rmk202.

Description: Develop quality criteria to evaluate the quality of SARS-CoV-2 genomes.

Description: We combine three meta-omics techniques (metagenomics, metatranscriptomics, and metaproteomics) to identify the microorganisms responsible for As methylation in two anoxic soil-derived microbial cultures.

Description: We performed transposon sequencing (TnSeq) to elucidate the genetic determinants involved in the sensitivity of Pseudomonas protegens towards phage tail-like particles.

Description: How plants respond to their microbiota is currently not well understood. We used a phylogenetically diverse set of 39 native bacterial strains from Arabidopsis thaliana leaves to assess host transcriptional and metabolic adaptations to bacterial encounters. We identified a molecular response, which we termed the general non-self response (GNSR) that involves the expression of a core set of 24 genes.

Description: Immunofluorenscence microscopy of intestinal tissue, RT-qPCR to measure gene expression, and ELISA to measure a marker of gut inflammation, from competitive infection experiments. The goal is to compare factors that affect a pathogen's ability to colonize the gut.

Description: MATLAB community simulations, MATLAB imaging script.

Description: We combine amplicon sequencing and bacterial culturing to characterize the viable bacterial community in 234 longitudinal bronchoalveolar lavage samples from 64 lung transplant recipients and establish links to viral loads, host gene expression, lung function, and transplant health.

Description: This R script shows an analysis example of using outwards-oriented paired-end reads (OPRs), identified using the OPR finder function in the mVIRs package, to identify p22 in S.

Description: We report the transcriptome of four strains of the Lactobacillus Firm5 phylotype obtained with in vivo and in vitro experiments under different nutrient conditions.

Description: Amplicon sequencing to disentangle a four Firm5 strain community composition over in vivo or in vitro passages.

Description: As part of this work, we established the Ocean Microbiomics Database (OMD), which can be interactively accessed at: https://www.microbiomics.io/ocean/. This Zenodo repository versions some of the files that make up the database while other (larger) files can be accessed at ENA under the project PRJEB45951 (https://www.ebi.ac.uk/ena/browser/view/PRJEB45951).

Description: Imaging, microscopy, bacterial culture, competition.

Description: Strain-level diversity and bacteria-phage interactions in domesticated microbial communities used to make cheese

Description: Profiling the taxonomic composition of microbial communities commonly involves the classification of ribosomal RNA gene fragments. As a trade-off to maintain high classification accuracy, existing tools are typically limited to the genus level. Here, we present mTAGs, a taxonomic profiling tool that implements the alignment of metagenomic sequencing reads to degenerate consensus reference sequences of small subunit ribosomal RNA genes. It uses DNA fragments, that is, paired-end sequencing reads, as count units and provides relative abundance profiles at multiple taxonomic ranks, including operational taxonomic units based on a 97% sequence identity cutoff. At the genus rank, mTAGs outperformed other tools across several metrics, such as the F1 score by >11% across data from different environments, and achieved competitive (F1 score) or better results (Bray–Curtis dissimilarity) at the sub-genus level. The software tool mTAGs is implemented in Python.

Description: The goal of this study was to quantify genome-wide gene expression differences of the aromatic-compound degrading bacterium Pseudomonas veronii 1YdBTEX2 upon inoculation in a variety of soils, contaminated or not with external toluene. Three growth phases were examined: a lag phase (1 h contact in the material), exponential growth and stationary phase.

Description: We followed microbial community changes in a freshwater lake sample that was incubated with small doses of polluting compounds, to be test whether the compounds can be biodegraded.

Description: These high-throughput sequencing data were used to locate inducible prophages, including those previously undiscovered, to quantify prophage activity and to investigate their replication.

Description: Composition of a soil microbial community grown inside agarose beads, in the presence or absence of an inoculant (Pseudomonas bacteria).

Description: The goals of this study were to examine difference in microbial diversity from washed soil communities, when they were incubated (1) in low or high connectivity environments and (2) with different substrates.

Description: In depth colony picking and sequencing of isolates of S. thermophilus and L. delbrueckii from the cheese starter culture RMK202 for Gruyere.

Description: The impact of different classes of compounds in the influent to wastewater treatment plants on the microbial community of aerobic granular sludge.

Description: CellCognize complements current sequencing-based methods by enabling rapid routine cell diversity analysis. The pipeline is suitable to optimize cell recognition for recurring microbiota types, such as in human health or engineered systems. Flow cytometry data; neural network data.

Description: Changes in a microbial community from a freshwater lake when it was grown in the presence of polluting compounds at low concentrations. The goal was to see which compounds might be biodegradable.

Description: Culture-independent profiling of the bacterial root microbiota shows that different plant species are colonized by distinct bacterial communities that provide beneficial services to the host. It is, however, not known to what extent the host actively selects these communities and whether commensal bacteria are adapted to a specific plant species. Here, we report a sequence-indexed culture collection from roots and nodules of the model legume Lotus japonicus that contains representatives from the majority of species found in culture-independent profiles.

Description: There is accumulating evidence that the lower airway microbiota impacts lung health. However, the link between microbial community composition and lung homeostasis remains elusive. We combine amplicon sequencing and bacterial culturing to characterize the viable bacterial community in 234 longitudinal bronchoalveolar lavage samples from 64 lung transplant recipients and establish links to viral loads, host gene expression, lung function, and transplant health.

Description: Here, we describe longitudinal tracking for four cystic fibrosis patients. Following metagenomics sequencing of lung sputum, we find that the taxonomic identity of individual colonizer lineages can be easily established. Crucially, even superficially clonal pathogens can be subdivided into multiple sub-lineages at the sequence level. By tracking individual allelic differences over time, an assembly-free clustering approach allows us to reconstruct multiple lineage-specific genomes with clear structural differences.

Description:

Description: We describe for the first time the microbial community found in the upper gastrointestinal tract of stunted children.