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1,438 results for “bacteria”
Picophytoplankton and bacteria total carbon estimates from cell counts analyzed with flow cytometry (FCM) from CCE-CalCOFI Augmented cruises in the California Current System, 2004 - 2023(ongoing).
Picophytoplankton populations and non-pigmented prokaryotes are sampled within the California Current Ecosystem (CCE) for abundances from 3 to 8 depths at CalCOFI stations. Seawater is collected from Niskin bottles and cells are fixed in the field aboard the survey cruises (since 2004, ongoing) with paraformaldehyde, and stained with a DNA-specific dye back in the laboratory. The cells are enumerated by an Altra flow cytometer (with a syringe pump for volumetric sample delivery) simultaniously with argon ion lasers, to distinguish three major populations of photoautotrophs (Prochlorococcus, Synechococcus, and pico-eukaryotes) and the assemblage of heterotrophic prokaryotes collectively referred to as H-Bact. FCM abundance estimates for each are converted to carbon biomass equivalents using mixed-layer estimates.
Source code and simulation datasets for the paper 'Migration and accumulation of bacteria with chemotaxis and chemokinesis'
<p>Source code and simulation data files for the paper 'Migration and accumulation of bacteria with chemotaxis and chemokinesis'</p> <p>The zipped folder 'SimulationCode.zip' contains Matlab source code files which have been used to generate the simulations in the paper: fixed attractant gradient, axisymmetric agar-plate like migration and transient attractant source. The file 'main.m' controls all simulations run with initial conditions specified in the files with suffix '_ic'. The file 'PDEsolver.m' specifies the finite difference solver used so solve the model PDEs, while 'FourthOrderFD.m' creates the matrices that are required<br> for the finite differnce solver. The chosen scheme is of fourth order accuracy.</p> <p>The zipped folder 'SimulationData.zip' contains Matlab data files generated by running the simulation code. The results correspont to the figures in the paper.</p>
16S gene and ASV sequences of bacteria isolated from soil and the phyllosphere of Arabidopsis thaliana
<p>Data from "Induction of antibiotic specialized metabolism by co-culturing in a collection of phyllosphere bacteria" by Qi et al. </p> <p>- 16S gene sequences of bacteria isolated from soil and the phyllosphere of Arabidopsis thaliana in FASTA format. </p> <p>- Filtered OTU (ASV) table across all samples </p> <p>- ASV sequences</p>
Data from: Temperature dependent effects of cutaneous bacteria on a frog's tolerance of fungal infection
<p>Defense against pathogens is one of many benefits that bacteria provide to animal hosts. A clearer understanding of how changes in the environment affect the interactions between animals and their microbial benefactors is needed in order to predict the impact and dynamics of emerging animal diseases. Due to its dramatic effects on the physiology of animals and their pathogens, temperature may be a key variable modulating the level of protection that beneficial bacteria provide to their animal hosts. Here we investigate how temperature and the makeup of the skin microbial community impact the susceptibility of amphibian hosts to infection by <em>Batrachochytrium</em> <em>dendrobatidis</em>, one of two fungal pathogens known to cause the disease chytridiomycosis. To do this, we manipulated the skin bacterial communities of susceptible hosts, northern cricket frogs (<em>Acris</em> <em>crepitans</em>), prior to exposing these animals to <em>Batrachochytrium</em> <em>dendrobatidis</em> under two different ecologically relevant temperatures. Our manipulations included one treatment where antibiotics were used to reduce the skin bacterial community, one where the bacterial community was augmented with the antifungal bacterium, <em>Stenotrophomonas</em> <em>maltophilia</em>, and one in which the frog's skin bacterial community was left intact. We predicted that frogs with reduced skin bacterial communities would be more susceptible (i.e., less resistant to and/or tolerant of <em>Bd</em> infection), and frogs with skin bacterial communities augmented with the known antifungal bacterium would be less susceptible to <em>Bd</em> infection and chytridiomycosis. However, we also predicted that this interaction would be temperature-dependent. We found a strong effect of temperature but not of skin microbial treatment on the probability and intensity of infection in <em>Bd</em>-exposed frogs. Whether temperature impacted survival, however, differed among our skin microbial treatment groups, with animals having more <em>S</em>. <em>maltophilia</em> on their skin surviving longer at 14 but not at 26 °C. Our results suggest that temperature was the predominant factor influencing <em>Bd</em>'s ability to colonize the host (i.e., resistance) but that the composition of the cutaneous bacterial community was important in modulating the host's ability to survive (i.e., tolerate) a heavy <em>Bd</em> infection.</p>
Modeling and measuring how codon usage modulates the relationship between burden and yield during protein overexpression in bacteria
<p>Additional data from experiments associated with paper revisions.</p> <p>Also added codon optimizer script.</p>
Plaque assay images from the article "Predicting phage-bacteria interactions at the strain level from genomes"
<p>This dataset contains the plaque assay images for (i) the construction of the 403 bacteria * 96 phages interaction matrix and (ii) the "cocktails" experiment (100 E. coli strains challenged with recommended cocktails vs. a baseline). </p>
Analysis of bacteria, inflammation, and exudation in epidermal suction blister wounds reveals dynamic changes during wound healing - Dataset
<p>Dataset for "<strong>Analysis of bacteria, inflammation, and exudation in epidermal suction blister wounds reveals dynamic changes during wound healing</strong>". Data were generated from samples collected to a biobank from suction blister wounds at various timepoints during a clinical trial (<a href="https://clinicaltrials.gov/study/NCT05378997?term=NCT05378997&rank=1"><strong>NCT05378997</strong></a>). Data include concentration of bacteria in swab and dressing fluid samples, neutrophil proteins (HNE, MPO, and HBP), cytokines (IFN-gamma, interleukin IL-1beta, IL-2, IL-4, IL-6, IL-8, IL-10, IL-12p70, IL-13, TNF-alpha) and total protein measured in dressing fluid samples, and bacterial species identified by MALDI-TOF in swab and dressing fluid samples.</p>
Dataset for article: Antimicrobial peptide induced colloidal transformations in bacteria-mimetic vesicles: Combining in silico tools and experimental methods
<p><strong>Dataset for publication:</strong></p><p>Antimicrobial peptide induced colloidal transformations in bacteria-mimetic vesicles: Combining in silico tools and experimental methods<br><i>Rafael V.M. Freire, Yeny Pillco-Valencia, Gabriel C.A. da Hora, Madeleine Ramstedt, Linda Sandblad, Thereza A. Soares, Stefan Salentinig</i><br>Journal of Colloid and Interface Science Volume 596, 15 August 2021, Pages 352-363 https://doi.org/10.1016/j.jcis.2021.03.060</p><p>Setup and conditions for the experiments are described in the experimental section of the published (open access) manuscript.</p><p>Data description in README.txt file.</p>
Algae-Bacteria Community Analysis for Drinking Water Taste and Odour Risk Management
<p>The datasets and accompanying R script included in this upload are provided to complement the manuscript titled <em>"Algae-Bacteria Community Analysis for Drinking Water Taste and Odour Risk Management."</em> These resources are intended to facilitate the replication and verification of the analyses presented in the paper.</p> <p> </p> <p> </p>
Fecal bacteria contamination of floodwaters and a coastal waterway from tidally-driven stormwater network inundation
<p>Inundation of coastal stormwater networks by tides is widespread due to sea-level rise (SLR). The water quality risks posed by tidal water rising up through stormwater infrastructure (pipes and catch basins), out onto roadways, and back out to receiving water bodies are poorly understood but may be substantial given that stormwater networks are a known source of fecal contamination. In this study, we (1) documented temporal variation in concentrations of <em>Enterococcus spp</em>. (ENT), the fecal indicator bacteria standard for marine waters, in a coastal waterway over a two-month period and more intensively during two perigean spring tide periods, (2) measured ENT concentrations in roadway floodwaters during tidal floods, and (3) explained variation in ENT concentrations as a function of tidal inundation, antecedent rainfall, and stormwater infrastructure using a pipe network inundation model and robust linear mixed effect models. We find that ENT concentrations in the receiving water body vary as a function of tidal stage and antecedent rainfall, but also site-specific characteristics of the stormwater network that drains to the waterbody. Tidal variables significantly explain measured ENT variance in the waterway, however, runoff drove higher ENT concentrations in the receiving waterway. Samples of floodwaters on roadways during both perigean spring tide events were limited, but all samples exceed thresholds for safe public use of recreational water. These results indicate that inundation of stormwater networks by tides could pose public health hazards in receiving water bodies and on roadways, which will likely be exacerbated in the future due to continued SLR.</p>
Identification of intratumoral bacteria that enhance breast tumor metastasis
<p>This file contains the supporting datasets for the manuscript entitled Identification of intratumoral bacteria that enhance breast tumor metastasis, by Gerbec et al. File includes 8 supporting datasets as well as a legend file with the description of each individual dataset.</p>
Thermal adaptation in Aedes aegypti does not constrain temperature-sensitive growth of bacteria or dengue virus
<p>Data set and R script used for the following manuscript : </p> <p><strong>Thermal adaptation in <em>Aedes aegypti</em> does not constrain temperature-sensitive growth of bacteria or dengue virus</strong></p> <p><span lang="EN-US">Alida Kropf<sup>1*#</sup>, Stéphanie Dabo<sup>2</sup>, Marine Amann<sup>3</sup>, Louis Lambrechts<sup>2</sup>, Jacob C Koella<sup>1</sup></span></p> <p><span lang="EN-US">PROCEEDINGS OF THE ROYAL SOCIETY B THE ROYAL SOCIETY B BIOLOGICAL SCIENCES</span></p> <p><strong><em><span lang="IT-CH">DOI: 10.1098/rspb.2025-0832.R1 </span></em></strong></p>
Dataset for Aqueous habitats and carbon inputs shape the microscale geography and interaction ranges of soil bacteria
<p>This repository hosts data for the paper entitled: "<em>Aqueous habitats and carbon inputs shape the microscale geography and interaction ranges of soil bacteria</em>" by Samuel Bickel and Dani Or.</p> <p>The following files are provided:</p> <p><strong>Microcosm experiment:</strong></p> <p>- Fluorescence microscopy images of the microcosm experiment (*.tif)</p> <p>- Code used for extracting cell locations from images (image_analysis.py)</p> <p><strong>Global model estimates from the bacterial interactions heuristic model:</strong></p> <p>- Maps of estimated cell density and proportion of biomass associated with anoxic cell clusters (*.nc)</p> <p> </p>
Oral bacteria from a community-based generation study RHINESSA in Bergen, Norway
<p>The oral cavity is the main gateway for oral bacteria and their components to enter the lungs. Disruption of the oral microbiota due to internal or external factors has been associated with respiratory diseases. This dataset is used to explore the association between oral bacteria, lung function, and lung inflammation in a generally healthy community-based generation study RHINESSA in Bergen, Norway. <strong>Study-specific metadata can be found in respective research articles linked to this dataset.</strong></p>
Data from: Pre-copulatory reproductive behaviours are preserved in Drosophila melanogaster infected with bacteria
<p>The activation of the immune system upon infection exerts a huge energetic demand on an individual, likely decreasing available resources for other vital processes, like reproduction. The factors that determine the trade-off between defensive and reproductive traits remain poorly understood. Here, we exploit the experimental tractability of the fruit fly <em>Drosophila melanogaster</em> to systematically assess the impact of immune system activation on pre-copulatory reproductive behaviour. Contrary to expectations, we found that male flies undergoing an immune activation continue to display high levels of courtship and mating success. Similarly, immune-challenged female flies remain highly sexually receptive. By combining behavioural paradigms, a diverse panel of pathogens and genetic strategies to induce the fly immune system, we show that pre-copulatory reproductive behaviours are preserved in infected flies, despite the significant metabolic cost of infection.</p>
Meta-omics-aided isolation of elusive anaerobic arsenic-methylating soil bacteria
<p>Data pertaining to the manuscript "<strong>Meta-omics-aided isolation of an elusive anaerobic arsenic-methylating soil bacterium"</strong> by Karen Viacava, Jiangtao, Qiao, Andrew Janowczyk, Suresh Poudel, Nicolas Jacquemin, Karin Lederballe Meibom, Him K. Shrestha, Matthew C. Reid, Robert L. Hettich and Rizlan Bernier-Latmani published in ISME journal.</p>
Bacteria and archaea of the Columbia and Willamette Rivers, 16S rRNA gene amplicon library metadata
<p>Bacterial and archaeal communities in the Columbia and Willamette Rivers in the Portland, OR, USA, region were characterized by 16S rRNA gene amplicon sequencing as part of the Lewis & Clark College spring 2022 Microbial Ecology course. Whole-water (>0.2 µm) samples were collected from: the Willamette River; the Columbia River above the confluence with the Willamette; and the Columbia River just downstream of the confluence with the Willamette.</p> <p>This dataset provides additional metadata to supplement the DNA sequences archived with the NCBI SRA at <a href="https://www.ncbi.nlm.nih.gov/sra/PRJNA865380">https://www.ncbi.nlm.nih.gov/sra/PRJNA865380</a></p>
Strains used in the paper "Bacteriophage cultivation for commensal human gut bacteria"
<p>Sequences of 16S rRNA genes of 411 strains for taxonomic detection;</p> <p>Genomic sequence of of 42 strains for taxonomic detection;</p> <p>Genomic sequence of Bacteroides fragilis and Parabacteroides merdae strains used for genomic analysis in phage-host range analysis experiments. </p>
dudesdb_201709 - Archaea and Bacteria - RefSeq - Complete Genomes
<p>bowtie2 index and dudes database for the set of Archaeal and Bacterial complete genomes from NCBI RefSeq, dating from 2017-09. The dudes database was made based on accession version numbers (DUDesDB.py option -m "av").</p>
dudesdb_201503 - Archaea and Bacteria - RefSeq - Complete Genomes
<p>bowtie2 index and dudes database (.ddb for version 0.06 and .npz for version 0.07) for the set of Archaeal and Bacterial complete genomes from NCBI RefSeq, dating from 2015-03. The dudes database was made based on accession version numbers (DUDesDB.py option -m "av").</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.