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Dataset results
287 results for “Bacterial communities”
Interspecies chemical signalling in a methane-oxidizing bacterial community
GEO Series GSE122293. Methylomonas sp. LW13. 8 samples. Type: Expression profiling by high throughput sequencing.
Allele specific expression and bacterial community composition in the Drosophila gut
GEO Series GSE263264. Drosophila melanogaster. 48 samples. Type: Expression profiling by high throughput sequencing.
Data from: Gut bacterial and fungal communities in ground-dwelling beetles are associated with host food habit and habitat
Beetles (Coleoptera) have the highest species diversity among all orders, and they have diverse food habits. Gut microbes may have contributed to this diversification of food habits. Here, we identified the pattern of the relationship between ground-dwelling beetles and their gut microbial communities (bacteria and fungi) in the field. We collected 46 beetle species of five families from secondary deciduous forests and grasslands in Japan and extracted microbial DNA from whole guts for amplicon sequencing. The gut bacterial and fungal communities differed among all habitats and all food habits of their hosts (carnivores, herbivores, omnivores, and scavengers) except for the fungal communities between carnivores and scavengers. Specifically, the abundant bacterial group varied among food habits: Xanthomonadaceae were abundant in scavengers, whereas Enterobacteriaceae were abundant in carnivores and herbivores. Phylogenetically closely related beetles had phylogenetically similar communities of Enterobacteriaceae, suggesting that the community structure of this family is related to the evolutionary change in beetle ecology. One of the fungal groups, Yarrowia species, which has been reported to have a symbiotic relationship with silphid beetles, was also detected from various carnivorous beetles. Our results suggest that the symbiotic relationships between ground-dwelling beetles and these microbes are widespread.
Data from: Social spider webs harbor largely consistent bacterial communities across broad spatial scales
Social animals that live in domiciles constructed from biomaterials may facilitate microbial growth. Spider webs are one of the most conspicuous biomaterials in nature, yet almost nothing is known about the potential for webs to harbor microbes, even in social spiders that live in dense, long-term aggregations. Here, we tested whether the dominant bacteria present in social spider webs vary across sampling localities and whether the more permanent retreat web harbors compositionally distinct microbes from the more ephemeral capture webs in the desert social spider Stegodyphus dumicola. We also sampled spider cuticles and prey items in a subset of colonies. We found that spider colonies across large spatial scales harbored similar web-associated bacterial communities. We also found substantial overlap in bacterial community composition between spider cuticle, prey, and web samples. These data suggest that social spider webs can harbor characteristic microbial communities and potentially facilitate microbial transmission among individuals, and this study serves as the first step towards understanding the microbial ecology of these peculiar animal societies.
Data from: Secondary successional trajectories of structural and catabolic bacterial communities in oil polluted soil planted with hybrid poplar
Poplars have widely been used for rhizoremediation of a broad range of organic contaminants for the past two decades. Still, there is a knowledge gap regarding the rhizosphere associated bacterial communities of poplars and their dynamics during the remediation process. It is envisaged that a detailed understanding of rhizosphere associated microbial populations will greatly contribute to a better design and implementation of rhizoremediation. In order to investigate the long-term succession of structural and catabolic bacterial communities in oil polluted soil planted with hybrid poplar, we carried out a 2-year field study. Hybrid aspen (Populus tremula x tremuloides) seedlings were planted in polluted soil excavated from an accidental oil-spill site. Vegetated and un-vegetated soil samples were collected for microbial community analyses at 7 different time-points during the course of 2 years and sampling time-points were chosen to cover the seasonal variation in the boreal climate zone. Bacterial community structure was accessed by means of 16S rRNA gene amplicon pyrosequencing whereas catabolic diversity was monitored by pyrosequencing of alkane hydroxylase and extradiol dioxygenase genes. We observed a clear succession of bacterial communities on both structural and functional levels from early to late phase communities. Sphingomonas type extradiol dioxygenases and alkane hydroxylase homologs of Rhodococcus clearly dominated the early phase communities. The high dominance-low diversity functional gene communities underwent a transition to low-dominance-high diversity communities in the late phase. These results pointed towards increased catabolic capacities and a change from specialist to generalist strategy of bacterial communities during the course of secondary succession.
Long read genome assembly of species from the synthetic HAMBI bacterial community
<p>We present complete genome sequences of 30 bacterial species that can be used to construct defined synthetic communities that stably form in the laboratory under controlled conditions.</p><p>This repository contains the final genome assemblies, logs, reports/summaries, scripts, and associated computational methods. All genomes were circularized (or in the case of <i>Agrobacterium tumefaciens</i> properly linearized) with the recovery of some small plasmids.</p><p>30 Species from the HAMBI community were sent for Oxford Nanopore or PacBio HiFi sequencing at <a href="https://www.seqcenter.com/">SeqCenter</a> early November 2022. I assembled multiple subsets of the read data for each genome and generated consensus assemblies using <a href="https://github.com/rrwick/Trycycler">Trycycler</a>.</p><p>All sequence data is available under BioProject <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1047486">PRJNA1047486</a></p><p>This is a mirror of the repository here: <a href="https://gitlab.utu.fi/slhogl/hambiLongRead">https://gitlab.utu.fi/slhogl/hambiLongRead</a></p>
Unexpected levels of antibiotic resistance in marine bacterial communities not solely explained by urban river discharge
<p>This data and the subsequent code were used in the manuscript "Unexpected levels of antibiotic resistance in marine bacterial communities not solely explained by urban river discharge". Any questions and comments about the data or analysis should be forward to Brandon Chan, lead author.</p>
Exposure to NSAIDs (Non Steroidal Anti-Inflammatory Drugs) and Severity of Community-acquired Bacterial Infections
ClinicalTrials.gov study NCT02794831. IPD Sharing: NO. Countries: 0. Publications: 0.
A Phase II Study of Faropenem in the Treatment of Adult Community-acquired Bacterial Pneumonia
ClinicalTrials.gov study NCT01886053. IPD Sharing: Not stated. Countries: 1. Publications: 0.
A P3 Comparator Trial in Community Acquired Bacterial Pneumonia
ClinicalTrials.gov study NCT02269644. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Efficacy and Safety Study of JNJ-32729463 Compared With Moxifloxacin for the Treatment of Subjects Requiring Hospitalization for Community-Acquired Bacterial Pneumonia
ClinicalTrials.gov study NCT01198626. IPD Sharing: Not stated. Countries: 6. Publications: 0.
A Phase III Study of Faropenem in the Treatment of Adult Community-acquired Bacterial Pneumonia
ClinicalTrials.gov study NCT01937832. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Blinded Efficacy and Safety Study of CAL02 IV Plus SOC in Subjects With Severe Community-Acquired Bacterial Pneumonia
ClinicalTrials.gov study NCT05776004. IPD Sharing: Not stated. Countries: 19. Publications: 0.
Bacterial Pathogens Associated With Community-acquired Pneumonia in Children
ClinicalTrials.gov study NCT06377163. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
Data from: Social spider webs harbor largely consistent bacterial communities across broad spatial scales
Open the record for dataset details and reuse information.
Data from: Gut bacterial and fungal communities in ground-dwelling beetles are associated with host food habit and habitat
Open the record for dataset details and reuse information.
Data from: Secondary successional trajectories of structural and catabolic bacterial communities in oil polluted soil planted with hybrid poplar
Open the record for dataset details and reuse information.
RNA-seq of Arabidopsis thaliana seedlings growing in the presence of a 185-members bacterial synthetic community under full and low phosphate conditions
GEO Series GSE129395. Arabidopsis thaliana. 24 samples. Type: Expression profiling by high throughput sequencing.
16S metabarcoding, a powerful tool to compare environmental and culture-derived bacterial communities, assess media selectivity and detect rare environmental bacterial species
<p>Processed raw data reads</p>
Data accompanying "The evolution of reduced facilitation in a four-species bacterial community"
<p>Dataset accompanying the paper.</p>
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Allen Brain Atlas
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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.