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20 results for “Microbial network”
Soil microbial community coupling network in response to diversified crop rotations
<p>Dataset of manuscript entitled “Soil microbial community coupling network in response to diversified crop rotations”. This manuscript includes the results of WP3 from the SOFT project (ref. 890874).</p>
Network analysis reflects the trophic relationship between microbial colonizers and deadwood resources - supporting information
<p>Supporting tables S2 - S5 of "Network analysis reflects the trophic relationship between microbial colonizers and deadwood resources".</p> <p>The file Table_Legends_S2-S5.txt contains all legends, as given below:</p> <p>Table S2: Module-associated trees and OTUs, their relative abundances and identities for the fungal sapwood network; module – name of the module, present – proportion of network version that the OTU is present in (1 = 1000/1000), inBestModule – proportion of the network versions where the OTU is associated with the respective module, percInBestModule – proportion of the network versions where the OTU is associated with the respective module provided that the OTU is part of the network (= inBestModule/present), meanAbundanceModuleSamples – mean relative abundance of the OTU in all samples belonging to the module, meanAbundanceOtherSamples – mean relative abundance of the OTU in all other samples, relAbundanceModuleSamplesVsOthers – meanAbundanceModuleSamples / meanAbundanceOtherSamples .</p> <p>Table S3: Module-associated trees and OTUs, their relative abundances and identities for the fungal heartwood network; module – name of the module, present – proportion of network version that the OTU is present in (1 = 1000/1000), inBestModule – proportion of the network versions where the OTU is associated with the respective module, percInBestModule – proportion of the network versions where the OTU is associated with the respective module provided that the OTU is part of the network (= inBestModule/present), meanAbundanceModuleSamples – mean relative abundance of the OTU in all samples belonging to the module, meanAbundanceOtherSamples – mean relative abundance of the OTU in all other samples, relAbundanceModuleSamplesVsOthers – meanAbundanceModuleSamples / meanAbundanceOtherSamples .</p> <p>Table S4: Module-associated trees and OTUs, their relative abundances and identities for the prokaryotic sapwood network; module – name of the module, present – proportion of network version that the OTU is present in (1 = 1000/1000), inBestModule – proportion of the network versions where the OTU is associated with the respective module, percInBestModule – proportion of the network versions where the OTU is associated with the respective module provided that the OTU is part of the network (= inBestModule/present), meanAbundanceModuleSamples – mean relative abundance of the OTU in all samples belonging to the module, meanAbundanceOtherSamples – mean relative abundance of the OTU in all other samples, relAbundanceModuleSamplesVsOthers – meanAbundanceModuleSamples / meanAbundanceOtherSamples .</p> <p>Table S5: Module-associated trees and OTUs, their relative abundances and identities for the prokaryotic heartwood network; module – name of the module, present – proportion of network version that the OTU is present in (1 = 1000/1000), inBestModule – proportion of the network versions where the OTU is associated with the respective module, percInBestModule – proportion of the network versions where the OTU is associated with the respective module provided that the OTU is part of the network (= inBestModule/present), meanAbundanceModuleSamples – mean relative abundance of the OTU in all samples belonging to the module, meanAbundanceOtherSamples – mean relative abundance of the OTU in all other samples, relAbundanceModuleSamplesVsOthers – meanAbundanceModuleSamples / meanAbundanceOtherSamples .</p>
Data from: Hierarchical social networks shape gut microbial composition in wild Verreaux's sifaka
<p>In wild primates, social behaviour influences exposure to environmentally acquired and directly transmitted microorganisms. Prior studies indicate that gut microbiota reflect pairwise social interactions among chimpanzee and baboon hosts. Here, we demonstrate that higher-order social network structure—beyond just pairwise interactions—drives gut bacterial composition in wild lemurs, which live in smaller and more cohesive groups than previously studied anthropoid species. Using 16S rRNA gene sequencing and social network analysis of grooming contacts, we estimate the relative impacts of hierarchical (i.e. multilevel) social structure, individual demographic traits, diet, scent-marking, and habitat overlap on bacteria acquisition in a wild population of Verreaux's sifaka (<em>Propithecus</em> <em>verreauxi</em>) consisting of seven social groups. We show that social group membership is clearly reflected in the microbiomes of individual sifaka, and that social groups with denser grooming networks have more homogeneous gut microbial compositions. Within social groups, adults, more gregarious individuals, and individuals that scent-mark frequently harbour the greatest microbial diversity. Thus, the community structure of wild lemurs governs symbiotic relationships by constraining transmission between hosts and partitioning environmental exposure to microorganisms. This social cultivation of mutualistic gut flora may be an evolutionary benefit of tight-knit group living.</p>
Reconstruction of a soil microbial network induced by stress temperature
<p>By applying a nonlinear time-series analysis to the metagenomic data of the soil microbiota cultured under suitable (30℃) or stressful (37℃) conditions, we show how the microbial interaction network responds to temperature stress. While the genera that persisted only under the suitable condition gave fewer positive effects, the genera that appeared only under the stressful condition received more positive effects in agreement with SGH. However, temperature changes also induce reconstruction of a community network, leading to an increased proportion of negative interactions at the whole community level. The anti-SGH pattern can be explained by the stronger competition caused by increased metabolic rate and population densities. </p>
Reconstruction of a soil microbial network induced by stress temperature
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Data from: Hierarchical social networks shape gut microbial composition in wild Verreaux's sifaka
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Universal microbial network decomposes mammals despite varied climate, location, and seasonal influence
<p>Microbial breakdown of organic material is one of the most important processes on earth, yet enormous knowledge gaps exist about its controls. We demonstrate that a universal, inter-kingdom microbial network assembles in response to nutrient-rich, terrestrial mammalian decomposition, despite selection effects of location, climate and season. We created the first metagenome-assembled genome library from mammalian decomposition-associated soils and combined it with metabolomics to identify a microbial decomposer network that interacts by cross-feeding to efficiently metabolize labile decomposition products. The key fungal and bacterial decomposers appear unique to the breakdown of terrestrial cadavers, and are rare in relative abundance across non-decomposition environments. Blow flies are suggested as an important decomposer vector and the observed lockstep of microbial interactions underlies a robust microbial forensic tool for predicting the time since death. </p>
Inferring microbial co-occurrence network from amplicon data: a systematic evaluation
<p>Supporting data for the manuscript "<em>Inferring microbial co-occurrence network from amplicon data: a systematic evaluation</em>".</p>
Data and code from: Thermodynamics underpinning the microbial community-level nitrogen networks
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Data from: Connectivity loss in experimental pond networks leads to biodiversity loss in microbial metacommunities
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Artificial neural network model and metabolomics data of selected microbial strains
<p>Metabolomics data, metadata, sample R code, and a pre-trained artificial neural network model to predict group memberships of the bacterial strains in the dataset.</p>
Data from: Fitness and microbial networks of the common wasp, Vespula vulgaris (Hymenoptera: Vespidae), in its native and introduced range
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Pollinators mediate floral microbial diversity and network under agrochemical disturbance
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Bioprospecting of soil-borne microorganisms and chemical dereplication of their anti-microbial constituents with the aid of UPLC-QTOF-MS and Molecular Networking approach
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The intestinal intermediate filament network responds to and protects against microbial insults and toxins II
GEO Series GSE125132. Caenorhabditis elegans. 6 samples. Type: Expression profiling by array.
The intestinal intermediate filament network responds to and protects against microbial insults and toxins I
GEO Series GSE125131. Caenorhabditis elegans. 6 samples. Type: Expression profiling by array.
The intestinal intermediate filament network responds to and protects against microbial insults and toxins
GEO Series GSE125133. Caenorhabditis elegans. 12 samples. Type: Expression profiling by array.
Dietary fat disturbance of of gut microbial diurnal patterns uncouples host metabolic networks.
GEO Series GSE53590. Mus musculus. 8 samples. Type: Expression profiling by array.
Community network analysis of complex microbial biofilms reveals characteristic microbial assemblages in health and disease
GEO Series GSE32159. Bacteria; Homo sapiens. 604 samples. Type: Non-coding RNA profiling by array.
A single early-in-life antibiotic course has long-lasting effect on microbial network topology and host immunity, in a murine model
GEO Series GSE98292. Mus musculus. 36 samples. Type: Expression profiling by array.
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.