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33 results for “OTU”
Environmental data and OTU table of bacteria and fungi in Jianfengling, Shennongjia and Xing'an Mountains
<p>Understanding the elevational pattern of soil microbial diversity is crucial for microbial biogeography, yet, the elevational patterns of diversity across different climatic zones, trophic levels and taxonomic levels remain unclear.</p> <p>In this study, we investigated the elevational patterns of species richness, evenness and the relationship between species richness and evenness (RRE) in the forest soil bacterial and fungal communities and individual phyla across three climatic zones (tropical, subtropical and cold temperate).</p> <p>Our results revealed that soil bacterial richness (alpha diversity) decreased with elevation, while fungi richness exhibited a hump-shaped pattern in tropical and cold temperate forests. Elevational patterns of evenness in bacterial and fungal communities showed hump-shaped patterns across climatic zones, except bacterial evenness in the tropical forest. Both bacterial and fungal richness and evenness were positively correlated in the subtropical and cold temperate forests, while negatively correlated for bacteria in the tropical forest. The richness and evenness of soil microorganisms across different regions were controlled by climatic and edaphic factors. Soil pH was the most important factor associated with the variations in bacterial richness and evenness, while mean annual temperature explained the major variations in fungal richness. Our results addressed the varieties of elevational patterns of microbial diversity in climate zones and taxonomic levels, further indicating that richness and evenness may respond differently to environmental gradients.</p>
Environmental data and OTU table of bacteria and fungi in Jianfengling, Shennongjia and Xing'an Mountains
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Achieving bio-protection in New Zealand ecosystems mesocosm fungal pathogen OTU table
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Raw sequence data and OTU tables of soil microorganisms obtained across a summit in the Lesotho highlands
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Supplementary material 1 from: Macher J, Macher T, Leese F (2017) Combining NCBI and BOLD databases for OTU assignment in metabarcoding and metagenomic datasets: The BOLD_NCBI _Merger. Metabarcoding and Metagenomics 1: e22262. https://doi.org/10.3897/mbmg.1.22262
The supplementary material contains the BOLD_NCBI_Merger script, the needed folder structure and the tutorial explaining how to use the script
OTU_Table1
<p>Unrarefied OTU table including dilutions series samples and controls. Taxonomy was assigned using the SILVA database. The V3-V4 region of the 16S rRNA genes were amplified using universal prokaryotic primer Pro341F and Pro805R.</p>
OTU_Table2
<p>Rarefied OTU table including Wyoming MX-80 bentonite samples. Taxonomy was assigned using the SILVA database. The V4-V5 region of 16S rRNA genes was amplified using universal prokaryotic primers 515F-Y and 926R.</p>
OTU data and analysis files for interspecies comparison of Philippine terrestrial small mammal diets
<p>Island radiations represent unique evolutionary histories in unique ecological contexts. These radiations provide opportunities to investigate ecological diversification in groups that typically exhibit niche partitioning among their constituents, including partitioning of food resources. DNA metabarcoding produces finer levels of diet identification than traditional methods, allowing us to examine dietary niche partitioning in communities or clades in which species share superficially similar diets. Here we use DNA metabarcoding to investigate dietary niche partitioning in an endemic radiation of mammals in the Philippines. Our data reveal niche partitioning as well as phylogenetically-uncorrelated adaptive evolution in this small mammal community. Because 70% of the focal species belong to the tribe Chrotomyini, an endemic Philippine radiation of murid rodents that feed extensively on earthworms, this study sheds light on dietary adaptation and its role in the co-occurrence of closely related species. Our results reveal fine-scale resource partitioning within this community; our data provide compelling evidence for niche partitioning of diet that was masked by previous diet categories and will help in further dissecting the model adaptive radiation of endemic small mammals on Luzon. This study reinforces the notion that DNA metabarcoding can be a valuable tool for investigating both ecological relationships and evolutionary ecology at the community and phylogenetic level, respectively.</p>
OTU data and analysis files for interspecies comparison of Philippine terrestrial small mammal diets
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Operational Taxonomic Unit (OTU) Counts at Sampling Subplots at HJA, HFR, BCI, CWT, LUQ, and NWT for N2O-reducing Microbial Communities
Patterns of biodiversity, such as the increase toward the tropics and the peaked curve during ecological succession, are fundamental phenomena for ecology. Such patterns have multiple, interacting causes, but temperature emerges as a dominant factor across organisms from microbes to trees and mammals, and across terrestrial, marine, and freshwater environments. However, there is little consensus on the underlying mechanisms, even as global temperatures increase and the need to predict their effects becomes more pressing. The purpose of this project is to generate and test theory for how temperature impacts biodiversity through its effect on biochemical processes and metabolic rate. A combination of standardized surveys in the field and controlled experiments in the field and laboratory measure diversity of three taxa -- trees, invertebrates, and microbes -- and key biogeochemical processes of decomposition in seven forests distributed along a geographic gradient of increasing temperature from cold temperate to warm tropical. N2O is reduced to N2 exclusively by microorganisms but little is known about the diversity and geographic distribution of N2O-reducing communities in forest soils across a temperature gradient. To this end, nosZ (N2O-reducing) amplicons were sequenced by MiSeq and sorted into Operational Taxonomic Units (OTUs) which could then be compared across sites for distribution, richness, and diversity indices. This work was completed by the University of Oklahoma Institute for Environmental Genomics as part of a macrosystems biodiversity and latitude project supported by the National Science Foundation under Cooperative Agreement DEB#1065836.
R_Rajsp_OTU_Table_Investigationg_Soil_Mycobiome_of_American_Ginseng
<p>OTU Table for MSc Thesis at Western University.</p>
Supplementary material 1 from: Cros M-J, Frigerio J-M, Peyrard N, Franc A (2024) Simple approaches for evaluation of OTU quality based on dissimilarity arrays. Metabarcoding and Metagenomics 8: e108649. https://doi.org/10.3897/mbmg.8.108649
Supplementary information
The list of top 50 most abundant phytoplankton taxa and the relative OTU abundance in Beibu Gulf summer and winter of 2022
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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.