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915 results for “metagenomics”
Rhizosphere metagenome of Punica granatum
<p>A comparison of microbial community of Rhizosphere and Bulk soil procured from a pomegranate farm.</p>
Supplementary material 1 from: Clasen LA, Detheridge AP, Scullion J, Griffith GW (2020) Soil stabilisation for DNA metabarcoding of plants and fungi. Implications for sampling at remote locations or via third-parties. Metabarcoding and Metagenomics 4: e58365. https://doi.org/10.3897/mbmg.4.58365
Combined Supplemntary Data Files 1–8
Supplementary material 9 from: Harper L, Watson H, Donnelly R, Hampshire R, Sayer C, Breithaupt T, Hänfling B (2020) Using DNA metabarcoding to investigate diet and niche partitioning in the native European otter (Lutra lutra) and invasive American mink (Neovison vison). Metabarcoding and Metagenomics 4: e56087. https://doi.org/10.3897/mbmg.4.56087
Figure S3
Supplementary material 10 from: Harper L, Watson H, Donnelly R, Hampshire R, Sayer C, Breithaupt T, Hänfling B (2020) Using DNA metabarcoding to investigate diet and niche partitioning in the native European otter (Lutra lutra) and invasive American mink (Neovison vison). Metabarcoding and Metagenomics 4: e56087. https://doi.org/10.3897/mbmg.4.56087
Figure S4
Supplementary material 11 from: Harper L, Watson H, Donnelly R, Hampshire R, Sayer C, Breithaupt T, Hänfling B (2020) Using DNA metabarcoding to investigate diet and niche partitioning in the native European otter (Lutra lutra) and invasive American mink (Neovison vison). Metabarcoding and Metagenomics 4: e56087. https://doi.org/10.3897/mbmg.4.56087
Figure S5
Supplementary material 8 from: Harper L, Watson H, Donnelly R, Hampshire R, Sayer C, Breithaupt T, Hänfling B (2020) Using DNA metabarcoding to investigate diet and niche partitioning in the native European otter (Lutra lutra) and invasive American mink (Neovison vison). Metabarcoding and Metagenomics 4: e56087. https://doi.org/10.3897/mbmg.4.56087
Figure S2
Supplementary material 12 from: Harper L, Watson H, Donnelly R, Hampshire R, Sayer C, Breithaupt T, Hänfling B (2020) Using DNA metabarcoding to investigate diet and niche partitioning in the native European otter (Lutra lutra) and invasive American mink (Neovison vison). Metabarcoding and Metagenomics 4: e56087. https://doi.org/10.3897/mbmg.4.56087
Figure S6
Supplementary material 7 from: Harper L, Watson H, Donnelly R, Hampshire R, Sayer C, Breithaupt T, Hänfling B (2020) Using DNA metabarcoding to investigate diet and niche partitioning in the native European otter (Lutra lutra) and invasive American mink (Neovison vison). Metabarcoding and Metagenomics 4: e56087. https://doi.org/10.3897/mbmg.4.56087
Figure S1
Supplementary material 3 from: Harper L, Watson H, Donnelly R, Hampshire R, Sayer C, Breithaupt T, Hänfling B (2020) Using DNA metabarcoding to investigate diet and niche partitioning in the native European otter (Lutra lutra) and invasive American mink (Neovison vison). Metabarcoding and Metagenomics 4: e56087. https://doi.org/10.3897/mbmg.4.56087
Appendix 3: Predator assignment
Supplementary material 6 from: Harper L, Watson H, Donnelly R, Hampshire R, Sayer C, Breithaupt T, Hänfling B (2020) Using DNA metabarcoding to investigate diet and niche partitioning in the native European otter (Lutra lutra) and invasive American mink (Neovison vison). Metabarcoding and Metagenomics 4: e56087. https://doi.org/10.3897/mbmg.4.56087
Table S1
Supplementary material 1 from: Harper L, Watson H, Donnelly R, Hampshire R, Sayer C, Breithaupt T, Hänfling B (2020) Using DNA metabarcoding to investigate diet and niche partitioning in the native European otter (Lutra lutra) and invasive American mink (Neovison vison). Metabarcoding and Metagenomics 4: e56087. https://doi.org/10.3897/mbmg.4.56087
Appendix 1: Fish inventory
Supplementary material 2 from: Harper L, Watson H, Donnelly R, Hampshire R, Sayer C, Breithaupt T, Hänfling B (2020) Using DNA metabarcoding to investigate diet and niche partitioning in the native European otter (Lutra lutra) and invasive American mink (Neovison vison). Metabarcoding and Metagenomics 4: e56087. https://doi.org/10.3897/mbmg.4.56087
Appendix 2: Methods
Supplementary material 4 from: Harper L, Watson H, Donnelly R, Hampshire R, Sayer C, Breithaupt T, Hänfling B (2020) Using DNA metabarcoding to investigate diet and niche partitioning in the native European otter (Lutra lutra) and invasive American mink (Neovison vison). Metabarcoding and Metagenomics 4: e56087. https://doi.org/10.3897/mbmg.4.56087
Appendix 4: Samples from non-focal mammal predators
Supplementary material 5 from: Harper L, Watson H, Donnelly R, Hampshire R, Sayer C, Breithaupt T, Hänfling B (2020) Using DNA metabarcoding to investigate diet and niche partitioning in the native European otter (Lutra lutra) and invasive American mink (Neovison vison). Metabarcoding and Metagenomics 4: e56087. https://doi.org/10.3897/mbmg.4.56087
Appendix 5: Non-focal mammal diet
Supplementary material 2 from: Basset Y, Donoso DA, Hajibabaei M, Wright MTG, Perez KHJ, Lamarre GPA, De León LF, Palacios-Vargas JG, Castaño-Meneses G, Rivera M, Perez F, Bobadilla R, Lopez Y, Ramirez JA, Barrios H (2020) Methodological considerations for monitoring soil/litter arthropods in tropical rainforests using DNA metabarcoding, with a special emphasis on ants, springtails and termites. Metabarcoding and Metagenomics 4: e58572. https://doi.org/10.3897/mbmg.4.58572
Appendix S2
Human genome for contaminant removal of metagenome reads
<p>See http://seqanswers.com/forums/archive/index.php/t-42552.html</p>
Data from: Comparing the effectiveness of metagenomics and metabarcoding for diet analysis of a leaf-feeding monkey (Pygathrix nemaeus)
Fecal samples are of great value as a non-invasive means to gather information on the genetics, distribution, demography, diet, and parasite infestation of endangered species. Direct shotgun sequencing of fecal DNA could give information on these simultaneously, but this approach is largely untested. Here we use two fecal samples to characterize the diet of two Red-Shanked Doucs Langurs (Pygathrix nemaeus) that were fed a known combination of foliage, fruits, vegetables and cereals. Illumina HiSeq sequencing produced ~70 million paired reads per sample, of which ~10000 (0.014%) and ~44000 (0.066%) respectively corresponded to chloroplast genomes. Sequences were matched against a database of available chloroplast 'barcodes' for angiosperms. The results were compared with 'metabarcoding' using PCR amplification of the P6 loop of trnL. Shotgun sequencing identified 7 and 9 of the likely 16 diet plants, against 6 and 5 plant species identified by metabarcoding. Metabarcoding produced thousands of reads that were consistent with the known diet, but the barcodes were too short to identify several diet plants to genus. Metagenomics could utilize multiple, longer barcodes that combined had greater power of identification, but rare diet items were not recovered. Read numbers for diet species in metagenomic and metabarcoding data were correlated, indicating that both approaches are useful for determining relative sequence abundance. Metagenomic reads were uniformly distributed across the chloroplast genomes; thus if chloroplast genomes were to be used as reference, the precision of identifications and species recovery would improve further. Metagenomics also recovered the host mitochondrial genome and numerous intestinal parasite sequences in addition to generating data useful for characterizing the microbiome.
Data from: Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics
Background: Microbial diversity and community structures in acidic hot springs have been characterized by 16S rRNA gene-based diversity surveys. However, our understanding regarding the interactions among microbes, or between microbes and environmental factors, remains limited. Results: In the present study, a metagenomic approach, followed by bioinformatics analyses, were used to predict interactions within the microbial ecosystem in Shi-Huang-Ping (SHP), an acidic hot spring in northern Taiwan. Characterizing environmental parameters and potential metabolic pathways highlighted the importance of carbon assimilatory pathways. Four distinct carbon assimilatory pathways were identified in five dominant genera of bacteria. Of those dominant carbon fixers, Hydrogenobaculum bacteria outcompeted other carbon assimilators and dominated the SHP, presumably due to their ability to metabolize hydrogen and to withstand an anaerobic environment with fluctuating temperatures. Furthermore, most dominant microbes were capable of metabolizing inorganic sulfur-related compounds (abundant in SHP). However, Acidithiobacillus ferrooxidans was the only species among key rare microbes with the capability to fix nitrogen, suggesting a key role in nitrogen cycling. In addition to potential metabolic interactions, based on the 16S rRNAs gene sequence of Nanoarchaeum-related and its potential host Ignicoccus-related archaea, as well as sequences of viruses and CRISPR arrays, we inferred that there were complex microbe-microbe interactions. Conclusions: Our study provided evidence that there were numerous microbe-microbe and microbe-environment interactions within the microbial community in an acidic hot spring. We proposed that Hydrogenobaculum bacteria were the dominant microbial genus, as they were able to metabolize hydrogen, assimilate carbon and live in an anaerobic environment with fluctuating temperatures.
Data from: A new plant virus discovered by immunocapture of double stranded RNA; assessment of a novel approach for viral metagenomics studies
Next-generation sequencing technologies enable the rapid identification of viral infection of diseased organisms. However, despite a consistent decrease in sequencing costs, it is difficult to justify their use in large-scale surveys without a virus sequence enrichment technique. As the majority of plant viruses have an RNA genome, a common approach is to extract the double-stranded RNA (dsRNA) replicative form, to enrich the replicating virus genetic material over the host background. The traditional dsRNA extraction is time-consuming and labour-intensive. We present an alternative method to enrich dsRNA from plant extracts using anti-dsRNA monoclonal antibodies in a pull-down assay. The extracted dsRNA can be amplified by reverse transcriptase–polymerase chain reaction and sequenced by next-generation sequencing. In our study, we have selected three distinct plant hosts: Māori potato (Solanum tuberosum), rengarenga (Arthropodium cirratum) and broadleaved dock (Rumex obtusifolius) representing a cultivated crop, a New Zealand-native ornamental plant and a weed, respectively. Of the sequence data obtained, 31–74% of the reads were of viral origin, and we identified five viruses including Potato virus Y and Potato virus S in potato; Turnip mosaic virus in rengarenga (a new host record); and in the dock sample Cherry leaf roll virus and a novel virus belonging to the genus Macluravirus. We believe that this new assay represents a significant opportunity to upscale virus ecology studies from environmental, primary industry and/or medical samples.
Data from: Potential and pitfalls of eukaryotic metagenome skimming: A test case for lichens
Whole genome shotgun sequencing of multi species communities using only a single library layout is commonly used to assess taxonomic and functional diversity of microbial assemblages. Here we investigate to what extent such metagenome skimming approaches are applicable for in-depth genomic characterizations of eukaryotic communities, e.g. lichens. We address how to best assemble a particular eukaryotic metagenome skimming data, what pitfalls can occur, and what genome quality can be expected from this data. To facilitate a project specific benchmarking, we introduce the concept of twin sets, simulated data resembling the outcome of a particular metagenome sequencing study. We show that the quality of genome reconstructions depends essentially on assembler choice. Individual tools, including the metagenome assemblers Omega and MetaVelvet, are surprisingly sensitive to low and uneven coverages. In combination with the routine of assembly parameter choice to optimize the assembly N50 size, these tools can preclude an entire genome from the assembly. In contrast, MIRA, an all-purpose overlap assembler, and SPAdes, a multi-sized de Bruijn graph assembler, facilitate a comprehensive view on the individual genomes across a wide range of coverage ratios. Testing assemblers on a real-world metagenome skimming data from the lichen Lasallia pustulata demonstrates the applicability of twin sets for guiding method selection. Furthermore, it reveals that the assembly outcome for the photobiont Trebouxia sp. falls behind the a-priori expectation given the simulations. Although the underlying reasons remain still unclear this highlights that further studies on this organism require special attention during sequence data generation and downstream analysis.
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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.