Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
1,076
datasets available to search
ShareScore release 0.7.1
Dataset results
1,076 results for “Metabarcoding”
Plant metabarcoding analysis in a Ptolemaic Egyptian Bes-vase
<p><strong>The investigation into origins and meaning of ancient religious rituals stands as a central pursuit within the fields of archaeology and anthropology. Today, we possess a wealth of well-preserved artifacts, often in their original form, that serve as compelling narratives from both cultural and material perspectives. Through the application of aDNA metabarcoding analysis, we have gained the ability to decipher those natural substances employed for ritualistic or medicinal purposes within the intricate and enigmatic religious and cultural framework of Egyptian civilization. </strong></p> <p><strong>here we deposit the sequences obtained from 16 mg of powder material recovered from the vase was processed for nucleic acid extraction in a laboratory area dedicated to the analysis of ancient DNA (aDNA). A brand new commercial kit, Quick-DNA Plant/Seed Kits (ZymoResearch), was used to extract the DNA, which was eluted in a volume of 50 µL. To ensure there were no possible contaminations, mock extractions without samples were systematically performed. DNA amplifications were conducted in a final volume of 25 µL, using 5 µL of undiluted DNA extract as the template. The amplification mixture contained 12.5 µL of AccuStart™ II PCR ToughMix (Quantabio), 0.1 µM of each primer, and 1 Evagreen to monitor the amplification kinetics on a BIO-RAD CFX96 thermal cycler. The mixture was denatured at 94°C for 3 minutes, followed by cycles of 15 seconds at 94°C, 10 seconds at 55°C, and 20 seconds at 72°C. The P6 loop region of the trnL (UAA) intron was amplified in triplicate using the universal primers g (5′-GGGCAATCCTGAGCCAA-3′) and h (5′-CCATTGAGTCTCTGCACCTATC-3′), which were modified by the addition of an adapter sequence (Illumina, San Diego, CA, USA) on the 5′ ends (81). Amplicon sequencing was performed using the 2 × 150-bp paired-end method on the MiSeq platform with a MiSeq Reagent Kit v2 Nano (Illumina). The reads obtained from the sequencing were processed using the CLC Genomics Workbench software environment ver. 22.0.</strong></p>
Data from: Predator-prey interactions in the Arctic: DNA-metabarcoding reveals that nestling diet of snow buntings reflects arthropod seasonality
<p>Tundra arthropods are of considerable ecological importance as a seasonal food source for many arctic-breeding birds. Dietary composition and food preferences are rarely known, complicating assessments of ecological interactions in a changing environment. In our field study, we investigated nestling diet of snow buntings (<em>Plectrophenax nivalis</em> (L., 1758)) breeding in Svalbard. We collected faecal samples from 8-day-old nestlings and assessed dietary composition by DNA-metabarcoding. Simultaneously, the availability of potential prey arthropods was measured by pitfall-trapping. Molecular analyses of nestling faeces identified 31 arthropod taxa in the diet, whose proportions changed throughout the brood-rearing period. Changes in nestling diet matched varying abundances and emergence patterns of the tundra arthropod community. Snow buntings provisioned their offspring mainly with Diptera (true flies) based on both presence/absence and relative read abundance of diet items. At the beginning of the season in June, Chironomidae (non-biting midges) and the scathophagid fly <em>Scathophaga furcata</em> (Say, 1823) dominated the diet, whereas the muscid fly <em>Spilogona dorsata </em>(Zetterstedt, 1845) dominated the diet later in July. When accounted for availability, muscid flies were selected positively amongst the most often provisioned food taxa. Our study demonstrates the ecological role of the snow bunting as a generalist arthropod predator and highlights DNA-metabarcoding as a non-invasive technique for diet analyses with high taxonomical precision if sufficient DNA-sequence libraries are available.</p>
Fastq sequence files supporting: Assessing the degradation of environmental DNA and RNA based on genomic origin in a metabarcoding context
<p>Molecular tools of species identification based on eNAs (environmental nucleic acids; eDNA and eRNA) have the potential to greatly transform biodiversity science. However, the ability of eNAs to obtain "real-time" biodiversity estimates may be complicated by the differential persistence and degradation dynamics of the molecular template (eDNA or eRNA) and the barcode marker used. Here, we collected water samples over a 28-day period to comparatively assess species detection using eDNA and eRNA metabarcoding of two distinct barcode markers—a mitochondrial mRNA marker (COI) and a nuclear rRNA marker (18S)—following complete removal of <em>Arthropoda </em>taxa in a semi-natural freshwater system. Our findings demonstrate that <em>Arthropoda </em>community composition was largely influenced by marker choice, rather than molecular template, individual microcosm, or sampling time point. Further, although eRNA may capture similar species diversity as the established eDNA method, this finding may be marker dependent. Although we found little to no difference in decay rates observed among sample groups (COI eDNA, COI eRNA, 18S eDNA, 18S eRNA), this result is likely due to limitations in the ability of eNA-based metabarcoding to provide a strong correlation between true eNA copy numbers present in the environment and final read counts obtained (following the metabarcoding workflow). Collectively, our findings provide further support for the use of multi-marker assessments in metabarcoding surveys to unravel the broadest taxonomic diversity possible, highlight the limitations of eNA metabarcoding methods in providing accurate decay rate estimates, as well as establish the need for further comparative studies using both metabarcoding and single-species detection methods to assess the persistence and degradation dynamics of eNAs for a diverse range of taxa.</p>
Data from: Foraging history of individual elephants using DNA metabarcoding
<p>Individual animals should adjust diets according to food availability. We used DNA metabarcoding to construct individual-level dietary timeseries for elephants from two family groups in Kenya varying in habitat use, social position, and reproductive status. We detected at least 367 dietary plant taxa, with up to 137 unique plant sequences in one fecal sample. Results matched well-established trends: elephants tended to eat more grass when it rained and other plants when dry. Nested within these switches from 'grazing' to 'browsing' strategies, dietary DNA revealed seasonal shifts in food richness, composition, and overlap between individuals. Elephants of both families converged on relatively cohesive diets in dry seasons but varied in their maintenance of cohesion during wet seasons. Dietary cohesion throughout the timeseries of the subdominant 'Artists' family was stronger and more consistently positive compared to the dominant 'Royals' family. The greater degree of individuality within the dominant family's timeseries could reflect more divergent nutritional requirements associated with calf-dependency and/or priority access to preferred habitats. Whereas theory predicts that individuals should specialize on different foods under resource scarcity, our data suggest family bonds may promote cohesion and foster the emergence of diverse feeding cultures reflecting links between social behavior and nutrition.</p>
Sequencing data for: Tracking climate-change induced biological invasions over 4 decades by metabarcoding archived natural eDNA samplers
<p><span>In a time of unprecedented global environmental change, understanding the response of biodiversity is paramount. However, our knowledge of anthropogenic impacts on ecosystems is limited by a lack of standardized retrospective biomonitoring data. Here, we use four-decade time series of archived blue mussels to trace spatiotemporal biodiversity change in coastal ecosystems. The filter-feeding mussels can serve as natural eDNA samplers, carrying an imprint of the surrounding aquatic community at the time of sampling. By sequencing the preserved DNA, we characterize highly diverse mussel-associated communities and reconstruct the invasion trajectory of an invasive species to the detriment of native taxa uncovering repeated population collapses and reinvasions after cold winters. Time series of natural eDNA samplers provide highly resolved temporal data on community assembly and global warming-driven invasion processes and overcome critical shortfalls in our understanding of biodiversity change in the Anthropocene.</span></p>
Data from: DNA metabarcoding reveals rangewide variation in aquatic diet of a riparian avian insectivore, the Prothonotary warbler
<p>Riparian avian insectivores not only depend on terrestrial insect prey but also benefit from the inclusion of aquatic prey during critical life history periods. Diets identified herein show that Prothonotary Warbler (<em>Protonotaria citrea</em>) nestlings were provisioned with aquatic prey throughout the breeding season across their range, but with variation in prey frequency of occurrence and taxonomy. Anthropogenic activity and climate change may impact the trophic link especially between aquatic and riparian habitats by altering the presence, abundance, and timing of prey availability. Thus, we used DNA metabarcoding of fecal samples to quantify the frequency of occurrence of nestling diet items at nine sites across their breeding range that differed in expected aquatic prey consumption. We analyzed spatial and temporal differences in the occurrence and multivariate diet assemblages of each prey source. Lepidoptera was the predominant terrestrial prey occurring in diets across space and time, whereas emergent aquatic insects and freshwater mollusks in aquatic diet exhibited greater variation. The frequency of emergent aquatic prey occurrence in nestling diets ranged from 61-100% across sites and was greater for early-season nestlings. The seasonal decrease in aquatic prey consumption indicates a potential temporal shift in the nutritional landscape from aquatic to terrestrial prey sources and a possible nutritional phenological mismatch for early nestlings as climate change advances the timing of insect emergence. Our findings also suggest that Prothonotary Warblers respond to environmental variability by consuming alternative prey and argue for future research investigating the extent to which shifting diets have nutritional consequences for riparian nestlings.</p>
DNA metabarcoding data from faecal samples of the lesser (Myotis blythii) and the greater (Myotis myotis) mouse-eared bats from Bulgaria
<p>A comprehensive understanding of trophic interactions in terrestrial ecosystems is crucial for ecological research and conservation. Recent advances in non-invasive methods, such as DNA metabarcoding, have enabled researchers to collect vast amounts of data on wild animal diets. However, sharing this data and metadata effectively and transparently presents new challenges. To address this, a new type of scholarly journal publication has emerged that aims to describe datasets rather than report research investigations. In this paper, we present a dataset of consumed prey species and parasites based on the metabarcoding of 113 faecal samples from the greater and lesser mouse-eared bats (<em>Myotis myotis</em> and <em>Myotis blythii</em>), along with a detailed description of the data sampling, laboratory analysis, and bioinformatics pipeline. Our dataset comprises 1018 unique Barcode Index Numbers (BINs) from 12 Classes and 43 Orders. In addition, we provide interactive Krona charts to visually summarize the taxonomic relationships and relative read abundance of the consumed prey species and parasites. This data can be used for meta-analysis, exploring new predator-prey and host-parasite interactions, studying inter and intraspecific ecological interactions, and informing protected area management, among other applications. By sharing this dataset, we hope to encourage other researchers to use it to answer additional ecological questions and advance our understanding of trophic interactions in terrestrial ecosystems.</p>
Bats are sentinels for invasive pest surveillance based on DNA metabarcoding
<p><span>Insectivorous bats have been identified as important agents for biological pest control in the agroecosystems and impose strong top-down pressure on pests</span><span> (</span><span>Ramirez-Francel</span><span> et al., 2022)</span><span>.</span><span> Without bats, it is estimated that the United States would spend more than $3 billion a year on pesticides alone</span><span> (</span><span>Boyles</span><span> et al., 2011)</span><span>. </span><span>Thus, b</span><span>ats are expected to be natural pest collectors</span><span> (Kunz, 2011)</span><span>. However, </span><span>it is still unproven assumption that bats can be used to efficiently monitor </span><span>invasi</span><span>ve</span><span> pest</span><span>s</span><span> in agroecosystems.</span> <span>Due to the wide distribution of bats, their high foraging efficiency, large activity range, and because most bats return to the same habitat and cluster in roosts together after foraging, collecting fecal samples is feasible and convenient. In our preliminary experiments, multiple bat species were found to normally consume FAW, which provides an excellent opportunity for verifying the practicability of DNA metabarcoding in monitoring the invasion of this pest.</span></p>
DNA metabarcoding illuminates the contribution of small and very small prey taxa to the diet of lions
<p><span>Knowledge of food web interactions is essential for understanding the role of carnivores in an ecosystem and designing appropriate conservation and management strategies to preserve them. These interactions can only be understood by studying carnivores' diets and obtaining comprehensive and unbiased diet data. For large carnivores – which typically rely on large herbivores as prey – the role of smaller prey species has not received attention. This study aims to quantify the contribution of small (5–50 kg) and very small (<5 kg) prey taxa in the diet of lions (</span><em><span>Panthera leo melanochaita</span></em><span>)</span><span> in four Kenyan National Parks (NPs). We use DNA metabarcoding to achieve higher-resolution insights into prey composition, which is less biased toward large prey species compared to traditional methods, such as carcass counts. Our study identified 24 prey taxa in a total of 171 lion fecal samples. Small and very small p</span><span>rey taxa together contributed 18.7% out of 278 prey occurrences in all fecal samples. With comparable small prey presence (ranging from 8% to 15%) in the diet for each NP studied. This approach </span><span>proved to be useful in detecting small and very small prey species in the diet of lions and can therefore be used in future research to uncover the diverse diet composition of these large carnivores. The consistent presence of smaller prey species in the diet indicates that lions generally supplement their large prey diet with smaller prey. </span></p>
Data from: Evaluation of fecal metabarcoding for studying the diets of sympatric dusky salamanders (Desmognathus)
<p>Amphibian diet studies often rely on visual identification of prey obtained through forced regurgitation or dissection. These approaches are somewhat invasive and often lack taxonomic specificity, which can discourage diet studies involving at-risk species and limit fine-scale investigations of diet composition. Here, we employ and assess a non-invasive molecular technique to characterize the diets of three co-occurring stream-dwelling salamander species (<em>Desmognathus ocoee</em>, <em>Desmognathus monticola</em>, and <em>Desmognathus quadramaculatus</em>) and investigate possible dietary partitioning within and among species. We used DNA metabarcoding to classify the arthropod prey communities from fecal samples of field-collected salamanders and investigated associations with predator species and snout-vent length (SVL). Of 200 salamanders captured and held for 24 hrs, 38 (19%) produced fecal samples containing arthropod DNA. We identified 53 prey taxa, of which 27 we could classify to species, 12 to genus, 10 to family, and 4 to order. We found no evidence of dietary partitioning among species or by SVL. Individual fecal samples generally contained few taxa, and few taxa were shared among samples, suggesting that our sample size likely limited the power of our inference. Our results support the utility of fecal metabarcoding as a non-invasive and taxonomically precise alternative to traditional diet analysis techniques. However, researchers should also consider the challenges associated with fecal metabarcoding (e.g., infrequent defecation by study organisms) before using it to complement more traditional methods.</p>
Gut content metabarcoding of specialized feeders is not a replacement for environmental DNA assays of their reef environment
<p>In tropical marine ecosystems, the coral-based diet of benthic-feeding reef fishes provides a window into the composition and health of coral reefs. In this study, for the first time, we compare multi-assay metabarcoding sequences of environmental DNA (eDNA) isolated from seawater and partially digested gut items from an obligate corallivore butterflyfish (<em>Chaetodon</em> <em>lunulatus</em>) resident at coral reef sites in the South China Sea. We specifically tested the proportional and statistical overlap of the different approaches (seawater versus gut content metabarcoding) in characterizing eukaryotic community composition on coral reefs. Based on 18S rRNA and ITS2 rRNA sequence data, which differed in their taxonomic sensitivity, we found that gut content detections were only partially representative of the eukaryotic communities detected in the seawater. Overall, our results indicate that dietary metabarcoding of specialized feeders can be complimentary to, but is no replacement for, more comprehensive environmental DNA assays of reef environments that can include the processing of different substrates (seawater, sediment, plankton) or traditional observational surveys. These molecular assays, in tandem, might be best suited to highly productive but cryptic oceanic environments (coral reefs, kelp forests, seagrass meadows) that contain an abundance of organisms that are often small, epiphytic, symbiotic, or cryptic.</p>
Complementary authentication of Chinese herbal products to treat endometriosis using DNA metabarcoding and HPTLC shows a high level of variability
<p>Traditional Chinese Medicine (TCM) is popular for the treatment of endometriosis, a complex gynecological disease that affects 10% of women globally. The growing market for TCMs has yielded a significant incentive for product adulteration, and although emerging technologies show promise to improve their quality control, many challenges remain. We tested the authenticity of two traditional Chinese herbal formulae used in women’s healthcare for the treatment of endometriosis, known as <em>Gui Zhi Fu Ling Wan</em> (FL) and <em>Ge Xia Zhu Yu Tang</em> (GX). Dual-locus DNA metabarcoding analysis coupled with high-performance thin-layer chromatography (HPTLC) were used to authenticate 19 FL and six GX commercial herbal products, as well as three ad hoc prepared artificial mixtures. HPTLC was able to detect most of the expected ingredients via comparative component analysis. DNA metabarcoding was able to detect an unexpected species diversity in the products, including 38 unexpected taxa. Chromatography has resolution for all species indirectly through identification of marker compounds for the different species ingredients. Metabarcoding on the other hand yields an overview of species diversity in each sample, but interpretation of the results can be challenging. Detected species might not be present in quantities that matter, and without validated quantification some detected species can be hard to interpret. Comparative analysis of the two analytical approaches also reveals that DNA for species might be absent or too fragmented to amplify as the relevant chemical marker compounds can be detected but no amplicons assigned to the same species. Our study emphasizes that integrating DNA metabarcoding with phytochemical analysis brings valuable data for comprehensive authentication of Traditional Chinese Medicines ensuring their quality and safe use.</p>
Hidden Phytophthora diversity unveiled in nurseries of the Czech Republic with metabarcoding
<p>This a subset of 105 demultiplexed Illumina MiSeq raw sequencing samples run at the James Hutton Institute in March 2022, consisting of two 96-well plates labelled with the Illumina A and D multiplexing kits with, 96 and 9 samples respectively.</p><p>There are 36 pairs of raw gzipped compressed FASTQ files (72 files), provided as a 336MB gzipped compressed tar-ball.</p><p>All 6 controls and 30 samples of interest are from the A multiplexing kit.</p><p>The sample filenames start with the sample name, followed by something like <i>CZ-N001-1910-S1Z1A-AD02_S38_L001_R1_001.fastq.gz</i> where <i>AD02</i> indicates well <i>D02</i> on the 96-well plate labelled with the <i>A</i> multiplexing set, and <i>S38</i> is the MiSeq sample number (from 1 to 192), and <i>R1</i> (or <i>R2</i>) indicate the Illumina forward (or reverse) paired read files.</p><p>The 6 controls have filenames starting <i>GL3A-0x</i>, shorthand for an undiluted synthetic sequence mix. Control <i>GL3A-0x-AB06_S18_L001</i> had the highest levels of non-synthetic sequence, with 422 copies of a biological sequence. This was therefore used by the THAPBI PICT pipeline as the minimum abundance threshold.</p>
Dietary adaptations along the Northern limit of distribution: What does the smooth snake (Coronella austriaca) eat in Norway? Metabarcoding of stomach content and visual analysis of faeces
Open the record for dataset details and reuse information.
Data from: Multi-tool marine metabarcoding bioassessment for baselining and monitoring species and communities in kelp habitats
Open the record for dataset details and reuse information.
Fungus and plant sedimentary ancient DNA metabarcoding data from five lakes in Siberia
Open the record for dataset details and reuse information.
Biomonitoring planktonic threats to salmon aquaculture: morphological and eDNA metabarcoding data
Open the record for dataset details and reuse information.
Fecal DNA metabarcoding-derived diets of deer in Sweden
Open the record for dataset details and reuse information.
Data from: Environmental DNA metabarcoding elucidates freshwater mussel diversity and occupancy to facilitate improved management and conservation
Open the record for dataset details and reuse information.
Combining sampling gear to optimally inventory species highlights the efficiency of eDNA metabarcoding
Open the record for dataset details and reuse information.
ScienceDex guides
Understand access before you commit
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.