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47 results for “metabarcoding analysis”
Data from: Metabarcoding analysis provides insight into the link between prey and plant intake in a large alpine cat carnivore, the snow leopard
<p>Species of the family Felidae (a group represented by cats) are thought to be obligate carnivores, specialized for hunting and consuming other animals. However, the detection of plants in the feces of felids raises questions about the role of plants in their diet. This is particularly true for the snow leopard (Panthera uncia), a big cat native to central and South Asia's high mountains. Our study aimed to comprehensively identify the prey and plants consumed by snow leopards as well as six other sympatric mammals. We applied DNA metabarcoding methods on 126 fecal samples collected from the Sarychat-Ertash Nature Reserve in Kyrgyzstan. We found that among the three most common plant families in snow leopard feces, Tamaricaceae (genus Myricaraia) was consumed often by snow leopards. The genus Myricaria frequently appeared in samples lacking any animal prey DNA, indicating that snow leopards might have consumed this plant especially when their digestive tracts were empty. We also observed a significant difference in plant composition between male and female snow leopards, and potentially between sampling seasons. We provide a comprehensive overview of the prey and plants detected in the feces of snow leopards and sympatric mammals. We believe our findings will help in formulating hypotheses and guiding future research to understand the adaptive significance of plant-eating behavior in felids and animal-plant relationships in the ecosystem.</p>
Otterly delicious: Spatiotemporal variation in the diet of a recovering population of Eurasian otters (Lutra lutra) revealed through DNA metabarcoding and morphological analysis of prey remains
<p>Eurasian otters are apex predators of freshwater ecosystems and a recovering species across much of their European range; investigating the dietary variation of this predator over time and space therefore provides opportunities to identify changes in freshwater trophic interactions and factors influencing the conservation of otter populations. Here we sampled faeces from 300 dead otters across England and Wales between 2007 and 2016, conducting both morphological analysis of prey remains and dietary DNA metabarcoding. Comparison of these methods showed that greater taxonomic resolution and breadth could be achieved using DNA metabarcoding but combining data from both methodologies gave the most comprehensive dietary description. All otter demographics exploited a broad range of taxa and variation likely reflected changes in prey distributions and availability across the landscape. This study provides novel insights into the trophic generalism and adaptability of otters across Britain, which is likely to have aided their recent population recovery, and may increase their resilience to future environmental changes.</p>
Data from: Metabarcoding analysis provides insight into the link between prey and plant intake in a large alpine cat carnivore, the snow leopard
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Data from: Comparative analysis of environmental DNA metabarcoding and spectro-fluorescence for phytoplankton community assessments
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Otterly delicious: Spatiotemporal variation in the diet of a recovering population of Eurasian otters (Lutra lutra) revealed through DNA metabarcoding and morphological analysis of prey remains
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Data from: Assessing springtime vertebrate prey of sympatric mesopredators in the southeastern United States using metabarcoding analysis
<p>Coyotes (<em>Canis latrans</em>) colonized the eastern United States over the last century and formed a 3-species predator guild with bobcats (<em>Lynx rufus</em>) and gray foxes (<em>Urocyon cinereoargenteus</em>) across much of the southeastern United States. Diets among the three species vary along with respective impacts on game species such as white-tailed deer (<em>Odocoileus virginianus</em>) and wild turkeys (<em>Meleagris gallopavo</em>). To determine predation impacts on vertebrate prey and dietary overlap in consumption of prey items, we assessed diets of coyote, bobcat, and gray fox during spring, coinciding with white-tailed deer fawning and wild turkey nesting and brood rearing. We sampled across three sites along the Savannah River in South Carolina from mid-May through mid-June of 2020-2021. We collected 180 scat samples along 295.9 kilometers (71.1 – 122.4 km/site) of unpaved secondary roads and used DNA metabarcoding to determine vertebrate diet items. We identified predator species of scat using DNA metabarcoding and species-specific mtDNA fragment analysis (153 were coyotes, 20 bobcats, and seven gray foxes). Overall, we found evidence that two species, coyote and bobcat, consumed deer while all three consumed turkeys. The frequency of deer in the diet varied across sites for coyotes from 62 – 86% and wild turkey was present with a frequency of occurrence of 9% for coyotes, 5% for bobcats, and 14% for gray fox. Vertebrate diet specialization was evident across predator species with a high frequency of deer in coyote diets, rabbits and small mammals in bobcat diets, and herpetofauna in gray fox diets. During deer fawning and wild turkey nesting and brood rearing, dietary overlap appears to be mediated by the disparate selection of prey items, which reduced competition among coyotes, bobcats, and gray foxes. The use of DNA metabarcoding may augment our understanding of dietary preferences within this predator guild by providing increased resolution of diet composition among important game species.</p>
Data from: Dietary partitioning among three cryptobentic reef fish mesopredators revealed by visual analysis, metabarcoding of gut content, and stable isotope analysis
<p>Understanding how mesopredators partition their diet and the identity of consumed prey can assist in understanding the ecological role predators and prey play in ecosystem trophodynamics. Here, we assessed the diet of three common coral reef mesopredators; <em>Pseudochromis flavivertex</em>, <em>Pseudochromis fridmani</em>, and <em>Pseudochromis olivaceus</em> from the family Pseudochromidae, commonly known as dottybacks, using a combination of i) visual stomach content analysis, ii) stomach content DNA metabarcoding (18S, COI), and iii) stable isotope analysis (δ<sup>15</sup>N, δ<sup>13</sup>C). In addition, <em>P. flavivertex</em> is found in two distinct color morphs in the Red Sea, providing an opportunity to analyze intra-morph differences. These techniques revealed partitioning in the dietary composition and resource use among species. Arthropods comprised the main dietary component of <em>P. flavivertex</em> (18S > 60%; COI > 10%), and <em>P. olivaceus</em> (18S = 57.2%) while <em>P. fridmani</em> ingested predominantly mollusks (18S = 51.3%, COI = 24.6%). Despite being small predators, microplastics were found in the gut content of some of these fishes. Stable isotope analysis showed differences in species' isotopic niche breadth and trophic position. <em>Pseudochromis olivaceus</em> presented the largest isotopic niche (SEA<sub>C</sub> = 1.61‰<sup>2</sup>), while <em>P. fridmani</em> showed the smallest isotopic niche (SEA<sub>C</sub> = 0.45‰<sup>2</sup>) among species. Although the two techniques used for stomach content analysis did not show differences in the diet within color morphs of <em>P. flavivertex</em>, they differed in the isotopic niche and resource use. Despite our limited sampling, our findings provide evidence of species-specific differences in the trophic ecology of dottybacks and demonstrate their important role as predators of cryptic invertebrates and small fishes. This study highlights the importance of combining several approaches (short-term: visual analysis and DNA metabarcoding; and long-term: isotope analysis) when assessing the feeding habits of coral reef fish, as they provide complementary information necessary to delimit their niches and understand the role that small mesopredators play in coral reef ecosystems.</p>
DNA metabarcoding sequence data for diet analysis of caribou
<p>Woodland caribou (<em>Rangifer tarandus caribou</em>) are threatened in Canada due to the drastic decline in population size caused primarily by human-induced landscape changes that decrease habitat and increase predation risk. Conservation efforts have largely focused on reducing predators and protecting critical habitat, whereas research on dietary niches and the role of potential food constraints in lichen-poor environments is limited. To improve our understanding of dietary niche variability, we used a next-generation sequencing approach with metabarcoding of DNA extracted from faecal pellets of woodland caribou located on Lake Superior in lichen-rich (mainland) and lichen-poor (island) environments. Amplicon sequencing of fungal ITS2 region revealed lichen-associated fungi as predominant in samples from both populations, but amplification at the chloroplast <em>trnL </em>region, which was only successful on island samples, revealed primary consumption of yew based on relative read abundance (<em>Taxus spp.</em>; 83.68%) with dogwood (<em>Cornus spp</em>.; 9.67%) and maple (<em>Acer spp.</em>; 4.10%) also prevalent. These results suggest that conservation efforts for caribou need to consider the availability of food resources beyond lichen to ensure successful outcomes. More broadly, we provide a reliable methodology for assessing ungulate diet from archived faecal pellets that could reveal important dietary shifts over time in response to climate change.</p>
Data for: Two is better than one: Coupling DNA metabarcoding and stable isotope analysis improves dietary characterizations for a riparian-obligate, migratory songbird
<p>While an increasing number of studies are adopting molecular and chemical methods for dietary characterization, these studies often employ only one of these laboratory-based techniques; an approach which may yield an incomplete, or even biased, understanding of diet due to each method's inherent limitations. To explore the utility of coupling molecular and chemical techniques for dietary characterizations, we applied DNA metabarcoding alongside stable isotope analysis to characterize the dietary niche of breeding Louisiana waterthrush (<em>Parkesia motacilla</em>), a migratory songbird hypothesized to preferentially provision their offspring with pollution-intolerant, aquatic arthropod prey. While DNA metabarcoding was unable to determine if waterthrush provision aquatic and terrestrial prey in different abundances, we found that specific aquatic taxa were more likely to be detected in successive seasons than their terrestrial counterparts, thus supporting the aquatic specialization hypothesis. Our isotopic analysis added greater context to this hypothesis by concluding that breeding waterthrush provisioned Ephemeroptera and Plecoptera, two pollution-intolerant, aquatic orders, in higher quantities than other prey groups, and expanded their functional trophic niche when such prey were not abundantly provisioned. Finally, we found that the dietary characterizations from each approach were often uncorrelated, indicating that the results gleaned from a diet study can be particularly sensitive to the applied methodologies. Our findings contribute to a growing body of work indicating the importance of high-quality, aquatic habitats for both consumers and their pollution-intolerant prey, while also demonstrating how the application of multiple, laboratory-based techniques can provide insights not offered by either technique alone.</p>
Row fastq files generated by 16S rRNA sequencing for the metabarcoding analysis of Hidalgo-Villeda et al. paper
<p>Fastq files used for the microbiome profiling of the terminal ileal and caecum content.</p> <p>Sequencing of the terminal ileal content was performed at the Institute Hospitalo-Universitaire Méditerannée Infection, Marseille, France.</p> <p>Sequencing of the caecum content was performed at Genoscreen, Lille, France</p> <p>The sequencing methodology is described on the methods part of the paper "A physiological mouse model of severe acute malnutrition reveals prolonged dysbiosis and altered immunity under nutritional intervention, Hidalgo-Villeda et al.".</p> <p>The metadata.xlsx table present the description and correspondance of each fastq files.</p>
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>
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
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Data from: To pool or not to pool: Pooled metabarcoding does not affect estimates of prey diversity in spider gut content analysis
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Data from: Assessing springtime vertebrate prey of sympatric mesopredators in the southeastern United States using metabarcoding analysis
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Data from: Dietary partitioning among three cryptobentic reef fish mesopredators revealed by visual analysis, metabarcoding of gut content, and stable isotope analysis
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DNA metabarcoding sequence data for diet analysis of caribou
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Data from: Seasonal differences in fish community structure in the upper Yangtze river based on eDNA metabarcoding: A multi-dimensional analysis
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Data for: Two is better than one: Coupling DNA metabarcoding and stable isotope analysis improves dietary characterizations for a riparian-obligate, migratory songbird
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Data from: Large-scale metabarcoding analysis of epipelagic and mesopelagic copepods in the Pacific
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Data from: Metabarcoding for the parallel identification of several hundred predators and their preys: application to bat species diet analysis
Assessing diet variability is of main importance to better understand the biology of bats and design conservation strategies. Although the advent of metabarcoding has facilitated such analyses, this approach does not come without challenges. Biases may occur throughout the whole experiment, from fieldwork to biostatistics, resulting in the detection of false negatives, false positives or low taxonomic resolution. We detail a rigorous metabarcoding approach based on a short COI minibarcode and two-step PCR protocol enabling the 'all at once' taxonomic identification of bats and their arthropod preys for several hundreds of samples. Our study includes faecal pellets collected in France from 357 bats representing 16 species, as well as insect mock communities that mimic bat meals of known composition, negative and positive controls. All samples were analysed using three replicates. We compare the efficiency of DNA extraction methods and we evaluate the effectiveness of our protocol using identification success, taxonomic resolution, sensitivity, and amplification biases. Our parallel identification strategy of predators and preys reduces the risk of mis-assigning preys to wrong predators and decreases the number of molecular steps. Controls and replicates enable to filter the data and limit the risk of false positives, hence guaranteeing high confidence results for both prey occurrence and bat species identification. We validate 551 COI variants from arthropod including 18 orders, 117 family, 282 genus and 290 species. Our method therefore provides a rapid, resolutive and cost-effective screening tool for addressing evolutionary ecological issues or developing 'chirosurveillance' and conservation strategies.
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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.