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43 results for “fecal samples”
Taxonomic Composition of Red Knot Fecal Samples on the Virginia Coast
Taxonomic Composition of Red Knot Fecal Samples on the Virginia Coast Understanding which prey birds use and how prey selection is related to prey availability is important to understanding avian ecology and for conservation planning. Abundant prey at stopovers during migration is a key to shorebird survival and breeding success. We determined which prey were available to foraging red knots (Calidris canutus rufa) using Virginia's barrier islands during spring migration by collecting substrate core samples containing prey on sand and peat substrates in May 2017 - 2019. We also collected red knot feces during the same period and used fecal DNA metabarcoding to determine which invertebrates red knots consumed. We used compositional analysis to determine which prey red knots selected on these islands. Crustaceans (Orders Amphipoda and Calanoida) were the most abundant prey on both sand and peat. Red knots consumed bivalves (Orders Venerida and Mytiloida), crustaceans (Orders Amphipoda and Calanoida), and insect larvae (Order Diptera). Red knots selected bivalves over non-bivalve prey, though non-bivalve prey may still be an important portion of the total caloric intake on Virginia's stopover, given their abundance and use. It is important that coastal conservation practices in the Western Mid-Atlantic stopover region continue to be designed to promote natural barrier island movement which leads to the formation of the peat banks used by many prey.
Data from: Wildlife fecal microbiota exhibit community stability across a semi-controlled longitudinal non-invasive sampling experiment
<p>Wildlife microbiome studies are being used to assess microbial links with animal health and habitat. The gold standard of sampling microbiomes directly from captured animals is ideal for limiting potential abiotic influences on microbiome composition, yet fails to leverage the many benefits of non-invasive sampling. Application of microbiome-based monitoring for rare, endangered, or elusive species creates a need to non-invasively collect scat samples shed into the environment. Since controlling sample age is not always possible, the potential influence of time-associated abiotic factors was assessed. To accomplish this, we analyzed partial 16S rRNA genes of fecal metagenomic DNA sampled non-invasively from Rocky Mountain elk (<em>Cervus canadensis</em>) near Yellowstone National Park. We sampled pellet piles from four different elk, then aged them in a natural forest plot for 1, 3, 7, and 14 days, with triplicate samples at each time point (i.e., a blocked, repeat measures (longitudinal) study design). We compared microbiomes of each elk through time with point estimates of diversity, bootstrapped hierarchical clustering of samples, and a version of ANOVA–simultaneous components analysis (ASCA) with PCA (LiMM-PCA) to assess the variance contributions of time, individual and sample replication. Our results showed community stability through days 0, 1, 3 and 7, with a modest but detectable change in abundance in only 2 genera (<em>Bacteroides</em> and <em>Sporobacter</em>) at day 14. The total variance explained by time in our LiMM-PCA model across the entire 2-week period was not statistically significant (p>0.195) and the overall effect size was small (<10% variance) compared to the variance explained by the individual animal (p<0.0005; 21% var.). We conclude that non-invasive sampling of elk scat collected within one week during winter/early spring provides a reliable approach to characterize microbiome composition in a 16S rDNA survey and that sampled individuals can be directly compared across unknown time points with minimal bias. Further, point estimates of microbiome diversity were not mechanistically affected by sample age. Our assessment of samples using bootstrap hierarchical clustering produced clustering by animal (branches) but not by sample age (nodes). These results support greater use of non-invasive microbiome sampling to assess ecological patterns in animal systems.</p>
Data From: what mandrills leave behind: using fecal samples to characterize the major histocompatibility complex in a threatened primate
<p>The major histocompatibility complex (MHC) can be useful in guiding conservation planning because of its influence on immunity, fitness, and reproductive ecology in vertebrates. The mandrill (<em>Mandrillus sphinx</em>) is a threatened primate endemic to central Africa. Considerable research in this species has shown that the MHC is important for disease resistance, mate choice, and reproductive success. However, all previous MHC research in mandrills has focused on an inbred semi-captive population, so their genetic diversity may have been underestimated. Here we expand our current knowledge of mandrill MHC variation by performing next-generation sequencing of non-invasively collected fecal samples from a large wild horde in central Gabon. We observe MHC lineages and alleles shared with other primates, and we uncover 45 putative new class II MHC DRB alleles, including representatives of the DRB9 pseudogene, which has not previously been identified in mandrills. We also document methodological challenges associated with fecal samples in NGS-based MHC research. Even with high read depth, the replicability of alleles from fecal samples was lower than that of tissue samples, and allele assignments are inconsistent between sample types. Further, the common assumption that variants with very high read depth should represent true alleles does not appear to be reliable for fecal samples. Nevertheless, the use of degraded DNA in the present study still enabled significant progress in quantifying immunogenetic diversity and its evolution in wild primates.</p>
Diet composition based on stable isotopic analysis of fecal samples revealed the preference of Black-faced Spoonbill (Platalea minor) for natural wetlands and fishponds
<p><span>Background:</span><span> Black-faced spoonbill (BFS) is a global endangered species, distributed only in the coastal zones of East Asia. Xinghua Bay is one of the main wintering sites and migration stopovers of BFS in mainland China. However, </span><span>with the </span><span>reduction and degradation of natural wetlands, it is uncertain whether the constructed wetland can provide habitat for the endangered BFS. Research on diet of BFS will help to understand their preference between natural and artificial wetlands, and also provide reference for their conservation and habitat restoration. </span></p> <p><span>Results:</span><span> In the early winter, the proportion of Palaemonidae in BFS's food was as high as 74.4%, while that of other food was only 3.0% to 6.0%. In the late winter, the food contribution of BFS was as follow: Portunidae </span><span>39.3% </span><span>> Palaemonidae </span><span>26.1% </span><span>> Cyprinidae </span><span>8.8% </span><span>></span> <span>Mugilidae </span><span>8.5% </span><span>> Gobiidae </span><span>7.3% </span><span>></span> <span>Crucian </span><span>5.1% </span><span>> Whiteshrimp </span><span>4.8%</span><span>. The proportion of Portunidae exceeded that of Palaemonidae, and together with Palaemonidae, it has become the main food of BFS in late winter. </span></p> <p><span>Conclusion: </span><span>The diet composition of BFS between the early and late winter was significantly different, which may be due to seasonal changes in food resources. Natural wetlands are the main feeding grounds of BFS, but artificial wetlands also provide them with supplementary feeding grounds and resting places. Aquaculture ponds play an important ecological function in maintaining the overwintering population of BFS in Xinghua Bay.</span></p>
Fig. 1 in An unexpected diversity of trypanosomatids in fecal samples of great apes
Fig. 1. Phylogenetic relationships of the detected trypanosomatids. An SSU rRNA-based Bayesian phylogenetic tree of trypanosomatid sequences (∼2 kb) obtained from gorilla and chimpanzee fecal samples collected in the Dja Faunal Reserve in Cameroon representing the most likely two new Herpetomonas species, one unknown Phytomonas species and two most likely new monoxenous trypanosomatid species of unnamed genera. These possible new species are assigned as new Typing Units (TUs) with numbers TU229–233. Bootstrap values from Bayesian posterior probabilities (MrBayes; 5 million generations) and bootstrap percentages for maximum-likelihood analysis (PhyML; 1000 replicates) are shown at the nodes; dashes indicate <50% bootstrap support or different topology; asterisks mark branches with maximal statistical support. The tree was rooted with Paratrypanosoma; the closest relative of the family Trypanosomatidae. Parasite names or names of strains supplemented with their GenBank accession numbers are given; the branch lengths are drawn proportionally to the amount of changes (scale bar).
Linked collectors and determiners for: NEON Biorepository Mammal Collection (Fecal Samples).
Natural history specimen data linked to collectors and determiners held within, "NEON Biorepository Mammal Collection (Fecal Samples)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/973879fb-3e36-49ca-ab09-01b87bea0deb">https://bionomia.net/dataset/973879fb-3e36-49ca-ab09-01b87bea0deb</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/973879fb-3e36-49ca-ab09-01b87bea0deb">https://gbif.org/dataset/973879fb-3e36-49ca-ab09-01b87bea0deb</a>. Formatted as a Frictionless Data package.
Comparison of fresh fecal samples from two populations (NAM and USA) (Part 2 of 2)
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Data from: Wildlife fecal microbiota exhibit community stability across a semi-controlled longitudinal non-invasive sampling experiment
Open the record for dataset details and reuse information.
Data From: what mandrills leave behind: using fecal samples to characterize the major histocompatibility complex in a threatened primate
Open the record for dataset details and reuse information.
Diet composition based on stable isotopic analysis of fecal samples revealed the preference of Black-faced Spoonbill (Platalea minor) for natural wetlands and fishponds
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Data from: Are fecal samples an appropriate proxy for amphibian intestinal microbiota?
<p>The intestinal microbiota, an invisible organ supporting a host's survival, has essential roles in metabolism, immunity, growth, and development. Since intestinal microbiota influences a host's biology, application of such data to wildlife conservation has gained interest. There are standard protocols for studying the human intestinal microbiota, but no equivalent for wildlife. A major challenge is sampling the intestinal microbiota in an effective, unbiased way. Fecal samples are a popular proxy for intestinal microbiota because collection is non-invasive, convenient, and allows for longitudinal sampling. Yet, it is unclear whether the fecal microbiota is representative of the intestinal microbiota. In amphibians, research on sampling methodology is limited. In this study, we characterize and compare microbiota (small intestine, large intestine, feces) of two Hong Kong stream-dwelling frog species: Lesser Spiny Frog (<em>Quasipaa exilispinosa</em>), and Hong Kong Cascade Frog (<em>Amolops hongkongensis</em>). We found that both species have similar dominant phyla and families, but diverge in terms of the dominant genera. Next, we assess the performance of fecal microbiota in representing the intestinal microbiota in these two species. We found that (1) microbiota of small and large intestine differs significantly, (2) feces are not an appropriate proxy of both intestinal sections, and (3) a set of microbial taxa significantly differs between sample types. Our cautions equating fecal and intestinal microbiota. Sampling feces can avoid sacrifice of an animal, but researchers should avoid over-extrapolation and interpret results carefully.</p>
16S And WGS Feature Tables: Tryptophan Metabolites And Their Predicted Microbial Sources In Fecal Samples Of Healthy Individuals
<p>The zip file contains 16S and WGS feature tables used in the following publication:</p> <p>Tryptophan Metabolites And Their Predicted Microbial Sources In Fecal Samples Of Healthy Individuals<br>Cynthia L. Chappell, Kristi L. Hoffman, Philip L. Lorenzi, Lin Tan, Joseph F. Petrosino, Richard A. Gibbs, Donna M. Muzny, Harsha Doddapaneni, Matthew C. Ross, Vipin K. Menon, Anil Surathu, Sara J. Javornik Cregeen, Anaid G. Reyes, Pablo C. Okhuysen bioRxiv 2023.12.20.572622; doi: https://doi.org/10.1101/2023.12.20.572622</p>
Data from: A genotyping-in-thousands by sequencing panel to inform invasive deer management using non-invasive fecal and hair samples
<p>Studies in ecology, evolution, and conservation often rely on non-invasive samples, making it challenging to generate large amounts of high-quality genetic data for many elusive and at-risk species. We developed and optimized a Genotyping-in-Thousands by sequencing (GT-seq) panel using non-invasive samples to inform the management of invasive Sitka black-tailed deer (<em>Odocoileus hemionus sitkensis</em>) in Haida Gwaii (Canada). We validated our panel using paired high-quality tissue and non-invasive fecal and hair samples to simultaneously distinguish individuals, identify sex and reconstruct kinship among deer sampled across the archipelago, then provided a proof-of-concept application using field-collected feces on SGang Gwaay, an island of high ecological and cultural value. Genotyping success across 244 loci was high (90.3%) and comparable to that of high-quality tissue samples genotyped using restriction-site associated DNA sequencing (92.4%), while genotyping discordance between paired high-quality tissue and non-invasive samples was low (0.50%). The panel will be used to inform future invasive species operations (culls or eradications) in Haida Gwaii by providing individual and population information to inform management. More broadly, our GT-seq workflow that includes quality control analyses for targeted SNP selection and a modified protocol may be of wider utility for other studies and systems where non-invasive genetic sampling is employed.</p>
Data from: Are fecal samples an appropriate proxy for amphibian intestinal microbiota?
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Plains and wood bison fecal samples, diet content, and diet quality
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Data from: A genotyping-in-thousands by sequencing panel to inform invasive deer management using non-invasive fecal and hair samples
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Data from: A pipeline for metabarcoding and diet analysis from fecal samples developed for a small semi-aquatic mammal
Metabarcoding allows the genetic analysis of pooled samples of various sources. It is becoming popular in the study of animal diet, especially because it allows the analysis of the composition of feces without the need of handling animals. In this work, we studied the diet of the Pyrenean desman (Galemys pyrenaicus), a small semi-aquatic mammal endemic to the Iberian Peninsula and the Pyrenees, by sequencing COI minibarcodes from feces using next-generation sequencing techniques. For the identification of assembled sequences, we employed a tree-based identification method that used a reference tree of sequences of freshwater organisms. The comparison of freshly collected fecal samples and older samples showed that fresh samples produced significantly more sequencing reads. They also rendered more operational taxonomical units (OTUs), but not significantly. Our analyses of 41 samples identified 224 OTUs corresponding to species of the reference tree. Ephemeroptera, Diptera excl. Chironomidae, and Chironomidae were the most highly represented groups in terms of reads as well as samples. Other groups of freshwater organisms detected were Plecoptera, Trichoptera, Neuropteroida, Coleoptera, Crustacea, and Annelida. Our results are largely in line with previous morphological and genetic studies on the diet of the Pyrenean desman, but allowed the identification of a higher diversity of OTUs in each sample. Additionally, the bioinformatic pipeline we developed for deep sequencing of fecal samples will enable the quantitative analysis of the diet of this and other species, which can be highly useful to determine their ecological requirements.
Changes in microbiome and metabolomic profiles of fecal samples stored with stabilizing solution at room temperature
<p>Metabolite profiles of samples stored at room temperature. </p> <p>Fecal samples from three individuals were stored in non-stabilization condition and in OMNIgene.GUT metagenome stabilization solution up to 21 days. Their metabolites were profiled with ultra-performance liquid chromatograph (UPLC) - quadrupole time-of-flight (Q-TOF) mass-spectrometry pipeline on an Acquity UPLC-Q-TOF instrument (Waters, Milford, MA, USA) equipped with an Acquity UPLC BEH C18 column. </p> <p> </p> <p>* MetabolitePeak.xlsx : Metabolite profile</p> <p>* MetabolitePeak.xlsx : Metabolite peak information</p> <p>* Sample.xlsx : Sample preservation condition</p> <p> </p>
Behavior and diet data collected from i) GPS video camera collars and ii) fecal samples collected from individuals from the Fortymile Caribou Herd
<p>Summer diets are crucial for large herbivores in the subarctic and are affected by weather, harassment from insects and a variety of environmental changes linked to climate. Yet understanding foraging behavior and diet of large herbivores is challenging in the subarctic because of their remote ranges. <a name="_Hlk82429015">We used GPS video-camera collars to observe behaviors and summer diets of the migratory Fortymile Caribou Herd (<i>Rangifer tarandus granti</i>) across Alaska, USA and the Yukon, Canada.</a> First, we characterized caribou behavior. Second, we tested if videos could be used to quantify changes in the probability of eating events. Third, we estimated summer diets at the finest taxonomic resolution possible through videos. Finally, we compared summer diet estimates from video collars to microhistological analysis of fecal pellets. We classified 18,134 videos from 30 female caribou over two summers (2018 – 2019). Caribou behaviors included eating (mean = 43.5%), ruminating (25.6%), travelling (14.0%), stationary awake (11.3%) and napping (5.1%). Eating was restricted by insect harassment. We classified forage(s) consumed in 5,549 videos where diet composition (monthly) highlighted a strong tradeoff between lichens and shrubs; shrubs dominated diets in June and July when lichen use declined. We identified 63 species, 70 genus and 33 family groups of summer forages from videos. After adjusting for digestibility, monthly estimates of diet composition were strongly correlated at the scale of the forage functional type (i.e., forage groups comprised of forbs, graminoids, mosses, shrubs, and lichens; <i>r = </i>0.79, <i>p</i> < 0.01). Using video collars, we identified i) a pronounced tradeoff in summer foraging between lichens and shrubs and ii) the costs of insect harassment on eating. Understanding caribou foraging ecology is needed to plan for their long-term conservation across the circumpolar north and video collars can provide a powerful approach across remote regions.</p>
Search Cytomegalovirus in Healthy Volunteers Stools Samples Selected as Potential Donor for Fecal Microbiota Transplant
ClinicalTrials.gov study NCT02694484. IPD Sharing: Not stated. Countries: 1. Publications: 1.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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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.
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