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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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Ensminger et al 2020 - Fecal glucocorticoid metabolites in harvested elk
<p>Raw data for modeling fecal glucocorticoid metabolites in Ensminger et al. 2020.</p>
Geography, seasonality, and host-associated population structure influence the fecal microbiome of a genetically depauparate Arctic mammal
<p>The Canadian Arctic is an extreme environment with low floral and faunal diversity characterized by major seasonal shifts in temperature, moisture and daylight. Muskoxen (<i>Ovibos moschatus</i>) are one of few large herbivores able to survive this harsh environment. Microbiome research of the gastrointestinal tract may hold clues as to how muskoxen exist in the Arctic, but also how this species may respond to rapid environmental changes. In this study, we investigated the effects of season (spring/summer/winter), year (2007-2016), and host genetic structure on population-level microbiome variation in muskoxen from the Canadian Arctic. We utilized 16S rRNA gene sequencing to characterize the fecal microbial communities of 78 male muskoxen encompassing two population genetic clusters.<a name="_Hlk534564036"> These clusters are defined by Arctic Mainland and Island populations, including; 1) two mainland sampling locations of the Northwest Territories and Nunavut; and 2) four locations of Victoria Island. </a>Between these geographic populations, we found that differences in the microbiome reflected host-associated genetic cluster with evidence of migration. Within populations, seasonality influenced bacterial diversity with no significant differences between years of sampling. We found evidence of pathogenic bacteria, with significantly higher presence in mainland samples. Our findings demonstrate the effects of seasonality and the role of host population-level structure in driving fecal microbiome differences in a large Arctic mammal.</p>
Data from: Estimation of energetic condition in wild baboons using fecal thyroid hormone determination
Understanding how environmental and social factors affect reproduction through variation in energetic condition remains understudied in wild animals, in large part because accurately and repeatedly measuring energetic condition in the wild is a challenge. Thyroid hormones (THs), such as triiodothyronine (T3) and thyroxine (T4), have a key role in mitigating metabolic responses to energy intake and expenditure, and therefore are considered important biomarkers of an animal's energetic condition. Recent method development has shown that T3 and T4 metabolites can be measured in feces, but studies measuring THs in wild populations remain rare. Here we measured fecal T3 metabolites (mT3) in baboons, and tested whether the conditions of collection and storage used for steroid hormones could also be used for mT3; we focused on mT3 as it is the biologically active form of TH and because fecal T4 metabolites (mT4) were below detection levels in our samples. We also tested if mT3 could be determined in freeze-dried samples stored for long periods of time, and if these concentrations reflected expected biological variations across seasons and reproductive states. Our results show that mT3 can be measured with accuracy and precision in baboon feces. The conditions of collection and storage we use for steroid hormones are appropriate for mT3 determination. In addition, mT3 concentrations can be determined in samples stored at -20 °C for up to 9 years, and are not predicted by the amount of time in storage. As expected, wild female baboons have lower mT3 concentrations during the dry season. Interestingly, mT3 concentrations are lower in pregnant and lactating females, possibly reflecting an energy sparing mechanism. Retroactive determination of mT3 concentration in stored, freeze-dried feces opens the door to novel studies on the role of energetic condition on fitness in wild animals.
High-resolution tracking of microbial colonization in Fecal Microbiota Transplantation experiments via metagenome-assembled genomes
<p>This project contains anvi'o profiles and contigs databases that is used and/or referenced from the Lee STM and Khan SA, <em>et al.</em> study titled "<strong>High-resolution tracking of microbial colonization in Fecal Microbiota Transplantation experiments via metagenome-assembled genomes</strong>". The pre-print of this study is available via http://dx.doi.org/10.1101/090993.</p> <p>To be able to work with the data files you will need anvi'o <strong>v2.1.0</strong> to be installed on your system. For installation instructions, or to have access to a Docker image for anvi'o, please visit this URL: http://merenlab.org/software/anvio</p> <p>Public data:</p> <ul> <li><strong>ANVIO-FMT-D-R01-R02-QUICK-VISUALIZATION.tar.gz</strong>: Data files for a quick visualization of the 97 MAGs and their distribution across the two FMT recipients. A run script in the archive explains how to use this data.<br> </li> <li><strong>ANVIO-FMT-D-R01-R02-MERGED-PROFILE.tar.gz</strong>: The merged anvi'o profile for the entire data, which also contains a collection of 97 MAGs identified in the donor. The profile database contains no hierarchical clustering of contigs, however, individual MAGs can be displayed via the following notation since the collection 'MAGs' describe the organization of contigs in each MAG referenced from the dataset `ANVIO-FMT-D-R01-R02-QUICK-VISUALIZATION`, as well as from the paper: "anvi-refine -c CONTIGS.db -p PROFILE.db -C MAGs -b <em>FMT-Donor_MAG_00054</em>". All MAG names are in the supplementary tables in our paper.<br> </li> <li><strong>ANVIO-FMT-D-R01-R02-MAGs-SUMMARY.tar.gz</strong>: A static HTML website that contains FASTA files for each MAG, and TAB-delimited matrices for coverage and detection values, and others. After unpacking, you can double-click the index.html file. </li> </ul>
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>
Data from: Metabarcoding of fecal pellets in wild muskox populations reveals negative relationships between microbiome and diet alpha diversity
<p>Microbiome diversity and diet composition concomitantly influence species health, fitness, immunity, and digestion. In environments where diet varies spatially and temporally, microbiome plasticity may promote rapid host adaptation to available resources. For northern ungulates in particular, metabarcoding of noninvasively collected fecal pellets presents unprecedented insights into their diverse ecological requirements and niches by clarifying the interrelationships of microbiomes, key to deriving nutrients, in context of altered forage availability in changing climates. Muskoxen (<em>Ovibos moschatus</em>) are Arctic-adapted species that experience fluctuating qualities and quantities of vegetation. Geography and seasonality have been noted to influence microbiome composition and diversity in muskoxen, yet it is unclear how their microbiomes intersect with diet. Following observations from other species, we hypothesized increasing diet diversity would result in higher microbiome diversity in muskoxen. We assessed diet composition in muskoxen using three common plant metabarcoding markers and explored correlations with microbiome data. Patterns of dietary diversity and composition were not fully concordant among the markers used, yet all reflected the primary consumption of willows and sedges. Individuals with similar diets had more similar microbiomes, yet in contrast to most literature, yielded negative relationships between microbiome and diet alpha diversity. This negative correlation may reflect the unique capacities of muskoxen to survive solely on high-fiber Arctic forage and provide insight into their resiliency to exploit changing dietary resources in a rapidly warming Arctic altering vegetation diversity.</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>
Advancing source tracking: systematic review and source-specific genome database curation of fecally shed prokaryotes
<p>This repository contains several files describing the data discussed in Lindner et al's "Advancing source tracking: systematic review and source-specific genome database curation of fecally shed prokaryotes". </p> <ol> <li>"database.fna" = concatenation of the (draft or complete) genome sequences described in the paper (n=12,730 source associated prokaryotic genomes) which passed quality checks and are species-level representatives (i.e., dereplicated at 95% ANI).</li> <li>"gdef.txt" = a manifest describing which sequences belong to which genomes.</li> <li>"sources.txt" = a manifest describing which genomes belong to which sources.</li> </ol> <p>The sources this database covers:</p> <table> <tbody> <tr> <td>Source Category</td> <td>Species-level <br>genome count</td> <td>Source-specific<br>species-level <br>genome count</td> </tr> <tr> <td>Bird</td> <td>56</td> <td>40</td> </tr> <tr> <td>Cat</td> <td>86</td> <td>6</td> </tr> <tr> <td>Chicken</td> <td>1314</td> <td>887</td> </tr> <tr> <td>Cow</td> <td>39</td> <td>15</td> </tr> <tr> <td>Dog</td> <td>139</td> <td>56</td> </tr> <tr> <td>Pig</td> <td>2764</td> <td>2035</td> </tr> <tr> <td>Ruminant</td> <td>740</td> <td>714</td> </tr> <tr> <td>Human</td> <td>4484</td> <td>3350</td> </tr> <tr> <td>Wastewater</td> <td>3108</td> <td>3097</td> </tr> </tbody> </table> <p> </p> <p>See publication for further details. </p>
Fecal standing crop with real time correction using scat detection dogs to estimate population density
<p>Population density is fundamental information for assessing the conservation status of species and support management and conservation actions for in situ populations, but is unknown for many forest species due to their difficulty in detection. The Fecal Standing Crop (FSC) method using detection dogs is an alternative for cryptic or elusive species. An intrinsic difficulty of FSC is the ability to find fecal samples in the field and to estimate the probability of which feces detection is influenced by degradation due to climatic conditions. Our goal was to propose a concurrent FSC parameter estimation using a scat detection dog under different climatic conditions and apply those parameters in a wild deer population. Ten fecal samples of gray brocket deer (Subulo gouazoubira) were placed weekly in a transect (24 x 1200 m) in both dry and wet seasons (12 weeks each). A scat detection dog was then employed to find experimental fecal samples to determine the FSC parameters that were subsequently used with naturally occurring fecal samples (also dog-detected) to estimate population density. The oldest dog found samples were 21 (Dry) and seven (Wet) days after placement, resulting in dog efficiency of 23% (Dry) and 30% (Wet). Adjusting the model to account for efficiency and scat durability, we estimated similar, seasonal, densities of 4.54 individuals km-2 (SD = 2.21, Dry) and 5.52 indiv. km-2 (SD = 3.71, Wet).</p> <p><em>Synthesis and applications:</em> Our results demonstrate that our concurrent methodology corrected the effects of weather and habitat on FSC parameters thereby allowing for accurate population density estimation. Additionally, this method can provide reasonably precise density estimates with a logistically feasible sample size, as demonstrated by simulation. Following our recommendations, this method allows a reliable estimate of population density because it incorporates any influence of study area, dog ability, and climate in fecal sample detection, providing fundamental information for the conservation of many cryptic and elusive species.</p>
Data from: Targeted genome-wide SNP genotyping in feral horses using non-invasive fecal swabs
<p>The development of high-throughput sequencing has prompted a transition in wildlife genetics from using microsatellites toward sets of Single Nucleotide Polymorphisms (SNPs). However, genotyping large numbers of targeted SNPs using non-invasive samples remains challenging due to relatively large DNA input requirements. Recently, target enrichment has emerged as a promising approach requiring little template DNA. We assessed the efficacy of Tecan Genomics' Allegro Targeted Genotyping (ATG) for generating genome-wide SNP data in feral horses using DNA isolated from fecal swabs. Total and host-specific DNA were quantified for 989 samples collected as part of a long-term individual-based study of feral horses on Sable Island, Nova Scotia, Canada, using dsDNA fluorescence and a host-specific qPCR assay, respectively. Forty-eight samples representing 44 individuals containing at least 10ng of host DNA (ATG's recommended minimum input) were genotyped using a custom multiplex panel targeting 279 SNPs. Genotyping accuracy and consistency were assessed by contrasting ATG genotypes with those obtained from the same individuals with SNP microarrays, and from multiple samples from the same horse, respectively. 62% of swabs yielded the minimum recommended amount of host DNA for ATG. Ignoring samples that failed to amplify, ATG recovered an average of 86.7% targeted sites per sample, while genotype concordance between ATG and SNP microarrays was 98.5%. The repeatability of genotypes from the same individual approached unity with an average of 99.9%. This study demonstrates the suitability of ATG for genome-wide, non-invasive targeted SNP genotyping, and will facilitate further ecological and conservation genetics research in equids and related species.</p>
Metagenome-assembled genomes obtained from fecal and salivary microbiomes of pancreatic cancer patients and controls
<p>7,546 MAGs obtained from fecal and salivary metagenomes of pancreatic cancer patients and controls</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>
Immune-mediated hematological disease in dogs is associated with alterations of the fecal microbiota: a pilot study
<div> <h3>Background</h3> <p>The dog is the most popular companion animal and is a valuable large animal model for several human diseases. Canine immune-mediated hematological diseases, including immune-mediated hemolytic anemia (IMHA) and immune thrombocytopenia (ITP), share many features in common with autoimmune hematological diseases of humans. The gut microbiome has been linked to systemic illness, but few studies have evaluated its association with immune-mediated hematological disease. To address this knowledge gap, 16S rRNA gene sequencing was used to profile the fecal microbiota of dogs with spontaneous IMHA and ITP at presentation and following successful treatment. In total, 21 affected and 13 healthy control dogs were included in the study.</p> <h3>Results</h3> <p>IMHA/ITP is associated with remodeling of fecal microbiota, marked by decreased relative abundance of the spirochete <em>Treponema</em> spp., increased relative abundance of the pathobionts <em>Clostridium septicum</em> and <em>Escherichia coli</em>, and increased overall microbial diversity. Logistic regression analysis demonstrated that <em>Treponema</em> spp. were associated with decreased risk of IMHA/ITP (odds ratio [OR] 0.24–0.34), while Ruminococcaceae UCG-009 and Christensenellaceae R-7 group were associated with increased risk of disease (OR =&thinsp;6.84 [95% CI 2–32.74] and 8.36 [95% CI 1.85–71.88] respectively).</p> <h3>Conclusions</h3> <p>This study demonstrates an association of immune-mediated hematological diseases in dogs with fecal dysbiosis, and points to specific bacterial genera as biomarkers of disease. Microbes identified as positive or negative risk factors for IMHA/ITP represent an area for future research as potential targets for new diagnostic assays and/or therapeutic applications.</p> </div>
Fathi Camel Microbiome Project (FCMP) Fecal Metagenome-assembled Genomes (MAGs)
<p>The Fathi Camel Microbiome Project (FCMP) aims to characterize the diversity and phenotypic associations of the dromedary camel microbiome. The gut microbiome of N = 55 camels was deeply sequenced via dropped stool. The raw reads, after QC, were assembled and binned into metagenome-assembled genomes (MAGs). We include here a collection of 3165 medium-quality or higher prokaryotic MAGs by MiMAG-like criteria (completeness >= 50%, contamination <= 5%). </p>
Data supporting the article: "Comparative analysis of fecal microbiota between adolescents with early-onset psychosis and adults with schizophrenia"
<p>This dataset supports the article titled <em>"Comparative analysis of fecal microbiota between adolescents with early-onset psychosis and adults with schizophrenia.", </em>available at<em> <a href="https://doi.org/10.3390/microorganisms12102071">https://doi.org/10.3390/microorganisms12102071</a></em><em>.</em></p> <p>The dataset includes fecal microbiota sequencing data from adolescent patients with early-onset psychosis, adult patients with schizophrenia, and non-psychotic controls. The data were generated using 16S rRNA gene sequencing and analyzed with QIIME2 and PICRUSt2 to assess microbial diversity and functional pathways. Variables such as age, diagnosis, and medication use are included.</p> <p>The dataset contains:</p> <ul> <li><strong>Processed results</strong> from fecal microbiota analysis (OTUs and taxonomic classifications)</li> <li><strong>Metadata</strong> associated with each sample (age, diagnosis, medication)</li> <li><strong>Results from diversity analysis</strong> (alpha and beta diversity metrics)</li> <li><strong>Functional analysis</strong> of microbial pathways (PICRUSt2)</li> </ul> <p>These data are essential for reproducing the findings discussed in the article. Note that the raw sequencing data are available upon request.</p>
Canis lupus fecal DNA dataset
<p>Sea otters (<em>Enhydra</em> <em>lutris</em>) and wolves (<em>Canis</em> <em>lupus</em>) are two apex predators with strong and cascading effects on ecosystem structure and function. After decades of recovery from near extirpation, their ranges now overlap, allowing sea otters and wolves to interact for the first time in the scientific record. We intensively studied wolves during 2015–2021 in an island system colonized by sea otters in the 2000s and by wolves in 2013. After wolf colonization, we quantified shifts in foraging behavior with DNA metabarcoding of 689 wolf scats and stable isotope analyses, both revealing a dietary switch from Sitka black-tailed deer (<em>Odocoileus</em> <em>hemionus</em>), the terrestrial in situ primary prey, to sea otters. Here we show an unexpected result of the reintroduction and restoration of sea otters, which became an abundant marine subsidy for wolves following population recovery. The availability of sea otters allowed wolves to persist and continue to reproduce, subsequently nearly eliminating deer. Genotypes from 390 wolf scats and telemetry data from 13 wolves confirmed island fidelity constituting one of the highest known wolf population densities and upending standardly accepted wolf density predictions based on ungulate abundance. Whereas marine subsidies in other systems are generally derived from lower trophic levels, here an apex nearshore predator became a key prey species and linked nearshore and terrestrial food webs in a recently deglaciated and rapidly changing ecosystem. These results underscore that species restoration may serve as an unanticipated nutrient pathway for recipient ecosystems even resulting in cross-boundary subsidy cascades.</p>
Inflammatory responses induced by the monophasic variant of Salmonella typhimurium in pigs play a role in the high shedder phenotype and fecal microbiota composition
<p>Pigs infected with <em><span>Salmonella</span></em> may excrete large amounts of <em><span>Salmonella</span></em>, increasing the risk of spread of this pathogen in the food chain. Identifying <em><span>Salmonella</span></em> high shedder pigs is therefore required to mitigate this risk. We analyzed immune-associated markers and composition of the gut microbiota in specific-pathogen-free pigs presenting different shedding levels after an oral infection with <span>Salmonella</span>. Immune response was studied through total blood cell counts, production of anti-<em><span>Salmonella</span></em> antibodies and cytokines, and gene expression quantification. Total <em><span>Salmonella</span></em> shedding for each pig was estimated and hierarchical clustering was used to cluster pigs into high, intermediate, and low shedders. Gut microbiota compositions were assessed using 16S rRNA microbial community profiling. Comparisons were made between control and inoculated pigs, then between high and low shedders pigs. Prior to infection, high shedders had similar immunological profiles compared to low shedders. As soon as 1 day postinoculation (dpi), significant differences in the cytokine production level and on the expression level of several host genes related to a proinflammatory response were observed between high and low shedders. Infection with <em><span>Salmonella</span></em> induced an early and profound remodeling of the immune response in all pigs, but the intensity of the response was stronger in high shedders. In contrast, low shedders seroconverted earlier than high shedders. Just after induction of the proinflammatory response (at 2 dpi), some taxa of the fecal microbiota were specific to the shedding phenotypes. This was related to the enrichment of several functional pathways related to anaerobic respiration in high shedders. In conclusion, our data show that the immune response to <em><span>Salmonella</span></em> modifies the fecal microbiota and subsequently could be responsible for shedding phenotypes. Influencing the gut microbiota and reducing intestinal inflammation could be a strategy for preventing <em><span>Salmonella</span></em> high shedding in livestock.</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>
Fecal Microbiota Transplantation for Pancreatitis
ClinicalTrials.gov study NCT02318134. IPD Sharing: Not stated. Countries: 1. Publications: 12.
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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
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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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