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87 results for “skin microbiome”
Effects of environmental translocation and host characteristics on skin microbiomes of sun-basking fish
<p>Variation in the composition of skin-associated microbiomes has been attributed to host species, geographic location, and habitat, but the role of intraspecific phenotypic variation among host individuals remains elusive. We explored if and how host environment and different phenotypic traits were associated with microbiome composition. We conducted repeated sampling of dorsal and ventral skin microbiomes of carp individuals (<em>Cyprinus</em> <em>carpio</em>) before and after translocation from laboratory conditions to a semi-natural environment. Both alpha and beta diversity of skin-associated microbiomes increased substantially within and among individuals following translocation, particularly on dorsal body sites. The variation in microbiome composition among hosts was significantly associated with body site, sun-basking, habitat switch, and growth, but not temperature gain while basking, sex, personality, or colour morph. We suggest that the overall increase in the alpha and beta diversity estimates among hosts were induced by individuals expressing greater variation in behaviours and thus exposure to potential colonizers in the pond environment compared to the laboratory. Our results exemplify how biological diversity at one level of organization (phenotypic variation among and within fish host individuals) together with the external environment impacts biological diversity at a higher hierarchical level of organisation (richness and composition of fish-associated microbial communities).</p>
Effects of exogenous elevation of corticosterone on immunity and the skin microbiome of Eastern Newts (Notophthalmus viridescens): Data & R scripts
<p>The amphibian chytrid fungus, <em>Batrachochytrium</em> <em>salamandrivorans</em> (<em>Bsal</em>) threatens salamander biodiversity. The factors underlying <em>Bsal</em> susceptibility may include glucocorticoid hormones (GCs). The effects of GCs on immunity and disease susceptibility are well studied in mammals, but less is known in other groups, including salamanders. We used <em>Notophthalmus</em> <em>viridescens</em> (Eastern Newts) to test the hypothesis that GCs modulate salamander immunity. We first determined the dose required to elevate corticosterone (CORT; primary GC in amphibians) to physiologically relevant levels. We then measured immunity (neutrophil-lymphocyte ratios, plasma bacterial killing ability [BKA], skin microbiome, splenocytes, melanomacrophage centers [MMCs]) and overall health in newts following treatment with CORT or an oil vehicle control. Treatments were repeated for a short (2 treatments over 5 days) or long (18 treatments over 26 days) time period. Contrary to our predictions, most immune and health parameters were similar for CORT and oil-treated newts. Surprisingly, differences in BKA, skin microbiome, and MMCs were observed between newts subjected to short and long-term treatments, regardless of treatment type (CORT, oil vehicle). Taken together, CORT does not appear to be a major factor contributing to immunity in Eastern Newts, although more studies examining additional immune factors are necessary.</p>
Data for: Skin bacterial microbiome diversity predicts lower activity levels in female, but not male, guppies, Poecilia reticulata
<p>While the link between the gut microbiome and host behaviour is well established, how the microbiomes of other organs correlate with behaviour remains unclear. Additionally, behaviour–microbiome correlations are likely sex-specific because of sex differences in behaviour and physiology, but this is rarely tested. Here, we tested whether the skin microbiome of the Trinidadian guppy, Poecilia reticulata , predicts fish activity level and shoaling tendency in a sex-specific manner. High-throughput sequencing revealed that the bacterial community richness on the skin (Faith's phylogenetic diversity) was correlated with both behaviours differently between males and females. Females with richer skin-associated bacterial communities spent less time actively swimming. Activity level was significantly correlated with community membership (unweighted UniFrac), with the relative abundances of 16 bacterial taxa significantly negatively correlated with activity level. We found no association between skin microbiome and behaviours among male fish. This sex-specific relationship between the skin microbiome and host behaviour may indicate sex-specific physiological interactions with the skin microbiome. More broadly, sex specificity in host–microbiome interactions could give insight into the forces shaping the microbiome and its role in the evolutionary ecology of the host.</p>
Data for: Skin bacterial microbiome diversity predicts lower activity levels in female, but not male, guppies, Poecilia reticulata
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Effects of exogenous elevation of corticosterone on immunity and the skin microbiome of Eastern Newts (Notophthalmus viridescens): Data & R scripts
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Effects of environmental translocation and host characteristics on skin microbiomes of sun-basking fish
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The skin microbiome facilitates adaptive tetrodotoxin production in poisonous newts
<p>Rough-skinned newts (<em>Taricha granulosa</em>) use tetrodotoxin (TTX) to block voltage-gated sodium (Na<sub>v</sub>) channels as a chemical defense against predation. Interestingly, newts exhibit extreme population-level variation in toxicity attributed to a coevolutionary arms race with TTX-resistant predatory snakes, but the source of TTX in newts is unknown. Here, we investigated whether symbiotic bacteria isolated from toxic newts could produce TTX. We characterized the skin-associated microbiota from a toxic and non-toxic population of newts and established pure cultures of isolated bacterial symbionts from toxic newts. We then screened bacterial culture media for TTX using LC-MS/MS and identified TTX-producing bacterial strains from four genera, including <em>Aeromonas</em>, <em>Pseudomonas</em>, <em>Shewanella</em>, and <em>Sphingopyxis</em>. Additionally, we sequenced the Na<sub>v</sub> channel gene family in toxic newts and found that newts expressed Na<sub>v</sub> channels with modified TTX binding sites, conferring extreme physiological resistance to TTX. This study highlights the complex interactions among adaptive physiology, animal-bacterial symbiosis, and ecological context. </p>
Fig. 3 in Skin Microbiome Of Free-Living European Pond Turtle (Emys Orbicularis (L.)) On The Northern Border Of Its Range In Silene Nature Park, Latvia
Fig. 3. Gram-positive (A) and Gram-negative bacteria (B) under the microscope. Magnification x1000.
Fig. 2 in Skin Microbiome Of Free-Living European Pond Turtle (Emys Orbicularis (L.)) On The Northern Border Of Its Range In Silene Nature Park, Latvia
Fig. 2. Sampled turtle with the biotope (Photo: M. Pupins).
Salamander skin microbiome sample metadata: Variation in amphibian skin microbes
<p>These data are associated with a study that explores variation in microbial communities on western tiger salamander skin (<em>Ambystoma</em> <em>mavortium</em>) through space, time, and across life history stages. Lake water and lake substrate microbiome samples were collected to observe microbial taxa which were disproportionately abundant between salamander skin and the environment. Microbiome samples were collected at two lakes during the summer and fall of 2018, and sampling occurred at each lake every other week. During each sampling event, water quality data were collected at four or five locations within the lake and are associated with microbiome samples collected in the lake's respective regions. For each sample, bacterial and fungal communities were examined through metabarcoding of the 16S and ITS metabarcoding regions, respectively, using Illumina next-generation sequencing. The dataset includes negative control samples to aid in detecting contamination, and the dataset includes mock community samples to aid in validating our bioinformatics methods. Each sample received spike-ins of cross-contamination oligos and synthetic genes to observe cross-contamination during library preparation and to allow for the estimation of absolute microbial abundances, respectively. This dataset includes spatiotemporal, ontogenetic, morphometric, and water quality metadata for microbiome samples along with essential information for processing the DNA sequence data.</p>
Data and code for "Dietary carotenoid supplementation has long-term and community-wide effects on the amphibian skin microbiome"
<p>Data, R code and R markdown report for the manuscript "Dietary carotenoid supplementation has long-term and community-wide effects on the amphibian skin microbiome" by Risely, A., Phillip G. Byrne, Bethany J. Hoye, and Aimee J. Silla</p> <p><strong>Data</strong></p> <p>frog_final.RDS = Processed phyloseq dataset of frog skin microbiome</p> <p><strong>Code</strong></p> <p>Frog_diet_analysis_V1.Rmd = Rmarkdown code</p> <p>Frog_diet_analysis_V1.html = Rmarkdown report (html version - need to download to view)</p> <p>Frog_diet_analysis_V1.pdf = Rmarkdown report (PDF version)</p>
Dynamics of Dysbiosis in the Skin and Gut Microbiome of Burn Patients
ClinicalTrials.gov study NCT07209007. IPD Sharing: NO. Countries: 1. Publications: 13.
Profiling the Skin Microbiome in Response to Altreno in Acne Patients
ClinicalTrials.gov study NCT04548349. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Nor climate, nor human impact factors: Chytrid infection shapes the skin microbiome of an endemic amphibian along a biodiversity hotspot
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Salamander skin microbiome sample metadata: Variation in amphibian skin microbes
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The skin microbiome facilitates adaptive tetrodotoxin production in poisonous newts
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Data from: Low-load pathogen spillover predicts shifts in skin microbiome and survival of a terrestrial-breeding amphibian
Wildlife disease dynamics are strongly influenced by the structure of host communities and their symbiotic microbiota. Conspicuous amphibian declines associated with the waterborne fungal pathogen Batrachochytrium dendrobatidis (Bd) have been observed in aquatic-breeding frogs globally. However, less attention has been given to cryptic terrestrial-breeding amphibians that have also been declining in tropical regions. By experimentally manipulating multiple tropical amphibian assemblages harboring natural microbial communities, we tested whether Bd spillover from naturally infected aquatic-breeding frogs could lead to Bd amplification and mortality in our focal terrestrial-breeding host: the pumpkin toadlet Brachycephalus pitanga. We also tested whether the strength of spillover could vary depending on skin bacterial transmission within host assemblages. Terrestrial-breeding toadlets acquired lethal spillover infections from neighboring aquatic hosts and experienced dramatic but generally non-protective shifts in skin bacterial composition primarily attributable to their Bd infections. In contrast, aquatic-breeding amphibians maintained mild Bd infections and higher survival, with shifts in bacterial microbiomes that were unrelated to Bd infections. Our results indicate that Bd spillover from even mildly infected aquatic-breeding hosts may lead to dysbiosis and mortality in terrestrial-breeding species, underscoring the need to further investigate recent population declines of terrestrial-breeding amphibians in the tropics.
Quantifying live bacteria in the human skin microbiome reveals reduced interpersonal variability
<p>Using flow-cytometry and metagenomics, coupled with an upstream pre-processing step to remove relic-DNA (DNA left behind from dead or dying cells) to determine the live population of the skin microbiome. Repository contains important feature tables, counts tables, sequencing preprocessing scripts and feature table analysis scripts.</p>
Skin microbiome alters attractiveness to Anopheles mosquitoes
<p>16S skin microbiome dataset V3/4 variable region and human attractiveness to mosquitoes</p> <p>MCRO-D-21-00316</p>
The effects of disinfectants on the gill and skin microbiome of striped catfish (Pangasianodon hypophthalmus)
<p>Overall classified reads of study.</p>
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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.