16s rRNA gene sequencing reads from the skin of spring peeper frogs
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ABSTRACT:
PROVIDER: PRJNA1013348 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Spring Peeper (Pseudacris crucifer) skin bacteria raw sequence reads
| PRJNA311585 | ENA
Project description:Contribution of macrophage subsets to scarless skin regeneration in Xenopus laevis frogs
| PRJNA1310604 | ENA
Project description:Xenopus laevis juvenile frogs are uniquely capable of scarless skin regeneration, but the cellular and molecular mechanisms guiding this process remain incompletely understood. Macrophages are known as key regulators of wound healing, yet how their phenotypes shift over time and influence downstream regeneration in X. laevis has not been previously defined. It is well established that macrophage functions are imperative to mammalian wound healing. In vertebrate biology, macrophage polarization is dictated by two colony-stimulating factor-1 (CSF1) receptor ligands: CSF1 and interleukin-34 (IL34). While IL34 in mammals is critical to the development of epidermal macrophages known as Langerhans cells, the contribution of CSF1- and IL34-derived macrophages to skin wound repair remains unexplored. Pertinently, using the X. laevis model, previous work from our lab showed that CSF1- and IL34- macrophages are functionally distinct, formulating our hypothesis that these subsets play distinct roles during different phases of cutaneous wound repair. We therefore characterized full-thickness (epidermis and dermis) skin wounds in juvenile X. laevis during regeneration, analyzing transcript levels reflecting: M( infiltration (csf1r) and phenotype abundance (csf1 and il34), fibroblast activation (αSMA/acta2), and wound bed collagen composition (Picrosirius red staining). To assess the functional roles of macrophage phenotypes, we enriched wounds with recombinant X. laevis CSF1, IL34, or a vector control 3 days post-wounding (dpw) and analyzed wound responses at 7 and 14 dpw. Normal scarless regeneration in these juveniles demonstrated that macrophages transiently accumulated in the wound bed, peaking at 7–14 dpw. This coincided with elevated csf1 expression, which later declined as il34 levels rose. Fibroblast activation into myofibroblasts as well as collagen deposition followed this cytokine shift and restored collagen to pre-wound levels by 60 dpw. Subcutaneous IL34 enrichment at 3 dpw led to significantly increased αSMA expression at 7 and 14 dpw, a higher type I:III collagen ratio at 7 dpw, and suppression of inflammatory mediators coupled with enhancement of other, anti-inflammatory mediators at 7dpw. CSF1 enrichment had no significant effect on αSMA expression or subsequent collagen deposition, but did show a bias towards inflammatory mediators and the suppression of resolving and pro-reparative transcripts at 7 dpw. These findings suggest that early IL34 supplementation promotes a pro-regenerative macrophage phenotype that enhances myofibroblast activation and matrix remodeling while early CSF1 supplementation may contribute to prolonged inflammation and impaired tissue regeneration. Temporal modulation of macrophage-derived signals, particularly IL34, plays a critical role in directing scarless skin regeneration in X. laevis. These findings identify a conserved immunoregulatory axis with potential relevance to improving wound healing in non-regenerative species. Xenopus laevis juvenile frogs are uniquely capable of scarless skin regeneration, but the cellular and molecular mechanisms guiding this process remain incompletely understood. Macrophages are known as key regulators of wound healing, yet how their phenotypes shift over time and influence downstream regeneration in X. laevis has not been previously defined. It is well established that M( functions are imperative to mammalian wound healing. In vertebrate biology, M( polarization is dictated by two colony-stimulating factor-1 (CSF1) receptor ligands: CSF1 and interleukin-34 (IL34). While IL34 in mammals is critical to the development of epidermal M(s known as Langerhans cells, the contribution of CSF1- and IL34-derived macrophages to skin wound repair remains unexplored. Pertinently, using the X. laevis model, previous work from our lab showed that CSF1- and IL34- M(s are functionally distinct, formulating our hypothesis that these subsets play distinct roles during different phases of cutaneous wound repair. We therefore characterized full-thickness (epidermis and dermis) skin wounds in juvenile X. laevis during regeneration, analyzing transcript levels reflecting: macrophage infiltration (csf1r) and phenotype abundance (csf1 and il34), fibroblast activation (αSMA/acta2), and wound bed collagen composition (Picrosirius red staining). To assess the functional roles of macrophage phenotypes, we enriched wounds with recombinant X. laevis CSF1, IL34, or a vector control 3 days post-wounding (dpw) and analyzed wound responses at 7 and 14 dpw. Normal scarless regeneration in these juveniles demonstrated that macrophages transiently accumulated in the wound bed, peaking at 7–14 dpw. This coincided with elevated csf1 expression, which later declined as il34 levels rose. Fibroblast activation into myofibroblasts as well as collagen deposition followed this cytokine shift and restored collagen to pre-wound levels by 60 dpw. Subcutaneous IL34 enrichment at 3 dpw led to significantly increased αSMA expression at 7 and 14 dpw, a higher type I:III collagen ratio at 7 dpw, and suppression of inflammatory mediators coupled with enhancement of other, anti-inflammatory mediators at 7dpw. CSF1 enrichment had no significant effect on αSMA expression or subsequent collagen deposition, but did show a bias towards inflammatory mediators and the suppression of resolving and pro-reparative transcripts at 7 dpw. These findings suggest that early IL34 supplementation promotes a pro-regenerative M( phenotype that enhances myofibroblast activation and matrix remodeling while early CSF1 supplementation may contribute to prolonged inflammation and impaired tissue regeneration. Temporal modulation of macrophage-derived signals, particularly IL34, plays a critical role in directing scarless skin regeneration in X. laevis. These findings identify a conserved immunoregulatory axis with potential relevance to improving wound healing in non-regenerative species.
2025-10-22 | GSE306422 | GEO
Project description:skin bacteria of metamorphosing frogs Targeted Locus (Loci)
| PRJNA300407 | ENA
Project description:Many terrestrial ectotherms have gone to great evolutionary lengths to adapt to long cold winters; some have even evolved the ability to tolerate the freezing of most of the water in the body. Now, however, high-elevation, and high-latitude winters are experiencing an accelerated period of warming. Specialized winter adaptations that promoted fitness in a seasonally frozen environment may soon be superfluous or even maladaptive. We ask whether winter adaptations include changes in immune functions, and whether changing winter conditions could exert disparate effects on populations of a wide-ranging terrestrial ectotherm, the wood frog (Lithobates sylvaticus). By rearing wood frogs from ancestral winter environments that vary in length and temperature in a common garden, and reciprocally crossing post-metamorphic frogs into unfrozen and frozen artificial winter conditions in the lab, we were able to decompose transcriptomic differences in ventral skin gene expression into those that were environmentally induced (responsive to temperature), genetically determined, and those that varied as an interaction between genotype and environment. We found that frogs from harsh ancestral winter environments upregulated immune processes, including cellular immunity, inflammatory processes, and adaptive immune processes, as compared to frogs from mild ancestral winter environments. Further, we saw that expression of several genes varied in an interaction between genotype and artificial winter environment, a pattern that was recapitulated at the level of hepatosomatic index (the proportion of body mass comprising liver). We suggest that just as winter climates likely served as the selective force resulting in remarkable winter adaptations such as freeze tolerance, they also induced constitutive changes in immune gene expression.
2025-04-14 | GSE266397 | GEO
Project description:Human skin microbiome dysbiosis can have clinical consequences. Characterizing taxonomic composition of bacterial communities associated with skin disorders is important for dermatological advancement in both diagnosis and novel treatments. This study aims to analyze and improve the accuracy of taxonomic classification of skin bacteria with MinION™ nanopore sequencing using a defined skin mock community and a skin microbiome sample. We compared the Oxford Nanopore Technologies recommended procedures and concluded that their protocols highly bias the relative abundance of certain skin microbiome genera, most notably a large overrepresentation of Staphylococcus and underrepresentation of Cutibacterium and Corynebacterium. We demonstrated that changes in the amplification protocols improved the accuracy of the taxonomic classification for these three main skin bacterial genera. This study shows that MinION™ nanopore could be an efficient technology for full-length 16S rRNA sequencing; however, the analytical advantage is strongly influenced by the methodologies. The suggested alternatives in the sample processing improved characterization of a complex skin microbiome community using MinION™ nanopore sequencing.
| S-EPMC8766866 | biostudies-literature
Project description:The emergence of massively parallel sequencing technology has revolutionized microbial profiling, allowing the unprecedented comparison of microbial diversity across time and space in a wide range of host-associated and environmental ecosystems. Although the high-throughput nature of such methods enables the detection of low-frequency bacteria, these advances come at the cost of sequencing read length, limiting the phylogenetic resolution possible by current methods. Here, we present a generic approach for integrating short reads from large genomic regions, thus enabling phylogenetic resolution far exceeding current methods. The approach is based on a mapping to a statistical model that is later solved as a constrained optimization problem. We demonstrate the utility of this method by analyzing human saliva and Drosophila samples, using Illumina single-end sequencing of a 750 bp amplicon of the 16S rRNA gene. Phylogenetic resolution is significantly extended while reducing the number of falsely detected bacteria, as compared with standard single-region Roche 454 Pyrosequencing. Our approach can be seamlessly applied to simultaneous sequencing of multiple genes providing a higher resolution view of the composition and activity of complex microbial communities.
| S-EPMC3905898 | biostudies-literature
Project description:Amphibian populations around the world are threatened by an emerging infectious pathogen, the chytrid fungus Batrachochytrium dendrobatidis (Bd). How can a fungal skin infection kill such a broad range of amphibian hosts? And why are certain species particularly susceptible to the impacts of Bd? Here we use a genomics approach to understand the genetic response of multiple susceptible frog species to Bd infection. We characterize the transcriptomes of two closely-related endangered frog species (Rana muscosa and Rana sierrae) and analyze whole genome expression profiles from frogs in controlled Bd-infection experiments. We integrate the Rana results with a comparable dataset from a more distantly-related susceptible species (Silurana tropicalis). We demonstrate that Bd-infected frogs show massive disruption of skin function and show no evidence of a robust immune response. The genetic response to infection is shared across the focal susceptible species, suggesting a common effect of Bd on susceptible frogs. A total of five (12-plex) chips were analyzed from 60 samples comprising 2 conditions (control and infected), 3 tissues (skin, liver and spleen) and 2 timepoints (early and late). Three biological replicates were used for each condition and tissue at each time point. Twentyfour arrays were analyzed for skin samples, 24 for liver, and 12 for spleen. The same dye, Cy5, was used for all samples.
2012-04-30 | E-GEOD-34235 | biostudies-arrayexpress
Project description:The fungal skin disease chytridiomycosis has caused the devastating decline and extinction of hundreds of amphibian species globally, yet the potential for evolving resistance, and the underlying pathophysiological mechanisms remain poorly understood. We exposed 406 naïve, captive-raised alpine tree frogs (Litoria verreauxii alpina) to the aetiological agent Batrachochytrium dendrobatidis in two concurrent and controlled infection experiments. We investigated (A) survival outcomes and clinical pathogen burdens between populations and clutches, and (B) individual host tissue responses to chytridiomycosis. Here we present multiple interrelated datasets associated with these exposure experiments, including animal signalment, survival and pathogen burden of 355 animals from Experiment A, and the following datasets related to 61 animals from Experiment B: animal signalment and pathogen burden; raw RNA-Seq reads from skin, liver and spleen tissues; de novo assembled transcriptomes for each tissue type; raw gene expression data; annotation data for each gene; and raw metabolite expression data from skin and liver tissues. These data provide an extensive baseline for future analyses.
2018-01-09 | MTBLS457 | MetaboLights