Phylogenomics as baseline for taxonomy description: Amphibiibacter pelophylacis gen. nov., sp. nov., a novel taxon of the family Sphaerotilaceae, class Betaproteobacteria, isolated from the skin microbiota of Pelophylax perezi from different populations

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Journal Year: 2025, Volume and Issue: 75(4)

Published: April 9, 2025

Bacterial strain SL12-8 T was characterized and isolated from the skin microbiota of Pelophylax perezi , Perez’s frog. Strain stained Gram-negative formed rod-shaped cells that grew optimally at 25 °C pH 7.0–7.5. The G+C content DNA 66.2 mol%. Ubiquinone 8 respiratory quinone identified in studied most closely related taxon. major fatty acids were summed feature 3 C 16:0 representing 84% total acids. Phylogenetic analyses based on 16S rRNA gene sequence placed within order Burkholderiales a distinct lineage. similarities to Rubrivivax albus Scleromatobacter humisilvae Piscinibacter aquaticus Azohydromonas caseinilytica Aquincola agrisoli 94.41, 94.08, 93.72, 93.72 93.64%, respectively. draft genome comprises 3,115,197 bases with 313-fold mapped coverage. assembled consists 53 large contigs more than 500 bp, encodes 2,814 putative coding sequences. analysis available genomes closest genera showed 124 core genes reveal novel genus-level clade including . Analysis revealed presence beta-lactone terpene biosynthetic clusters. phylogenomic, phylogenetic, phenotypic chemotaxonomic data (=UCCCB 131 =CECT 30762 ) represents type species genus, for which we propose name Amphibiibacter pelophylacis gen. nov., sp. nov.

Language: Английский

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Near-infrared spectroscopy as a diagnostic screening tool for lethal chytrid fungus in eastern newts

Communications Biology, Journal Year: 2025, Volume and Issue: 8(1)

Published: April 17, 2025

The emergence of Batrachochytrium salamandrivorans (Bsal) poses an imminent threat to caudate biodiversity worldwide, particularly through anthropogenic-mediated means such as the pet trade. Bsal is a fungal panzootic that has yet reach Americas, Africa, and Australia, presenting significant biosecurity risk naïve amphibian populations lacking innate immune defenses necessary for combating invasive pathogens. We explored capability near-infrared spectroscopy (NIRS) coupled with predictive modeling rapid, non-invasive screening tool in live caudates. Using eastern newts (Notopthalmus viridescens) model species, NIR spectra were collected tandem dermal swabs used confirmatory qPCR analysis. identified spectral profiles differed significantly by physical location (chin, cloaca, tail, foot) well pathogen status (control vs. exposed individuals; p < 0.05). support vector machine algorithm achieved mean classification accuracy 80% sensitivity 92% discriminating Bsal-control (-) from Bsal-exposed (+) individuals. This approach offers promising method identifying Bsal-compromised populations, potentially aiding early detection mitigation efforts alongside existing techniques.

Language: Английский

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Framework for multi-stressor physiological response evaluation in amphibian risk assessment and conservation

Frontiers in Ecology and Evolution, Journal Year: 2024, Volume and Issue: 12

Published: March 13, 2024

Controlled laboratory experiments are often performed on amphibians to establish causality between stressor presence and an adverse outcome. However, in the field, identification of lab-generated biomarkers from single stressors interactions multiple impacts difficult discern ecological context. The ubiquity some pesticides anthropogenic contaminants results potentially cryptic sublethal effects or synergistic among stressors. Although biochemical pathways regulating physiological responses toxic well-conserved vertebrates, different exposure regimes life stage vulnerabilities can yield variable risk species. Here we examine stress-related biomarkers, highlight endpoints commonly linked apical effects, discuss differences ontogeny ecology that could limit interpretation across Further identify promising field-based measures indicative potential health development be useful anuran conservation. We outline common context altered functional pathways, presenting stage-specific for species, discussing multi-stressor vulnerability larger framework amphibian history ecology. This overview identifies points physiological, ecological, demographic provide evaluating impacting populations worldwide strategic conservation planning.

Language: Английский

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Microbiome and climate: skin microbial diversity and community functions of Polypedates megacephalus (Anura: Rhacophoridae) associated with bioclimate

Microbiology Spectrum, Journal Year: 2025, Volume and Issue: unknown

Published: March 5, 2025

The microbiome inhabiting animal skin plays a crucial role in host fitness by influencing both the composition and function of microbial communities. Environmental factors, including climate, significantly impact diversity functional attributes these However, it remains unclear how specific climatic factors affect amphibian composition, community function, relationship between two aspects. Understanding effects is particularly important because amphibians are poikilotherms and, thus, more susceptible to temperature fluctuations. Here, we investigated rhacophorid tree frog Polypedates megacephalus across different regimes using 16S rRNA gene sequencing. Skin swab samples were collected from nine populations P. adults Guangxi region, China. majority core microbiota found belong genus Pseudomonas. Our findings indicate that diversity, associated with changes conditions. Specifically, taxonomic increased response higher climate variability, Additionally, traits communities changed parallel shifts composition. significant correlations redundancy index suggest environmental filtering driven change impacts stability. These results highlight critical influence on microbiomes offer new insights into contribute adaptation varying conditions.IMPORTANCEThis study understanding association amphibians, which vulnerable due their poikilothermic nature. Amphibians rely for key functions like disease resistance, yet little known about fluctuations By analyzing regimes, our analysis reveals warmer climates could reduce redundancy, indicating stability be hosts adapted relatively cooler potential ecological consequences emphasize need integrate health conservation strategies.

Language: Английский

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Compositional Graphical Lasso Resolves the Impact of Parasitic Infection on Gut Microbial Interaction Networks in a Zebrafish Model

Journal of the American Statistical Association, Journal Year: 2023, Volume and Issue: 118(543), P. 1500 - 1514

Published: Jan. 6, 2023

Understanding how microbes interact with each other is key to revealing the underlying role that microorganisms play in host or environment and identifying as an agent can potentially alter environment. For example, understanding microbial interactions associate parasitic infection help resolve potential drug diagnostic test for infection. To unravel interactions, existing tools often rely on graphical models infer conditional dependence of abundances represent their interactions. However, current methods do not simultaneously account discreteness, compositionality, heterogeneity inherent microbiome data. Thus, we build a new approach called "compositional lasso" upon by incorporating above characteristics into model explicitly. We illustrate advantage compositional lasso over under variety simulation scenarios benchmark study, Tara Oceans Project. Moreover, present our results from analysis dataset Zebrafish Parasite Infection Study, which aims gain insight gut parasite burden covary during infection, thus uncovering novel putative disrupting success. Our identifies changes interaction degree between infected uninfected individuals three taxa, Photobacterium, Gemmobacter, Paucibacter, are inversely predicted methods. Further investigation these method-specific taxa reveals biological plausibility. In particular, speculate pathobiotic roles Photobacterium Gemmobacter zebrafish gut, probiotic Paucibacter. Collectively, analyses demonstrate provides powerful means accurately resolving microbiota drive discovery.

Language: Английский

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The Binding, Infection, and Promoted Growth of Batrachochytrium dendrobatidis by the Ranavirus FV3

Viruses, Journal Year: 2024, Volume and Issue: 16(1), P. 154 - 154

Published: Jan. 20, 2024

Increasing reports suggest the occurrence of co-infection between Ranaviruses such as Frog Virus 3 (FV3) and chytrid fungus Batrachochytrium dendrobatidis (Bd) in various amphibian species. However, potential direct interaction these two pathogens has not been examined to date. In this study, we investigated whether FV3 can interact with Bd vitro using qPCR, conventional microscopy, immunofluorescent microscopy. Our results reveal unexpected ability bind, promote aggregation, productively infect, significantly increase growth vitro. To extend vivo, assessed impact on Xenopus tropicalis frogs previously infected Bd. Consistent results, exposure Bd-infected X. increased loads decreased host’s survival.

Language: Английский

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Probing the functional significance of wild animal microbiomes using omics data

Published: Feb. 13, 2024

Host-associated microbiomes are thought to play a key role in host physiology and fitness, but this conclusion mainly derives from studies of handful animal models humans. To test the generality conclusion, non-model wild animals needed. However, whilst microbiome taxonomic diversity has recently received much attention, characterization its functional potential is lagging behind. Functional “omics” approaches, such as metagenomics, metatranscriptomics, metabolomics, represent promising techniques probe significance host-associated wild. In review, we propose (1) briefly define main available omics tools along with their strengths limitations, (2) summarise advances enabled by understand function human models, (3) showcase examples how these methods have already brought invaluable insights into (4) provide guidelines on implement address outstanding questions field microbiomes. conclude, suggest that approach once presence an abundant resident microbiota been established using more traditional (and less expensive) approaches qPCR metabarcoding.

Language: Английский

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Environmental and Anthropogenic Factors Shape the Skin Bacterial Communities of a Semi-Arid Amphibian Species

Microbial Ecology, Journal Year: 2022, Volume and Issue: 86(2), P. 1393 - 1404

Published: Nov. 29, 2022

Abstract The amphibian skin microbiome is important in maintaining host health, but vulnerable to perturbation from changes biotic and abiotic conditions. Anthropogenic habitat disturbance emerging infectious diseases are both potential disrupters of the microbiome, addition being major drivers decline globally. We investigated how environment (hydrology, disturbance), pathogen presence, biology (life stage) impact wild Dhofar toads ( Duttaphrynus dhufarensis ) Oman. detected ranavirus (but not Batrachochytrium dendrobatidis across all sampling sites, constituting first report this Oman, with reduced prevalence disturbed sites. show that beta diversity driven by life stage, water source, disturbance, infection. Finally, although trends bacterial differential abundance were evident versus undisturbed co-occurrence patterns determined through network analyses revealed high site specificity. Our results therefore provide support for taxa associated (and likely broader aspects microbial community ecology) largely specific.

Language: Английский

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A conceptual framework for host‐associated microbiomes of hybrid organisms

Methods in Ecology and Evolution, Journal Year: 2024, Volume and Issue: 15(3), P. 511 - 529

Published: Jan. 30, 2024

Abstract Hybridization between organisms from evolutionarily distinct lineages can have profound consequences on organismal ecology, with cascading effects fitness and evolution. Most studies of hybrid focused traits, for example, various aspects morphology physiology. However, the recent emergence holobiont theory, there has been growing interest in understanding how hybridization impacts is impacted by host‐associated microbiomes. Better interplay host microbiomes potential to provide insight into both roles as dictators performance well fundamental rules governing microbiome assembly. Unfortunately, a current lack frameworks structure organisms. In this paper, we develop four conceptual models describing possible relationships hybrids their progenitor or ‘parent’ taxa. We then integrate these quantitative ‘4H index’ present new R package calculation, visualization analysis index. demonstrate 4H index be used compare across disparate plant animal systems. Our analyses data sets show variation systems based taxonomy, site microbial taxonomic group. models, paired our associated tools, facilitate comparison This, turn, allows systematic exploration different impact

Language: Английский

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Temporal microbiome changes in axolotl limb regeneration: Stage‐specific restructuring of bacterial and fungal communities with a Flavobacterium bloom during blastema proliferation

Wound Repair and Regeneration, Journal Year: 2024, Volume and Issue: 32(6), P. 826 - 839

Published: Aug. 6, 2024

Abstract The intricate relationship between regeneration and microbiota has recently gained attention, spanning diverse model organisms. Axolotl ( Ambystoma mexicanum ) is a critically endangered salamander species organism for regenerative developmental biology. Despite its significance, noticeable gap exists in understanding the interplay axolotl microbiome. Here, we analyse depth bacterial 16S rRNA amplicon dataset that reported before as data resource profile fungal community by sequencing ITS amplicons at critical stages of limb (0–1–4–7–30–60 days post amputation, ‘dpa’). Results reveal decline richness evenness course regeneration, with recovering beyond 30 dpa unlike fungi community. Beta diversity analysis reveals precise restructuring along three phases contrasting less congruent changes Temporal dynamics highlight prevalent anaerobic bacteria initiation phase Flavobacterium bloom early correlating blastema proliferation. Predicted functional mirrors these shifts, emphasising transition from amino acid metabolism to lipid control. Fungal communities shift Blastomycota Ascomycota dominance late stage. Our findings provide ecologically relevant insights into stage specific role microbiome contributions regeneration.

Language: Английский

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