MicrobiomeStatPlots: Microbiome statistics plotting gallery for meta‐omics and bioinformatics

iMeta, Год журнала: 2025, Номер unknown

Опубликована: Фев. 17, 2025

Abstract The rapid growth of microbiome research has generated an unprecedented amount multi‐omics data, presenting challenges in data analysis and visualization. To address these issues, we present MicrobiomeStatPlots, a comprehensive platform offering streamlined, reproducible tools for This integrates essential bioinformatics workflows with pipelines provides 82 distinct visualization cases interpreting datasets. By incorporating basic tutorials advanced R‐based strategies, MicrobiomeStatPlots enhances accessibility usability researchers. Users can customize plots, contribute to the platform's expansion, access wealth knowledge freely on GitHub ( https://github.com/YongxinLiu/MicrobiomeStatPlot ). Future plans include extending support metabolomics, viromics, metatranscriptomics, along seamless integration into omics workflows. bridges gaps visualization, paving way more efficient, impactful research.

Язык: Английский

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Topical transdermal administration of lenalidomide nanosuspensions-based hydrogels against melanoma: In vitro and in vivo studies

International Journal of Pharmaceutics X, Год журнала: 2025, Номер 9, С. 100316 - 100316

Опубликована: Янв. 18, 2025

Язык: Английский

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Selection and Validation of Appropriate Reference Genes for qRT‐PCR Analysis of Iris germanica L. Under Various Abiotic Stresses

Food Science & Nutrition, Год журнала: 2025, Номер 13(1)

Опубликована: Янв. 1, 2025

ABSTRACT Choosing the appropriate reference genes for quantitative real‐time PCR (qRT‐PCR) is very important accurately evaluating expression of target genes. Iris germanica L. a widely used horticultural plant with high ornamental value, which also shows strong ability to tolerate abiotic stresses. No comprehensive research has been carried out on optimal in under stress. In this study, nine were selected as candidates based transcriptome sequencing data The assessment stability various stress was conducted using four distinct methods (GeNorm, NormFinder, BestKeeper, and RefFinder). It found that ACT F3H drought different temperature EF1α exhibited superior performance salt IgP5CS gene evaluated provide additional validation accuracy genes, indicating inappropriate may lead significant deviations results. This identified reliable I. across conditions, thereby facilitating investigation into molecular mechanisms responsible tolerance

Язык: Английский

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Comparative Genomics of Bryopsis hypnoides: Structural Conservation and Gene Transfer Between Chloroplast and Mitochondrial Genomes

Biomolecules, Год журнала: 2025, Номер 15(2), С. 278 - 278

Опубликована: Фев. 13, 2025

Bryopsis hypnoides, a unicellular multinucleate green alga in the genus Bryopsis, plays vital ecological roles and represents key evolutionary link between multicellular algae. However, its weak genetic baseline data have constrained progress of research. In this study, we successfully assembled annotated complete circular chloroplast mitochondrial genomes B. hypnoides. The genome has total length 139,745 bp contains 59 protein-coding genes, 2 rRNA 11 tRNA with 31 genes associated photosynthesis. 408,555 41 3 18 involved oxidative phosphorylation. Based on data, conducted comparison involving repeat sequences, phylogenetic relationships, codon usage preferences, gene transfer two organellar genomes. major results highlighted that (1) favors A/T repeats, whereas prefers C/G repeats; (2) preference analysis indicated both prefer codons ending A/T, stronger bias observed genome; (3) sixteen fragments high sequence identity were identified genomes, indicating potential transfer. These findings provide critical insights into characteristics evolution

Язык: Английский

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Fermentation-enriched quinoa β-glucan ameliorates disturbed gut microbiota and metabolism in type 2 diabetes mellitus mice

International Journal of Biological Macromolecules, Год журнала: 2025, Номер 306, С. 141666 - 141666

Опубликована: Март 1, 2025

Язык: Английский

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Exposure to thiazole pesticides disrupts pathogens and undermines keystone status of rare taxa within bacterial ecological networks

Ecotoxicology and Environmental Safety, Год журнала: 2025, Номер 292, С. 117983 - 117983

Опубликована: Март 1, 2025

Considering the sensitivity of rare microbial taxa to environmental disturbances and their critical roles in ecosystems, it is essential investigate how soil communities (particularly microbes) respond pesticide exposure. In this study, we found that thiazole pesticides significantly reduced severity potato common scab effectively disrupted pathogen's cell membrane integrity. Notably, hierarchical partitioning analysis indicated geocaulosphere constitute key clusters influencing disease incidence. Within bacterial molecular ecological networks, nodes corresponding these generally exhibited higher degrees compared those more abundant taxa. However, exposure number keystone substantially weakened hub status networks. These findings suggest that, although eradicate pathogens, they may also pose a non-negligible potential risk agricultural ecosystems.

Язык: Английский

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EasyPubPlot: A Shiny Web Application for Rapid Omics Data Exploration and Visualization

Journal of Proteome Research, Год журнала: 2025, Номер unknown

Опубликована: Март 7, 2025

Computational toolkits for data exploration and visualization from widely used omics platforms often lack flexibility customization. While many tools generate standardized output, advanced programming skills are necessary to create high-quality visualizations. Therefore, user-friendly that simplify this crucial, yet time-consuming, step essential. We developed EasyPubPlot (Easy Publishable Plotting), a straightforward, easy-to-use, no-coding, user experience-oriented, open-source, shiny web application along with its associated R package streamline functional omics-empowered research. generates publishable scores plots, volcano heatmaps, box dot bubble plots minimal steps. The tool was designed guide new users accurate efficient navigation. Step-by-step tutorials each type of plot also provided. Herein, we demonstrated EasyPubPlot's competent functionality versatility by showcasing metabolomics, proteomics, transcriptomics data. Collectively, reduces the gap between analysis stunning visualization, thereby diminishing friction focusing on science. app can be downloaded installed locally (https://github.com/Pharmaco-OmicsLab/EasyPubPlot) or through (https://pharmaco-omicslab.shinyapps.io/EasyPubPlot).

Язык: Английский

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Genome-wide identification of the SmPHR gene family in Salvia miltiorrhiza and SmPHR7-mediated response to phosphate starvation in Arabidopsis thaliana

Plant Cell Reports, Год журнала: 2025, Номер 44(4)

Опубликована: Март 12, 2025

Язык: Английский

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Comparative analysis of deep dentinal caries microbiota in teeth with normal pulp, reversible pulpitis, symptomatic and asymptomatic irreversible pulpitis

International Endodontic Journal, Год журнала: 2025, Номер unknown

Опубликована: Март 14, 2025

Abstract Aim To characterize the deep dentinal caries microbiota in teeth diagnosed with normal pulp (NP), reversible pulpitis (RP), symptomatic irreversible (SIP), and asymptomatic (AIP), to identify potential key pathogens associated progression, exploring their roles disease advancement. Methodology In this cross‐sectional study, we collected 108 samples, categorized into NP ( n = 27), RP SIP AIP according American Association of Endodontists' diagnostic criteria. 2 samples were excluded due contamination. Samples processed using Illumina MiSeq high‐throughput sequencing. Alpha beta diversity, taxa abundance differences, co‐occurrence network analysis, functional prediction evaluated. Correlation analysis between bacteria clinical diagnosis, signs, exposure status was performed Spearman Mantel test. Results The bacteriome exhibited statistically significant differences among NP, RP, SIP, groups. showed similar microbial community structures, comparable alpha bacterial phenotypes, functions, structures. contrast, displayed distinct profiles. characterized by higher diversity a greater gram‐negative bacteria, Propionibacterium Prevotella_7 identified as pathogenesis. On other hand, lower facultative anaerobes, Lactobacillus Limosilactobacillus Fusobacterium , Prevotella Treponema Selenomonas both SIP. Compared networks are more complex contain endodontic pathogens. These form positive correlations each numerous negative lactic acid bacteria. Conclusions differs significantly across AIP, exhibit communities, whereas display

Язык: Английский

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Correlation between oral microbiota and dry socket at different time periods on tooth extraction

Journal of Oral Microbiology, Год журнала: 2025, Номер 17(1)

Опубликована: Апрель 4, 2025

Dry socket is a common post-extraction complication, characterized by the exposure of bone surfaces to oral environment, leading severe pain and potential infection. This study investigates relationship between microbial composition dry incidence in tooth extraction patients. From 87 patients (56 normal healing, 31 socket), 321 samples were collected at pre-, med-, stages from saliva sites, all information was documented. All underwent 16S rDNA sequencing amplicon analysis. exhibited distinct diversity composition. Prevotella, Fusobacterium, Haemophilus strongly associated with occurrence socket. The profiles revealed clearer temporal changes healing/dry distinctions. network key node/edge differences med/post stages. Random forest analysis using pre-extraction microbes predict symptoms, achieving 75% accuracy rate identifying healthy group. Fusobacterium development prediction. Functional caused alterations structure might have been reason for different symptoms observed after extraction.

Язык: Английский

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