Science Bulletin, Journal Year: 2025, Volume and Issue: unknown
Published: Jan. 1, 2025
Language: Английский
iMeta, Journal Year: 2024, Volume and Issue: 3(1)
Published: Feb. 1, 2024
The increasing application of meta-omics approaches to investigate the structure, function, and intercellular interactions microbial communities has led a surge in available data. However, this abundance human environmental microbiome data exposed new scalability challenges for existing bioinformatics tools. In response, we introduce Wekemo Bioincloud-a specialized platform -omics studies. This offers comprehensive analysis solution, specifically designed alleviate tool selection users face expanding sets. As now, Bioincloud been regularly equipped with 22 workflows 65 visualization tools, establishing itself as user-friendly widely embraced studying diverse Additionally, enables online modification vector outputs, registration-independent personalized dashboard system ensures privacy traceability. is freely at https://www.bioincloud.tech/.
Language: Английский
Citations
102
iMeta, Journal Year: 2024, Volume and Issue: 3(3)
Published: April 11, 2024
Abstract Venn diagrams serve as invaluable tools for visualizing set relationships due to their ease of interpretation. Widely applied across diverse disciplines such metabolomics, genomics, transcriptomics, and proteomics, utility is undeniable. However, the operational complexity has been compounded by absence standardized data formats need switch between various platforms generating different diagrams. To address these challenges, we introduce EVenn platform, a versatile tool offering unified interface efficient exploration visualization ( http://www.ehbio.com/test/venn ) streamlines upload process with format, enhancing capabilities multimodule analysis. This comprehensive protocol outlines applications EVenn, featuring representative results multiple diagrams, uploads in centralized center, step‐by‐step case demonstrations. Through functionalities, emerges valuable user‐friendly in‐depth multiomics data.
Language: Английский
Citations
44
Environment International, Journal Year: 2024, Volume and Issue: 183, P. 108431 - 108431
Published: Jan. 1, 2024
Microplastic (MP) pollution is a rapidly growing global environmental concern that has led to the emergence of new compartment, plastisphere, which hotspot for accumulation antibiotic resistance genes (ARGs) and human bacterial pathogens (HBPs). However, studies on effects long-term organic fertilizer application dispersal ARGs virulence factor (VFGs) in plastisphere farmland soil have been limited. Here, we performed field culture experiment by burying nylon bags filled with MPs paddy had treated different fertilizers over 30 years explore changes VFGs plastisphere. Our results show amplified ARG VFG caused fertilization 1.5 1.4 times, respectively. And it also 2.7-fold increase risk horizontal gene transfer. Meanwhile, tended promote deterministic process community assembly HBPs, an times. Network analysis found significant correlation between ARGs, VFGs, bacteria Correlation highlight important role mobile genetic elements (MGEs) communities shaping abundance findings provide insights into health associated due derived from fertilizers.
Language: Английский
Citations
40
Biomarker Research, Journal Year: 2024, Volume and Issue: 12(1)
Published: Sept. 27, 2024
Abstract Cells, as the fundamental units of life, contain multidimensional spatiotemporal information. Single-cell RNA sequencing (scRNA-seq) is revolutionizing biomedical science by analyzing cellular state and intercellular heterogeneity. Undoubtedly, single-cell transcriptomics has emerged one most vibrant research fields today. With optimization innovation technologies, intricate details concealed within cells are gradually unveiled. The combination scRNA-seq other multi-omics at forefront field. This involves simultaneously measuring various omics data individual cells, expanding our understanding across a broader spectrum dimensions. precisely captures aspects transcriptomes, immune repertoire, spatial information, temporal epitopes, in diverse contexts. In addition to depicting cell atlas normal or diseased tissues, it also provides cornerstone for studying differentiation development patterns, disease heterogeneity, drug resistance mechanisms, treatment strategies. Herein, we review traditional technologies outline latest advancements multi-omics. We summarize current status challenges applying biological clinical applications. Finally, discuss limitations potential strategies address them.
Language: Английский
Citations
26
iMeta, Journal Year: 2024, Volume and Issue: 3(2)
Published: March 11, 2024
Abstract Inflammatory bowel disease (IBD) is a significant global health concern. The gut microbiota plays an essential role in the onset and development of IBD. Sanghuangporus (SH), traditional Chinese medicinal mushroom, has excellent anti‐inflammatory effects effective at modulating microbiota. Despite these attributes, specific anticolitic SH mechanisms through which mediates its benefits remain unclear. Herein, we demonstrated that polyphenol‐rich extract from effectively alleviated pathological symptoms dextran sodium sulfate (DSS)‐induced colitis mice by Treatment with distinctly enriched Alistipes , especially onderdonkii metabolite 5‐hydroxyindole‐3‐acetic acid (5HIAA). Oral gavage live A. or 5HIAA potently mitigated DSS‐induced mice. Moreover, both significantly activated aromatic hydrocarbon receptor (AhR), administration AhR antagonist abrogated their protective against colitis. These results underscore potent efficacy diminishing promotion 5HIAA, ultimately activating signaling. This study unveils potential avenues for developing therapeutic strategies based on interplay between
Language: Английский
Citations
24
Journal of genetics and genomics/Journal of Genetics and Genomics, Journal Year: 2024, Volume and Issue: unknown
Published: Sept. 1, 2024
Language: Английский
Citations
20
iMeta, Journal Year: 2025, Volume and Issue: unknown
Published: Feb. 14, 2025
Abstract Shotgun metagenomics has become a pivotal technology in microbiome research, enabling in‐depth analysis of microbial communities at both the high‐resolution taxonomic and functional levels. This approach provides valuable insights diversity, interactions, their roles health disease. However, complexity data processing need for reproducibility pose significant challenges to researchers. To address these challenges, we developed EasyMetagenome, user‐friendly pipeline that supports multiple methods, including quality control host removal, read‐based, assembly‐based, binning, along with advanced genome analysis. The also features customizable settings, comprehensive visualizations, detailed parameter explanations, ensuring its adaptability across wide range scenarios. Looking forward, aim refine by addressing contamination issues, optimizing workflows third‐generation sequencing data, integrating emerging technologies like deep learning network analysis, further enhance accuracy. EasyMetageonome is freely available https://github.com/YongxinLiu/EasyMetagenome .
Language: Английский
Citations
5
iMeta, Journal Year: 2025, Volume and Issue: unknown
Published: Feb. 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.
Language: Английский
Citations
4
Environmental Science & Technology, Journal Year: 2025, Volume and Issue: unknown
Published: Jan. 21, 2025
Viruses are considered to regulate bacterial communities and terrestrial nutrient cycling, yet their effects on metabolism the mechanisms of carbon (C) dynamics during dissolved organic matter (DOM) mineralization remain unknown. Here, we added active inactive bacteriophages (phages) soil DOM with original incubated them at 18 or 23 °C for 35 days. Phages initially (1–4 days) reduced CO2 efflux rate by 13-21% 3–30% but significantly (p < 0.05) increased 4–29% 9–41% after 6 days, raising cumulative emissions 14% 21% °C. decreased dominant taxa community diversity (consistent a "cull-the-winner" dynamic), thus altering predicted microbiome functions. Specifically, phages enriched some (such as Pseudomonas, Anaerocolumna, Caulobacter) involved in degrading complex compounds consequently promoted functions related C cycling. Higher temperature facilitated phage-bacteria interactions, diversity, enzyme activities, boosting 16%. Collectively, impact shifting microbial functions, moderate changes modulating magnitude these processes not qualitatively behavior.
Language: Английский
Citations
3
Protein & Cell, Journal Year: 2023, Volume and Issue: 14(10), P. 709 - 712
Published: May 23, 2023
With its critical role in human health and disease, the microbiome has transformed modern biology. Over past few years, research evolved rapidly, with microbiologists gradually shifting their focus from cataloging microorganisms to understanding functional roles how they interact host. Here, we present global trends summarize current work on published Protein & Cell. In closing, highlight some of major advancements research, including technical, practical, conceptual advancements, that aim enhance disease diagnosis, medicine development, personalized interventions
Language: Английский
Citations
28