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Related Concept Videos

Two-Dimensional Microscopy in Microbiology01:29

Two-Dimensional Microscopy in Microbiology

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Two-dimensional (2D) microscopy encompasses a range of optical techniques that capture images within a single focal plane, offering detailed representations of microscopic structures. These techniques are essential in biological and medical research, enabling the visualization of cellular and subcellular structures with different levels of contrast and specificity.There are several major types of 2D microscopy, each with strengths and applications.Bright-Field MicroscopyBright-field microscopy...
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Three-dimensional imaging techniques are essential in cell biology, allowing researchers to visualize intricate cellular structures with high resolution. Two prominent methods, Differential Interference Contrast Microscopy (DIC) and Confocal Scanning Laser Microscopy (CSLM), provide distinct advantages for imaging live and thick specimens, respectively.Differential Interference Contrast MicroscopyDIC microscopy enhances contrast in transparent, unstained samples by converting phase...
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Bacterial and archaeal cells exhibit remarkable diversity in shape and structure, critical in their adaptability and functionality. Among bacteria, the most commonly observed shapes include cocci and bacilli. Cocci are spherical and may exist singly or in groupings such as pairs (diplococci), chains (streptococci), clusters (staphylococci), or tetrads. Bacilli, in contrast, are rod-shaped and can also occur as single cells, in pairs, or chains, depending on their environmental and genetic...
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Classification is the process of organizing organisms into hierarchically inclusive groups based on their phenotypic similarities or evolutionary relationships. A species comprises one or more strains, and closely related species are grouped into genera. Genera are further classified into families, families into orders, orders into classes, and so forth, up to the domain level, which is the broadest taxonomic rank derived from a combination of phenotypic and genotypic data.The nomenclature of...
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Microorganisms play a pivotal role in maintaining ecosystem balance by recycling essential elements such as carbon, nitrogen, and phosphorus, as well as supporting processes like bioremediation, wastewater treatment, and biofuel production.Microbes in Elemental CyclesIn the carbon cycle, microorganisms decompose organic matter, releasing carbon dioxide via aerobic respiration. This carbon dioxide is subsequently used by photosynthetic organisms to synthesize organic compounds, closing the...
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Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
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Related Experiment Video

Updated: Sep 25, 2025

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
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MicrobioSee: A Web-Based Visualization Toolkit for Multi-Omics of Microbiology.

JinHui Li1, Yimeng Sang1, Sen Zeng1

  • 1State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China.

Frontiers in Genetics
|April 25, 2022
PubMed
Summary

MicrobioSee simplifies microbial multi-omics data analysis with an interactive visualization tool. This free, open-source toolkit aids researchers, especially microbiologists, in understanding complex datasets without coding expertise.

Keywords:
MicrobioSeeintegration analysismetagenomestacked column chartvisualization toolkit

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Computational Biology

Background:

  • High-throughput sequencing enables low-cost acquisition of microbial multi-omics data.
  • Existing analysis tools present high learning curves, complex dependencies, and costs for researchers.
  • A user-friendly toolkit is needed to streamline microbial multi-omics data interpretation.

Purpose of the Study:

  • To develop MicrobioSee, a real-time interactive visualization tool for microbial multi-omics data.
  • To simplify complex plotting methods for omics data analysis.
  • To provide an accessible tool for microbiologists without extensive coding experience.

Main Methods:

  • Development of MicrobioSee, a web-based visualization tool.
  • Integration of 17 modules covering major omics data (transcriptome, metagenome, proteome).
  • Implementation of simplified plotting functions for diversity, ROC, and enrichment pathways.

Main Results:

  • MicrobioSee offers real-time, interactive visualization of microbial multi-omics data.
  • The tool simplifies visualization of diversity, ROC curves, and differentially expressed gene (DEG) enrichment pathways.
  • Three case studies demonstrate the tool's functional application and utility.

Conclusions:

  • MicrobioSee provides a concise, user-friendly, time-saving, and cross-platform toolkit.
  • The open-source nature and simplified interface benefit researchers, particularly those lacking coding skills.
  • MicrobioSee is freely available, promoting broader accessibility in microbial multi-omics research.