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Related Concept Videos

Methods to Assess Microbial Communities01:19

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Microbial communities, comprising bacteria, archaea, and eukaryotic microorganisms, inhabit diverse ecosystems and play crucial roles in environmental and biological processes. Their diversity is defined by three main parameters: species richness (the number of distinct species), species abundance (the relative quantity of each species), and species evenness (how uniformly individual species are distributed in various locations). These factors together shape the structure and ecological balance...
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Assessing microbial populations is crucial for understanding microbial roles in health, ecology, and industry. Various complementary techniques—both culture-based and molecular—enable detailed analysis of microbial abundance, diversity, and function.Viable Plate CountThe viable plate count is a traditional culture-based method used to estimate the number of living microbes in a sample. After serial dilution, the sample is spread onto nutrient agar plates. Each viable cell forms a...
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Microbial biosensors are analytical devices that utilize living microbes to detect specific substances through measurable signals. These devices consist of two main components: biosensing organisms and signal-transducing elements. Biosensing organisms, such as Escherichia coli or Saccharomyces cerevisiae, are typically housed in multiwell plates connected to transducers, enabling rapid, real-time detection of target analytes.Signal Generation MechanismWhen a target analyte—such as...
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Automated diagnostic analyzers have transformed clinical microbiology by providing rapid and reliable methods for pathogen identification and antibiotic susceptibility testing. Among these systems, the Vitek 2 is widely used because it automates the traditionally labor-intensive processes of microbial identification (ID) and antibiotic susceptibility testing (AST), delivering standardized and timely results that are essential for effective patient care.Microbial Identification with ID CardsThe...
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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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Updated: Mar 27, 2026

Automated and High-throughput Microbial Monoclonal Cultivation and Picking Using the Single-cell Microliter-droplet Culture Omics System
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Microbial Omics.

Ahmet Arıhan Erözden1,2, Nalan Tavşanlı1,2, Mahmut Çalışkan1

  • 1Biotechnology Division, Department of Biology, Faculty of Science, Istanbul University,Vezneciler, Istanbul, Türkiye.

Progress in Molecular and Subcellular Biology
|March 26, 2026
PubMed
Summary
This summary is machine-generated.

Omics technologies offer powerful tools for microbiology research. This chapter guides researchers on using genomics, transcriptomics, proteomics, metabolomics, and meta-omics for microbial ecosystem analysis.

Keywords:
GenomicsMeta-metabolomicsMetabolomicsMetagenomicsMetaproteomicsMetatranscriptomicsProteomicsTranscriptomics

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Area of Science:

  • Microbiology
  • Molecular Biology
  • Bioinformatics

Background:

  • Omics technologies have transformed scientific research.
  • Their application in microbiology offers novel insights into microbial life and community interactions.
  • Understanding microbial ecosystems requires multi-level molecular investigation.

Purpose of the Study:

  • To provide a comprehensive overview of single-organism and meta-omics techniques in microbiology.
  • To detail the experimental and bioinformatic workflows for various omics approaches.
  • To serve as a practical guide for researchers studying microbial structure, function, and interactions.

Main Methods:

  • Genomics, transcriptomics, proteomics, metabolomics for individual organisms.
  • Metagenomics, metatranscriptomics, metaproteomics, meta-metabolomics for microbial communities.
  • Integrative multi-omics strategies for holistic ecosystem analysis.

Main Results:

  • Detailed descriptions of key omics methods, including their features and applications.
  • Outlines of experimental and bioinformatic pipelines for each technique.
  • Discussion of commonly used computational tools for omics data analysis.

Conclusions:

  • Omics technologies provide a powerful toolkit for microbial research.
  • Multi-omics approaches are essential for a comprehensive understanding of microbial ecosystems.
  • This chapter equips researchers with practical knowledge for exploring microbial life at multiple molecular levels.