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Related Concept Videos

Methods to Assess Microbial Communities01:19

Methods to Assess Microbial Communities

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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Methods to Assess Microbial Populations

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 visible...
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

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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Rapid Identification of Pathogens

MALDI-TOF MS has transformed clinical microbiology by offering a rapid and reliable method for pathogen identification. The traditional approach to microbial identification typically involves time-consuming culture techniques and biochemical tests, which can delay the initiation of appropriate antimicrobial therapy. MALDI-TOF MS avoids these delays by using characteristic ribosomal protein mass patterns of microbial cells, enabling accurate species-level identification within minutes.Principle...
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Microbial Growth Measurement: Direct Methods

Direct methods for measuring microbial populations in a culture are essential tools in microbiology, providing quantitative data for various applications. Among these, microscopic counts, plate counts, and serial dilution are widely used techniques, each with unique principles and applications.Microscopic CountsMicroscopic counting involves the use of a Petroff-Hausser chamber, a specialized microscope slide with a grid and defined depth. By observing a liquid culture under a microscope,...
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Automated Microbial Diagnostics

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Related Experiment Video

Updated: Jun 7, 2026

High Throughput Co-culture Assays for the Investigation of Microbial Interactions
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Published on: October 15, 2019

BIPES, a cost-effective high-throughput method for assessing microbial diversity.

Hong-Wei Zhou1, Dong-Fang Li, Nora Fung-Yee Tam

  • 1Department of Environmental Health, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, Guangdong, China. biodegradation@gmail.com

The ISME Journal
|October 22, 2010
PubMed
Summary

A new barcoded Illumina paired-end sequencing (BIPES) method enhances microbial diversity analysis by improving accuracy and reducing costs compared to traditional pyrosequencing. This cost-effective approach enables deeper insights into environmental and human microbiomes.

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Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
11:22

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

Published on: October 15, 2019

Area of Science:

  • Microbial Ecology
  • Genomics
  • Bioinformatics

Background:

  • Pyrosequencing of 16S rRNA variable tags is standard for microbial diversity but is expensive for large-scale studies.
  • High sequencing depth is crucial for accurate microbial community analysis.
  • Current methods face limitations in cost-effectiveness and scalability.

Purpose of the Study:

  • To develop a cost-effective and accurate sequencing method for microbial diversity analysis.
  • To improve the assessment of microbial communities in environmental and human samples.
  • To overcome the limitations of pyrosequencing for large-scale microbiome studies.

Main Methods:

  • Developed the barcoded Illumina paired-end sequencing (BIPES) method for 16S V6 tags.
  • Sequenced tags from both ends using Illumina HiSeq 2000 and overlapped paired-end reads.
  • Implemented quality control steps including mismatch removal and primer error checking.

Main Results:

  • BIPES achieved high base sequencing accuracy (99.93%) by overlapping paired-end reads.
  • The method yields 20-50 times more 16S V6 tags than pyrosequencing per run.
  • BIPES reads cost less than 1/40 of pyrosequencing reads, offering significant cost savings.

Conclusions:

  • BIPES is a labor-saving and cost-effective method for microbial ecology studies.
  • The method provides accurate and high-throughput analysis of microbial communities.
  • BIPES is suitable for routine analysis of environmental and human microbiomes.