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Related Concept Videos

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...
Methods to Assess Microbial Populations01:30

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...
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...
Applications of Molecular Taxonomy01:20

Applications of Molecular Taxonomy

Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...
RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...

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Guided Protocol for Fecal Microbial Characterization by 16S rRNA-Amplicon Sequencing
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Guided Protocol for Fecal Microbial Characterization by 16S rRNA-Amplicon Sequencing

Published on: March 19, 2018

High throughput sequencing methods and analysis for microbiome research.

Julia M Di Bella1, Yige Bao, Gregory B Gloor

  • 1Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada.

Journal of Microbiological Methods
|September 14, 2013
PubMed
Summary
This summary is machine-generated.

High-throughput sequencing enables comprehensive microbiome analysis, covering prokaryotic communities across diverse environments. This review details methods and bioinformatics tools for analyzing microbiome sequence data, aiming to establish a baseline for this evolving field.

Keywords:
BioinformaticsHigh-throughput sequencingMetagenomeMetatranscriptomeMicrobiome

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Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing

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Last Updated: May 7, 2026

Guided Protocol for Fecal Microbial Characterization by 16S rRNA-Amplicon Sequencing
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Published on: March 19, 2018

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

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Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing
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Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing

Published on: August 25, 2018

Area of Science:

  • Microbiology and Bioinformatics
  • Genomics and Molecular Biology

Background:

  • High-throughput sequencing technology advancements are driving increased use in studying microbial communities.
  • Prokaryotic community analysis is crucial across various environmental niches.

Purpose of the Study:

  • To review current high-throughput sequencing techniques for microbiome analysis.
  • To discuss bioinformatic tools for analyzing amplicon, metagenome shotgun, and metatranscriptome sequences.
  • To provide a foundational understanding of microbiome analysis methods and identify future research challenges.

Main Methods:

  • Review of nucleic acid extraction protocols from diverse environments.
  • Description of sample preparation workflows for microbiome studies.
  • Overview of high-throughput sequencing platforms and associated bioinformatic pipelines.

Main Results:

  • Detailed discussion of techniques for microbiome sample processing and sequencing.
  • Comprehensive summary of bioinformatic tools for sequence data analysis (amplicon, metagenome, metatranscriptome).
  • Identification of current limitations in sensitivity, specificity, and interpretation of microbiome sequence data.

Conclusions:

  • High-throughput sequencing offers powerful tools for microbiome research.
  • Standardized methods and advanced bioinformatics are essential for accurate microbiome analysis.
  • Further research is needed to address challenges in data interpretation and analytical sensitivity/specificity.