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Related Concept Videos

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...
DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

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Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization
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Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization

Published on: April 14, 2016

High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when

Todd Z DeSantis1, Eoin L Brodie, Jordan P Moberg

  • 1Lawrence Berkeley National Laboratory, Center for Environmental Biotechnology, 1 Cyclotron Road, Mail Stop 70A-3317, Berkeley, CA 94720, USA.

Microbial Ecology
|March 6, 2007
PubMed
Summary

A novel microarray offers a faster, more comprehensive method for detecting diverse prokaryotic DNA sequences in environmental samples compared to traditional clone sequencing. This method reveals greater microbial diversity, aiding ecological studies.

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Last Updated: Jul 16, 2026

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12:37

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Published on: April 14, 2016

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

Published on: October 15, 2019

Area of Science:

  • Microbial Ecology
  • Molecular Biology
  • Bioinformatics

Background:

  • Environmental prokaryotic detection often uses polymerase chain reaction (PCR) with broad-specificity primers to amplify 16S rRNA genes.
  • Traditional clone-and-sequence methods for classifying these genes can be unwieldy and may miss diverse taxa.
  • Microarray hybridization offers a potential alternative for rapid and comprehensive prokaryotic community profiling.

Purpose of the Study:

  • To evaluate the breadth and accuracy of a novel high-density 16S rRNA gene microarray.
  • To compare microarray performance against the clone-and-sequence method for analyzing environmental DNA samples.
  • To assess the microarray's ability to detect diverse prokaryotic sequence types across different environments.

Main Methods:

  • Environmental DNA samples (urban aerosol, soil, water) were amplified using universal 16S rRNA gene primers.
  • PCR products were analyzed using both traditional clone-and-sequence methods and a novel high-density microarray.
  • The microarray contained 297,851 probes targeting 842 prokaryotic subfamilies.

Main Results:

  • The clone libraries yielded 1391 high-quality sequences, with ~8% identified as novel.
  • Microarray analysis confirmed most clone-detected subfamilies and revealed greater amplicon diversity, including previously unobserved phyla.
  • Sequences from Nitrospira, Planctomycetes, and TM7, uniquely detected by the array, were verified via specific PCR and sequencing.
  • Microarray-detected subfamily richness correlated well with clone-based predictions, except in water samples where clone-based estimates were significantly lower.

Conclusions:

  • The microarray, while not ideal for novel taxa identification, demonstrates superior diversity detection in environmental samples compared to standard clone libraries.
  • The microarray provides a rapid, replicable method for evaluating microbial communities, offering significant advantages for microbial ecology research.
  • This technology enhances the comprehensive view of prokaryotic community composition in environmental studies.