16S rRNA gene sequencing for deciphering the colorectal cancer gut microbiome: Current protocols and workflows

Research output: Contribution to journalShort survey

Abstract

The human gut holds the densest microbiome ecosystem essential in maintaining a healthy host physiology, whereby disruption of this ecosystem has been linked to the development of colorectal cancer (CRC). The advent of next-generation sequencing technologies such as the 16S rRNA gene sequencing has enabled characterization of the CRC gut microbiome architecture in an affordable and culture-free approach. Nevertheless, the lack of standardization in handling and storage of biospecimens, nucleic acid extraction, 16S rRNA gene primer selection, length, and depth of sequencing and bioinformatics analyses have contributed to discrepancies found in various published studies of this field. Accurate characterization of the CRC microbiome found in different stages of CRC has the potential to be developed into a screening tool in the clinical setting. This mini review aims to concisely compile all available CRC microbiome studies performed till end of 2016 and to suggest standardized protocols that are crucial in developing a gut microbiome screening panel for CRC.

LanguageEnglish
Article number767
JournalFrontiers in Microbiology
Volume9
Issue numberAPR
DOIs
Publication statusPublished - 27 Apr 2018

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Workflow
rRNA Genes
Colorectal Neoplasms
Microbiota
Ecosystem
Computational Biology
Nucleic Acids
Gastrointestinal Microbiome
Technology

Keywords

  • 16S rRNA gene
  • 16S rRNA gene sequencing
  • Colorectal cancer
  • Colorectal cancer screening
  • Gut microbiome
  • Metagenomics
  • Next-generation sequencing

ASJC Scopus subject areas

  • Microbiology
  • Microbiology (medical)

Cite this

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title = "16S rRNA gene sequencing for deciphering the colorectal cancer gut microbiome: Current protocols and workflows",
abstract = "The human gut holds the densest microbiome ecosystem essential in maintaining a healthy host physiology, whereby disruption of this ecosystem has been linked to the development of colorectal cancer (CRC). The advent of next-generation sequencing technologies such as the 16S rRNA gene sequencing has enabled characterization of the CRC gut microbiome architecture in an affordable and culture-free approach. Nevertheless, the lack of standardization in handling and storage of biospecimens, nucleic acid extraction, 16S rRNA gene primer selection, length, and depth of sequencing and bioinformatics analyses have contributed to discrepancies found in various published studies of this field. Accurate characterization of the CRC microbiome found in different stages of CRC has the potential to be developed into a screening tool in the clinical setting. This mini review aims to concisely compile all available CRC microbiome studies performed till end of 2016 and to suggest standardized protocols that are crucial in developing a gut microbiome screening panel for CRC.",
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author = "Osman, {Muhammad Afiq} and Neoh, {Hui Min} and {Ab Mutalib}, {Nurul Syakima} and Chin, {Siok Fong} and {A. Jamal}, {A. Rahman}",
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AU - Neoh, Hui Min

AU - Ab Mutalib, Nurul Syakima

AU - Chin, Siok Fong

AU - A. Jamal, A. Rahman

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N2 - The human gut holds the densest microbiome ecosystem essential in maintaining a healthy host physiology, whereby disruption of this ecosystem has been linked to the development of colorectal cancer (CRC). The advent of next-generation sequencing technologies such as the 16S rRNA gene sequencing has enabled characterization of the CRC gut microbiome architecture in an affordable and culture-free approach. Nevertheless, the lack of standardization in handling and storage of biospecimens, nucleic acid extraction, 16S rRNA gene primer selection, length, and depth of sequencing and bioinformatics analyses have contributed to discrepancies found in various published studies of this field. Accurate characterization of the CRC microbiome found in different stages of CRC has the potential to be developed into a screening tool in the clinical setting. This mini review aims to concisely compile all available CRC microbiome studies performed till end of 2016 and to suggest standardized protocols that are crucial in developing a gut microbiome screening panel for CRC.

AB - The human gut holds the densest microbiome ecosystem essential in maintaining a healthy host physiology, whereby disruption of this ecosystem has been linked to the development of colorectal cancer (CRC). The advent of next-generation sequencing technologies such as the 16S rRNA gene sequencing has enabled characterization of the CRC gut microbiome architecture in an affordable and culture-free approach. Nevertheless, the lack of standardization in handling and storage of biospecimens, nucleic acid extraction, 16S rRNA gene primer selection, length, and depth of sequencing and bioinformatics analyses have contributed to discrepancies found in various published studies of this field. Accurate characterization of the CRC microbiome found in different stages of CRC has the potential to be developed into a screening tool in the clinical setting. This mini review aims to concisely compile all available CRC microbiome studies performed till end of 2016 and to suggest standardized protocols that are crucial in developing a gut microbiome screening panel for CRC.

KW - 16S rRNA gene

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KW - Colorectal cancer

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KW - Metagenomics

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