16S rRNA Gene Sequencing for Deciphering the Colorectal Cancer Gut Microbiome: Current Protocols and Workflows

Frontiers in Microbiology
Muhammad-Afiq OsmanRahman Jamal

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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Citations

Feb 10, 2020·Environmental Science and Pollution Research International·Yijie YangLihong Chai
Aug 8, 2020·Chembiochem : a European Journal of Chemical Biology·Agne SveistyteKristoffer R Brandvold
Feb 7, 2021·Communications Biology·Nathan Dumont-LeblondCaroline Duchaine
Mar 7, 2021·International Journal of Molecular Sciences·Sheeana GangadooJames Chapman
Nov 29, 2020·Current Opinion in Biotechnology·Seo-Young ParkArul Jayaraman
Apr 18, 2021·International Journal of Medical Microbiology : IJMM·Stephan C BischoffBenjamin Seethaler

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Methods Mentioned

BETA
PCR
biopsy
nucleic acid extraction
biopsies

Software Mentioned

EzBioCloud
MOTHUR
MetaHIT
Quantitative Insight into Microbial Ecology ( QIIME )
QIIME

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