16S rRNA gene sequencing

Overview

Amplicon sequencing of the bacterial 16S rRNA gene used to characterize microbial community composition in tumor and matched normal tissue PMID:37202560.

Used by

• PMID:41941260 — 16S/ITS microbiome sequencing performed in ImmunoRad MCT1 rectal-cancer patients; post-RT sequencing showed increases in Clostridiales and Trichocomaceae relative to baseline PMID:41941260.
• PMID:37202560 — applied to 348 AC-ICAM treatment-naive primary colon cancer tumor/normal pairs, plus an additional 42 tumor-only samples (ICAM42), to derive a Ruminococcus bromii-driven microbiome signature combined with the ICR signature into the mICRoScore PMID:37202560.
• Used in all 18 case–control studies meta-analyzed (predominantly V3–V4 region; platforms including Illumina MiSeq/HiSeq/NovaSeq and Ion Torrent) to characterize the oral microbiome in esophageal cancer cases vs. controls; significant beta-diversity differences reported in 12/17 studies PMID:24670651
• Multiple 16S rRNA sequencing studies (Zhang Q, Ito Z, Deng T, Zhang T, Jia X) synthesized in this CCA review, profiling gut microbiota dysbiosis in cholangiocarcinoma; documented depletion of Faecalibacterium/Roseburia/Bacteroides and enrichment of Escherichia-Shigella/Enterobacteriaceae in iCCA patients vs healthy controls PMID:25608663

Notes

• In the AC-ICAM workflow, 16S sequencing was paired with tumor whole-genome sequencing for microbiome read mining and validation PMID:37202560.
• Microbiome composition is sensitive to sample handling, diet, and geography, so the R. bromii signal requires external validation PMID:37202560.

Sources

• PMID:37202560
• PMID:41941260

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