Comparative analysis of full-length 16s ribosomal RNA gene sequencing in human oropharyngeal swabs using primer sets with different degrees of degeneracy.

ABSTRACT:

Background

Full-length 16S rRNA gene sequencing using nanopore technology has become increasingly relevant for profiling complex microbial communities, including the human oral microbiome. Primer selection plays a critical role in amplification bias and taxonomic resolution, yet remains insufficiently investigated for oropharyngeal samples.

Methods

We conducted a comparative analysis of two primer sets with differing degrees of degeneracy - Oxford Nanopores (ONT) standard 27F primer (27F-I) and a more degenerate variant (27F-II) - for full-length 16S rRNA gene sequencing of 80 human oropharyngeal swab samples using ONTs MinION Mk1C. Alpha diversity and taxonomic profiles were statistically compared between primer sets and benchmarked against a large-scale salivary microbiome

SUBMITTER: Waechter C 

PROVIDER: S-EPMC12665744 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature