Evaluation of V3-V4 and FL-16S rRNA amplicon sequencing approach for microbiota community analysis of tracheostomy aspirates.

ABSTRACT: Respiratory infections pose a significant risk for people requiring prolonged mechanical ventilation, yet limited information exists regarding the complex microbiome dynamics of people with tracheostomies during chronic critical illness. Oxford Nanopore Technologies (ONT) long-read sequencing allows for full-length 16S rRNA amplicon sequencing, providing enhanced species-level understanding of the respiratory microbiome. We validated ONT-based FL-16S amplicon sequencing for microbial insights from tracheal aspirates by comparing results with those of Illumina V3-V4 amplicon sequencing. Comparisons were made on a standardized microbial community and tracheal aspirates using multiple DNA extraction kits. Conventional short-read bioinformatic pipelines are suboptimal for processing longer, er

SUBMITTER: Gupta A 

PROVIDER: S-EPMC12379586 | biostudies-literature | 2025 Aug

REPOSITORIES: biostudies-literature