GigaByte
Bacterial metagenome in plaque, saliva, and tumor samples from individuals with and without OSCC by next-generation sequencing
By Erira A, Robayo DAG, Gamboa FO and 6 others.
Abstract
Background
Oral dysbiosis has been associated with oral squamous cell carcinoma (OSCC); however, most microbiome studies rely on 16S ribosomal RNA (rRNA) gene sequencing, limiting species-level taxonomic resolution.
Methods
Dental plaque, saliva, and tumor tissue samples from 10 patients with OSCC and dental plaque and saliva samples from 10 healthy controls were analyzed in this exploratory cross-sectional study. DNA was extracted and subjected to shotgun metagenomic sequencing using the Illumina MiSeq platform. Sequence reads were quality filtered with fastp, taxonomically classified using Kraken2 v2.1.3, and species-level abundances were re-estimated with Bracken v2.9 following the removal of human reads and low abundance taxa. Relative abundances were compared using the Mann-Whitney U test with the Benjamini-Hochberg false discovery rate correction, while the Bray-Curtis principal coordinate analysis was used as an exploratory approach to visualize microbial community patterns.