The Core and Variable Oral Microbiome of a Group Sri Lankan Oral Squamous Cell Carcinoma (OSCC) Male Patients

EasyChair Preprint no. 6989

Abstract

Present study was conducted to identify core and variable microbiome of a group of Sri Lankan OSCC male patients. The universal prokaryotic 16S rRNA gene, with V1- V9 hyper variable regions and the internal transcribed spacer (ITS) with a non-functional DNA segment that is located between 18S, 5.8S and 28S rRNA genes infungi are ideal candidates for sequencing after amplification with the specific degenerate primers, for profiling of microbiome. Representative sub sample comprising 25 OSCC cases and 27 fibro-epithelial polyp (FEP) controls as well as 22 OSCC cases and 24 fibro-epithelial polyp (FEP) controls were selected from a large multi-centre field study conducted in Sri Lanka for profiling of bacteriome and mycobiome respectively. DNA were extracted from all frozen tissues according to the manufacturer’s instructions. In the present study, the V1 to V3 region of the prokaryotic 16S rRNA gene and fungal ribosomal internal transcribed spacer 2 (ITS2) were used for amplification with degenerate specific primers, followed by sequencing using (Illumina) 2x300 bp chemistry. Raw reads were subjected for pre and final processing procedures to obtain high-quality non-chimeric merged reads. As a result, 89.0 % of bacterial and 97.4 % of fungal processed reads were classified into species. Bacterial classification up to species level was done by prioritized BLASTN-based algorithm and fungal species level using a BLASTN-algorithm with UNITE’s named species sequences as reference. Downstream compositional analyses were performed with QIIME and LEFSe software. The core microbiome was consisted of common genera of Streptococcus, Rothia, Leptotrichia, Gemella, Capnocytophaga, Fusobacterium, Prevotella, Haemophillus, Granulicatella and Neisseria as well as Candida, Malassezia, Cladosporium and Aspergillus which were common to FEP controls as well as OSCC cases. Obviously, certain species were differently abundant in the variable microbiome of OSCC patients.

Keyphrases: Core Oral Microbiome, Universal prokaryotic 16S rRNA gene, Variable Oral Microbiome

@Booklet{EasyChair:6989,
  author = {Manosha Perera and Irosha Perera},
  title = {The Core and Variable Oral Microbiome of a Group Sri Lankan Oral Squamous Cell Carcinoma (OSCC) Male Patients},
  howpublished = {EasyChair Preprint no. 6989},

  year = {EasyChair, 2021}}