Oral Bacteriome Compositions Identified by 16S rRNA Metagenomics in a Randomly Selected “Healthy” Nigerian Male and Female Subjects

Abstract

Background: There is a dearth of information on the core oral bacteriome compositions of healthy Africans especially Nigerians, mostly due to the non-existence of apt molecular techniques. Objectives: In this study, we sought to determine the core oral bacteriome compositions of ‘healthy’ Nigerian males and females. Methods: Oral samples were collected from nineteen adult subjects comprising 11 females and 8 males. DNA was extracted and 16S rRNA V4 region amplified using pattern barcoded primers prior to sequencing with the Illumina MiSeq program. Quantitative Insights into Microbial Ecology (QIIME) pipeline was used for 16S rRNA identification. The core genera were defined as taxa present in all subjects and over 2.0% in abundance, while core species defined as taxa found in at least 17/19 samples and over 0.1% in abundance. Results: Overall, 111 genera and 151 species representing 14 phyla were identified from the 19 subjects. Firmicutes (43.6%) were the most abundant phyla followed by Proteobacteria (33.62%), Bacteroidetes (9.67%), Actinobacteria (8.48%),  Fusobacteria (4.31%) and others. The most abundant genera were Streptococcus (27.28%) followed by Haemophilus (14.95%), Neisseria (9.67%), Veillonella (7.22%),  Gemella(5.77%), Rothia (3.11%), Prevotella (3.03%), Porphyromonas (2.94%),  Lautropia (2.86%), Corynebacterium(2.74%), and Leptotrichia (2.61%). The most abundant core species identified were Haemophilus parainfluenzae (29.31%), followed by Haemophilus influenzae (6.91%), Lautropia sp TeTO (6.82%), Porphyromonas catoniae (6.0%), Streptococcus thermophilus (5.23%), Actinobacillus porcinus (4.80%), Rothia dentocariosa (3.32%), Rothia mucilaginosa (2.95%), Neisseria elongata (2.66%), and Streptococcus gordonii (2.55%). Conclusions: The genera and species-level core oral bacteriome identified could be used as a reference for comparison with larger population studies.