Metagenomic rDNA Profiles of the Oral Microbiome in Healthy Subjects Are Distinctive Compared to That in Smokers and Disease Subjects Despite High Variations between Subjects

Abstract

The vital role of oral microbiome in the well-being of humans is only beginning to be unraveled. Employing a rigorous analysis of PCR-restriction fragment length polymorphisms (PCR-RFLP) and DNA fingerprints from denatured gradient gel electrophoresis (PCR-DGGE) of the 16S rDNA gene in metagenomic samples, this study evaluated the stability of the oral microbiome and contrasted the PCR-DGGE profiles of subjects belonging to three groups—healthy, smokers and oral diseases; in search of distinctive patterns predictive of each group. The DNA band size, intensity and profile generated by three restriction enzymes from a 1500 bp amplicon showed a fairly stable microbial community structure (P < 0.05) in PCR-RFLP samples collected from each individual over a 3-month period. Microbial diversity indices and cluster analysis of amplicons from the V4 region of the 16S gene from the three study groups were consistent with a stable core of bacterial DNA fingerprint within and between subjects despite the enormous beta variations. Statistical analysis including multi-dimensional scaling of the DGGE fingerprints in smokers and oral disease subjects aligned both banding patterns (P-value 0.08, Student’s t-test), suggesting some similarity between the microbial consortia of smokers and subjects with dental caries and gingivitis. There was a significant difference between bacterial genomic profiles in healthy mouth and smokers/disease (P = 0.002; paired-sample Student’s t-test). Operational taxonomic unit diversity and species richness determined by the GelCompare II software were higher in smokers ( H' = 0.99 ± 0.12; S = 2.87 ± 0.75) and oral disease mouths ( H' = 1.06 ± 0.085; S = 2.86 ± 0.31), than in healthy subjects ( H' = 0.926 ± 0.07; S = 1.79 ± 0.56) suggesting that smoking is associated with a microbial community shift towards the structure found in poor oral health. It is clear that the human oral bacteria symbionts are not all random colonizers. Rather some of them constitute a fragile stable dynamic community whose disturbance could lead to disease or be indicative of disease. Understanding the dynamics of the bacterial community structure in health and disease states is a prerequisite to developing effective preventive healthcare and rapid diagnosis of diseases.