African Journal of Microbiology Research Vol. 6(10), pp. 2559-2566, 16 March, 2012 Available online at http://www.academicjournals.org/AJMR DOI: 10.5897/AJMR12.115 ISSN 1996-0808 ©2012 Academic Journals Full Length Research Paper Microbial profiling of dental caries and periodontitis patients using denaturing gradient gel electrophoresis Ayaz Ahmed 1 , Jianjun Liu 1 , Yousuf Moosa 2 , Li Tang 3 , Shizhu Zang 1 and Yi Xin 1 * 1 Department of Biotechnology, Dalian Medical University, Dalian, P. R. China. 2 First affiliated Hospital of Dalian Medical University, Dalian, P. R. China. 3 Department of Microecology, Dalian Medical University, Dalian, P.R. China. Accepted 08 February, 2012 Oral cavity contains a diverse group of microorganisms which changes from normal to diseased condition like dental caries and periodontitis. It is hard to depict the complete picture of microbial environment as some species are uncultivable. In this study we detected the microbial diversity of normal, dental caries and periodontal group by using culture independent PCR based denaturing gradient gel electrophoresis (DGGE). DNA was extracted from plaque samples from patients, and PCR was conducted for the 16s rRNA gene with universal primer, followed by DGGE, excision of bands, cloning and sequencing. It was determined that the number of bands detected in normal group (17.06 ± 4.34) was more than dental caries (12.73 ± 3.2) and periodontitis group (10.36 ± 3.5). On clustering they formed mixed clusters. Sequencing results showed that dental caries group contained large proportion of Gram positive bacteria, while periodontitis group contained mostly Gram negative bacteria. Diversity in dental caries and periodontitis groups were less as compared to normal group which suggested that the presence of only cariogenic bacteria and those who tolerate low pH contributes in dental caries and some typical bacteria responsible for causing periodontitis. DGGE is the effective tool to dissect any microbial niche in the body. Key words: Dental caries, periodontitis, denaturing gradient gel electrophoresis (DGGE), microbial diversity. INTRODUCTION Metagenomics allow us to know that microorganisms present within human body are ten times more than the cells in the body and contains in aggregate of 100 times more genes (Gill et al., 2006). Most of the micro- organisms play an important role in human physiological processes while some cause disease. Oral cavity is one of the most complex microbial habitats in the human body that comprises of more than 600 diverse arrays of bacterial species (Kazor et al., 2003). More than 250 oral microbes have been isolated and characterized by the cultivation method but over 450 microbial species have *Corresponding author. E-mail: jimxin@hotmail.com. been identified by the culture independent molecular methods (Aas et al., 2008a; Paster et al., 2006). Oral microbiota beside its importance in oral health reflects the health and disease status of the host as it effects many other systemic diseases like bacterial endocarditis, pneumonia, preterm low birth weight and coronary heart disease (Beck et al., 2005a; 2005b; Offenbacher et al., 2006; Paju and Scannapieco, 2007). Among many oral diseases dental caries and periodontitis are common diseases. Dental caries is characterized by the acid demineralization of the tooth enamel followed by damage to the hard tooth structure, which results in the formation of cavities on tooth surface. Mutans group Streptococci are closely associated with the caries formation and frequently isolated from dental