The study and practice of endodontics aims to prevent and treat pulp and periapical disease and an understanding of the mechanisms of biofilm formation, dental caries development, and bacterial invasion of dentinal tubules are central to these aims. Studies using open-ended methods report a higher microbial diversity in health than that found in caries. Dental caries is caused by complex highly active biofilm microbiotas, which in the presence of dietary carbohydrates act as a consortium to produce an acidic environment that demineralizes teeth. Molecular-based studies including cloning and sequencing strategies and 16S rRNA probe studies revealed a wide diversity of species in plaque of young children with early childhood caries (ECC), including in clinically healthy oral sites. Updated microbiological methods incorporating 16S rRNA gene sequencing for bacterial identification have expanded the understanding of the microbiota of the oral cavity, including that of dental caries and dentinal tubule invasion.