The microbiota of the oral cavity plays a significant role in pulpal and periapical diseases. Historically, 100 years ago little was known on microbiota, but after a century of investigations, only now can many of the intimate secrets of microbial growth, expansion, persistence, communal activities, and virulence be revealed. However, with the capabilities of the microbiota for mutation, quorum sensing, and information transference, researchers are hard-pressed to keep up with both the changes and challenges that an amazingly wide range of bacterial species pose for both the scientist and clinician. Fortunately, the development and expansion of a vast array of molecular biological investigative techniques have enabled dentistry and its associated medical fields to attempt to keep pace with the wide and fascinating world of oral microbiology.

The techniques for root canal obturation have undergone several changes in the last 10 years. While warm vertical compaction had been the major method of filling the canal, which included the use of core carriers made of structurally stable gutta-percha, recent developments in the manufacturing of precision-tapered, gutta-percha cones and the use of bioceramic root canal sealers have become the clinician's choice in the past few years. The impact of these revolutionary changes is explored with open ended questions and challenges for the reader.

Recalcitrant bacteria play an important role of the persistence of periapical disease following root canal procedures, especially when they a part of a complex and stable biofilms that are found in the intricacies of the apical root canal anatomy. This is particularly true in cases that are deemed as a “failure in root canal treatment.” However, the literature is replete with confusion with regard to this concept of failure, as general terms, such as endodontic pathology or endodontic infection are used to denote factors implicated in the failure, without specifically identifying the issues of concern and their eradication, especially as they relate to the overall systemic health of the patient. Thus, attention for the cause of the failure immediately focuses on bacterial species without considering a vast array of potential causes. In doing so many studies tend to look at only one specific species as being the causative agent in the presence of the diagnosed failure (E. faecalis) and this bacterial species has been the focus of a wide range of investigative studies used for proof of concept. Is it possible that this focus has missed the bigger picture and potentially more virulent, invasive, and persistent species are involved? Have too many studies relied on short-term, single-bacterial biofilms, negating the very essence of the long-term interplay of multiple species within these colonies? This short communication will address this perspective, attempting to expand the investigative process for the presence and persistence of periapical disease and its impact on the host.