A peer-reviewed journal that offers evidence-based clinical information and continuing education for dentists.

The Human Microbiome Revisited

As noted in last month’s editorial, the bacteria, fungi, viruses, protozoa and archaea found in the body are collectively known as the human microbiome.


As noted in last month’s editorial, the bacteria, fungi, viruses, protozoa and archaea found in the body are collectively known as the human microbiome. In particular, the oral microbiome consists of an incredibly diverse group of microorganisms; it has been estimated the oral cavity holds more than 1000 bacterial species alone. Currently, we have limited knowledge of how all these species interact.

Previously, it was not possible to identify the vast majority of these organisms, mainly because of problems in cultivating the multiple organisms found in the oral cavity. As a result, it has been difficult to target specific etiologic factors for oral disease. Advances in cloning and polymerase chain reaction (PCR) technology are changing this, however. The latter technique is a molecular genetics tool that analyzes short sequences of deoxyribonucleic acid and ribonucleic acid (better known as DNA and RNA). In addition, pyrosequencing is overcoming the initial limitations imposed by cloning and PCR, as this sequence-based detection technology enables rapid and accurate quantification of sequence variation.


A study using pyrosequencing to evaluate the oral microbiome was published by Spain’s Department of Genomics and Health, Center for Advanced Research in Public Health. Researchers obtained supragingival plaque from 25 subjects, who were also evaluated for oral health. In subjects with active caries, one set of samples was taken without touching the lesions. A second sampling of biofilm was taken from inside each lesion. Two subjects who had never experienced caries served as controls. The bacterial samples from the caries subjects were separated into two groups: individuals who had been treated for caries in the past, but currently had a low number of active lesions, and subjects with a high number of active caries. All of the subjects in this last group had poor oral hygiene. Even with low sample numbers, the authors found diversity between healthy and diseased microbiomes. Health was more often associated with Bacilli and Gammaproteobacteria, while anaerobic bacteria (including Bacteroides) were more closely associated with disease.

Dental caries is the most prevalent infectious human disease and affects more than 80% of the world’s dentate population. Research into the etiology of the disease process has been ongoing, and while several hypotheses have been suggested, so far no single agent has been able to meet Koch’s postulates for this disease. The study cited above, as well as others, run counter to the once widely held belief that Streptococcus mutans is the sole etiologic factor. Of interest is that the study found almost a complete absence of S. mutans in caries lesions.

If these new approaches to identifying organisms in the oral microbiome hold true, they will spur significant progress in preventing and treating this worldwide problem. These findings may lead the dental community to develop new compounds to fight caries, and possibly encourage increased use of targeted probiotics to increase the number of favorable microorganisms in the oral cavity.

Thomas G. Wilson Jr., DDS
Editor in Chief

From Decisions in Dentistry. February 2017;3(2):8.

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