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Table 2 Summary of obstacles to determining the microbial etiology of caries

From: Are the mutans streptococci still considered relevant to understanding the microbial etiology of dental caries?

Obstacle or Confounder
Sampling Choices
 - saliva instead of dental plaque
 - plaque pooled from sites of caries and intact enamel
 - microbiology of carious sites can vary considerably over small distances
Substrate Susceptibility
 - tooth sites may vary in susceptibility to dental plaque of similar composition
Caries Process
 - the microbiology of caries evolves as the lesion progresses in severity
Genetic Contributions
 - salivary composition and constituents may elevate or depress caries risk
Determination of the Plaque Microbiome
 - culture-based methods have a narrow focus
 - next generation sequencing outcomes may differ from lab to lab analyzing the same sample
 - 16S gene-based sequencing poorly differentiates species of oral streptococci
Biological Significance
 - little evidence for what constitutes biologically significant levels of individual plaque species
Caries Incidence
 - the microbial basis for occasional caries may typically differ from that for rampant caries