Research approaches to biofilm are stratified by a series of analyses: (1) microbial number and species; (2) microbial proteins, such as enzymes; and (3) microbial activity, such as metabolic activity. On the other hand, the hierarchical structure of biology includes the genome, proteome, and metabolome, in which the metabolome is the final output of biological function. Metabolome analysis is the comprehensive analysis of the metabolome, a new strategy for biological research in the 21st century. The stratified structure of biofilm research corresponds to the biological hierarchy, and the analysis of microbial activity, especially metabolic activity, is comparable to metabolome analysis; however, oral biofilm samples are too small to analyze the metabolome by conventional methods. Recently, a new device involving capillary electrophoresis (CE) and time-of-flight mass spectrometry (MS) has been developed, facilitating metabolomic investigation of the central carbon metabolic pathways (i.e., the EMP pathway, pentose phosphate pathway, and TCA cycle) in oral biofilm. Using CE-MS, we analyzed metabolome profiles of oral biofilm after oral rinsing with glucose in vivo and evaluated the effects of oral rinsing with fluoride and xylitol on the metabolome profiles of oral biofilm. The results were somewhat consistent with previous in vitro data obtained from single bacterial strains, namely, Streptococcus and Actinomyces; however, new information describing the metabolic properties of oral biofilm was also obtained. This metabolomic approach will reveal the functional characteristics of oral biofilm in vivo, potentially providing new insights into the nature of oral biofilm in health and disease.
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