Beyond microbial community composition: functional activities of the oral microbiome in health and disease

Abstract

The oral microbiome plays a relevant role in the health status of the host and is a key element in a variety of oral and non-oral diseases. Despite advances in our knowledge of changes in microbial composition associated with different health conditions the functional aspects of the oral microbiome that lead to dysbiosis remain for the most part unknown. In this review, we discuss the progress made towards understanding the functional role of the oral microbiome in health and disease and how novel technologies are expanding our knowledge on this subject.

Keywords: Caries; Dysbiosis; Microbiome; Omics; Oral; Periododontitis.

Fig. 1. Schematic representation of the different ‘omic’ levels in the ecology of microbial communities

Different strategies of study would results in different levels of knowledge when studying microbial communities. DNA based analysis would only give information about the potential activities of the community. Metatrancriptome and metaproteome give functional information while only the metabolome would give information about the final products of microbial acitivity. Adapted from Maron et al. [23].

Fig. 2. Rank distribution of relative increase in number of hits for the metagenome and metatranscriptome results

The ratio of counts in disease vs health was log2 transformed and plotted according to ranks. Only species with significant differences either in metagenomic or metatranscriptomic counts are presented. The statistical significance was calculated using the non-parametric test implemented in the program NOISeq as described in the methods section. In green species with statistical differences in both metagenome and metatranscriptome. In blue species with statistical differences in metagenomic counts. In orange species with statistical differences in metatranscriptome counts. Red start indicate major periodontal pathogens previously assigned to the ‘red-complex’.

Fig. 3. GO enrichment analysis summarized and visualized as a scatter plot using REVIGO

a) Biological processes in disease. b) Biological processes in health. c) Molecular functions in disease. d) Molecular functions in healthy. GO terms are represented by circles and are plotted according to semantic similarities to other GO terms (adjoining circles are most closely related). Circle size is proportional to the frequency of the GO term, while color indicates the log10 p value (red higher, blue lower).