Glossary

Biofilm: In general, a biofilm is a well-organized, cooperative community of microorganisms that is found on surfaces anywhere in nature that typically form under fluid conditions.⁷

Plaque Biofilm: The biofilm unique to the oral cavity occurring on numerous surfaces such as the cheeks, tongue and teeth comprised of a sticky mass of proteins, lipids, glycoproteins, and glycolipids housing oral microbial communities with special chemical and nutritional gradients.^3,8,9

Microbiome: The human microbiota consists of the 10-100 trillion symbiotic microbial cells harbored by each person; the human microbiome consists of the genes these cells harbor.¹⁰

Symbionts: Symbiont is the term used to refer to an organism living in symbiosis.¹¹

Pathobionts: Pathobionts are opportunistic microbes that emerge as a result of perturbations in the healthy microbiome due to complex interactions of various genetic, exposomal, microbial, and host factors that lead to their selection and expansion.¹²

Commensal organisms: Beneficial bacterial species that protect against pathogens, perform multiple immunological functions and maintain health.¹³

Symbiosis: A condition that occurs in health dominated by commensal gram-positive organisms that are in homeostasis with the host.⁴

Dysbiosis: The transition of the polymicrobial community from largely gram-positive commensal microbes to a gram-negative enriched inflammogenic community.⁴

Metagenomics: Is a set of techniques which detects bacteria that cannot be cultured and identifies the genomic diversity of microbes by genomic analysis of the DNA of the entire community of microbes that involves the whole-genome shotgun sequencing (WGS).³

16S rRNA sequencing: Involves sequencing of the conserved 16S rRNA gene.³

Metabolomics: the study of molecules in biological samples which may be produced by the host or its microbiome.¹⁴

Meta-transcriptomics: Sequencing of mRNA in a sample providing a snapshot of transcriptionally active microbes.¹⁴

Keystone Pathogens: specific microbes that are present in low numbers such as Porphyromonas gingivalis (P. gingivalis) and Filifactor alocis (F. alocis) that are capable of triggering inflammation by interfering with the innate immune system causing a shift in the host response.¹⁵