High‐throughput methods for analysis of the human oral microbiome

Abstract

The vast majority (ca. 90%) of cells in the humanbody are not human at all – but rather microbial(64). Many of these microbial cells play importantroles in normal human physiology because they areinvolved in nutrient absorption (5, 6, 10), synthesisof vitamins and protection of human cells frominfection (39, 134). The human body containsnumerous ecological niches (such as the oral cavity)that are suitable for acquiring and retaining micro-bial cells. The oral cavity is a warm, wet and nutri-ent-rich environment that is ideal for supportingmicrobial growth. It also shelters microbes by pro-viding specific ecological niches (e.g. the tongue,and supra- and subgingival areas of the tooth),which protect microbes from mechanical and envi-ronmental stress caused by brushing, chewing, pHand temperature (58). These benefits are not with-out consequences: some microbes are a burden onthe host because they continually challenge oraltissues for resources. The host deals with thesemicrobes by regulating microbial growth throughenzymes and by influencing the composition of oralmicrobes through defence mechanisms (e.g.immune effectors and defensins). Hence, the hostand the microbial cells co-exist in the oral cavity bymaintaining a dynamic balance that arises out ofnumerous host–microbe interactions (79). In healthyindividuals, this balance is regarded as dynamicbecause it changes in response to endogenous (e.g.stress) and exogenous (e.g. smoking) factors. Asubstantial disruption of this balance, however, canlead to a variety of chronic oral infectious diseases,including periodontitis, peri-implant diseases anddental decay (47).Thousands of diverse species of microorganismscolonize the human oral cavity. Most of thesemicroorganisms are found in complex biofilms thatare attached to soft and hard tissues in the oral cavity(57, 89). These biofilms are assembled in an orderedprocess that begins with the adherence of microbialcolonizers to a surface and is followed by the colo-nization of different microbial species that attach tothe initial colonizers (65, 100, 101, 119). The initialcolonizers are predominantly gram-positive aerobes,such as streptococci (93). These microbes normallyexist in commensal harmony with host cells, whilesecondary colonizers, which are predominatelygram-negative bacteria, may or may not exist inharmony with host cells. Host cells provide specificreceptor ligands that coordinate the initial microbialcolonization of a surface, while subsequent biofilmassembly depends upon the physiology and meta-bolic capabilities of the interacting microbial cells(52). Hence, the physiological processes of both thehost and microbial cells are responsible for biofilmassembly (61). Differences in the composition of oralmicrobial biofilms within the same individual ondifferent tissue surfaces, such as mucosa vs. tooth, orwithin the same habitat (e.g. one vs. another peri-odontal pocket) (7–9, 55, 77, 89, 97) are presumablycaused by variations in endogenous and exogenousfactors.The perception of oral microbial communities,biofilm formation and host–microbe interactions bythe scientific community is inherently linked to theavailability and capability of technologies that can beused to describe biological events. These techno-logies have enabled researchers to study known(previously described) microbes, and have helped toelucidate the role of microbes in oral disease.However, most conventional technologies are basedon detecting only one nucleic acid sequence (e.g. by