Advancements toward a systems level understanding of the human oral microbiome

Abstract

Oral microbes represent one of the most well studied microbial communities owing to the fact that they are a fundamental part of human development influencing health and disease, an easily accessible human microbiome, a highly structured and remarkably resilient biofilm as well as a model of bacteria-bacteria and bacteria-host interactions. In the last 80 years since oral plaque was first characterized for its functionally stable physiological properties such as the highly repeatable rapid pH decrease upon carbohydrate addition and subsequent recovery phase, the fundamental approaches to study the oral microbiome have cycled back and forth between community level investigations and characterizing individual model isolates. Since that time, many individual species have been well characterized and the development of the early plaque community, which involves many cell–cell binding interactions, has been carefully described. With high throughput sequencing enabling the enormous diversity of the oral cavity to be realized, a number of new challenges to progress were revealed. The large number of uncultivated oral species, the high interpersonal variability of taxonomic carriage and the possibility of multiple pathways to dysbiosis pose as major hurdles to obtain a systems level understanding from the community to the gene level. It is now possible however to start connecting the insights gained from single species with community wide approaches. This review will discuss some of the recent insights into the oral microbiome at a fundamental level, existing knowledge gaps, as well as challenges that have surfaced and the approaches to address them.

The Oral Microbiome of Children: Development, Disease, and Implications Beyond Oral Health

“…During this process, particular community dynamics involving sucrose metabolism, pH homeostasis and biofilm formation, impact oral disease development [55, 64]. For instance, tooth decay and enamel demineralization seem to be promoted by a community shift in biofilm populations towards acidogenic (acid producing) and aciduric (acid tolerant) cariogenic bacteria, likely triggered by low pH after sucrose fermentation [65]. Additionally, sucrose seems to be a substrate for the production of extracellular and intracellular polysaccharides, two components that determine biofilm formation and structure [66, 67].…”

“…For instance, S. mutans can trigger pH conditions as low as 3.0 after sugar stimuli through fermentation, a scenario that has been linked to enamel demineralization [73, 74]. In contrast, other species within the Streptococcus genus, such as S. salivarius and S. mitis are associated with an increase of pH through alkali generating pathways, and therefore are linked to a protective effect against caries[64, 65]. …”

“…Thus, it is necessary to improve and standardize microbial community profiling in early oral disease by refining diversity at deeper taxonomic levels (e.g., species and strains). Additionally, adopting a system-level approach to profile microbemicrobe and microbe-metabolite interactions in the early oral ecosystem should improve our understanding of microbial function in disease, beyond taxonomic characterizations [65, 83]. …”

What could you do with 400 years of biological history on african americans? Evaluating the potential scientific benefit of systematic studies of dental and skeletal materials on African Americans from the 17th through 20th centuries

“…across 20 generations are possible with the 4Cs database and would be an important addition to the literature since changes in the oral microbiome over time may reflect the effects of exposure to environmental toxins, dietary patterns, and differential pharmaceutical use (see Dewhirst et al, 2010). Oral microbes are a fundamental part of human development and easily accessible part of the human microbiome (McLean, 2014). Studies of the oral microbiome could be central to the reconstructions of the effects of the built and social environments on the episome as the oral cavity and upper respiratory track are the main ports of entry of microorganisms into the human body (Macovei et al, 2015).…”

Bacterial adhesion and biofilm formation on yttria-stabilized, tetragonal zirconia and titanium oral implant materials with low surface roughness - an in situ study

“…Due to the considerable differences in composition between the pellicles formed by human sterilized saliva in vitro and those formed in the oral cavity in situ, results of in vitro studies could differ significantly from those of in situ investigations Yao et al, 2003). Furthermore, the oral microbiota consists of 700-1000 different species (Dewhirst et al, 2010;Griffen et al, 2012), and contributes to the formation of microbial biofilms with high microbial diversity within the oral cavity (McLean, 2014). As a result, the characterization of the complex process of oral biofilm formation on implant materials can only be simulated to a limited extent in vitro, although a high diversity of adherent oral bacteria on implant materials has been demonstrated in vitro (Nascimento et al, 2015).…”