The Human Oral Microbiome in Health and Disease: From Sequences to Ecosystems

Abstract

The human oral cavity is home to an abundant and diverse microbial community (i.e., the oral microbiome), whose composition and roles in health and disease have been the focus of intense research in recent years. Thanks to developments in sequencing-based approaches, such as 16S ribosomal RNA metabarcoding, whole metagenome shotgun sequencing, or meta-transcriptomics, we now can efficiently explore the diversity and roles of oral microbes, even if unculturable. Recent sequencing-based studies have charted oral ecosystems and how they change due to lifestyle or disease conditions. As studies progress, there is increasing evidence of an important role of the oral microbiome in diverse health conditions, which are not limited to diseases of the oral cavity. This, in turn, opens new avenues for microbiome-based diagnostics and therapeutics that benefit from the easy accessibility of the oral cavity for microbiome monitoring and manipulation. Yet, many challenges remain ahead. In this review, we survey the main sequencing-based methodologies that are currently used to explore the oral microbiome and highlight major findings enabled by these approaches. Finally, we discuss future prospects in the field.

Gallstone Disease and Microbiome

“…The total surface area of the oral cavity is about 214.7 ± 12.9 cm 2 [ 28 ]. The oral microbiome is a unique and extensive ecosystem—including viruses, fungi, protozoa, archaea, and bacteria [ 29 , 30 ]—with over 700 prokaryote species [ 28 ] that interact in various ways to form biofilms. Individuals’ oral microbiomes are highly specific at the species level, although the human oral microbiome shows few geographical differences overall [ 30 ]; however, the number of microbes of different types can fluctuate.…”

“…Individuals’ oral microbiomes are highly specific at the species level, although the human oral microbiome shows few geographical differences overall [ 30 ]; however, the number of microbes of different types can fluctuate. In the oral cavity, 50–200 types of microorganisms belonging to 15 genera are isolated, which are found in almost every person [ 29 , 31 ]. The microbiome of a healthy oral cavity contains five predominant types: 96% of the total number of taxa belong to Firmicutes (genus Streptococcus , family Veillonellaceae , genus Granulicatella ), Proteobacteria (genus Neisseria , Haemophilus ), Actinobacteria (genus Corynebacterium , Rothia , Actinomyces ), Bacteroidetes (genus Prevotella , Capnocytophaga, Porphyromonas ), Fusobacteria (genus Fusobacterium ) [ 31 ], and Spirocheetes [ 32 ]; the remaining types, Euryarchaeota , Chlamydia , Chloroflexi , SR1, Synergistetes , Tenericutes , and TM7 represent the remaining 4% of taxa [ 32 ].…”

43-Year Temporal Trends in Immune Response to Oral Bacteria in a Swedish Population

“…We anticipate that the generally higher immune responses to oral opportunistic species among the older participants compared to the younger participants reflect age-related dental disease progression and the associated microbiota profile in the underlying population [27,28]. However, it is less clear why the antibody levels of several dental disease-associated bacteria increased over time in cross-sectional samples in the same age stratum.…”

Dysbiosis of Oral Microbiota and Its Effect on Epithelial-Mesenchymal Transition: a Review

“…The oral ecosystem has significantly different niches such as saliva, soft tissue surface (tongue surface, oral mucosa), hard tissue (surface of the gum and palette), and palatine tonsil. Each niche provides a distinct ecosystem and optimal growth conditions for the growth of different oral microbiota [10,17]. It has been reported that the profiles of 40 different cultivable bacterial species differ in saliva, soft tissue surface and hard tissue surface, and supragingival and subgingival plaques of healthy individuals [18].…”

“…A number of aerobic and anaerobic bacteria uptake nutrients and moisture from the saliva in order to develop biofilms on the surface of the teeth, soft palate, and hard palate [19]. Microorganisms are divided into five further sub-divisions, such as obligate aerobic, obligate anaerobic (Fusobacterium and Veillonella), facultative anaerobes (Actinomyces and Streptococci), microaerophilic (grow best at low CO 2 level, e.g., Lactobacillus), and capnophiles (best grow in high CO 2 concentration, such as Neisseria) [17,20].…”