Characterization of saliva microbiota’s functional feature based on metagenomic sequencing

Abstract

Objective Saliva, a mixture of exocrinally secretive fluids, amounts to ~1.5 L daily and harbors numerous microbial inhabitants. However, except the organismal structure of saliva microbiota, the functional profile of saliva microbiota remain elusive.MethodsHere we used metagenomic sequencing to experimentally reconstruct the global genomic profile of saliva by sequencing total saliva DNA from two healthy and two caries-active (DMFT ≧ 6) adults.ResultsWe found that saliva microbiota, representing 30–60% of total saliva DNA in our samples, might carry functional signatures that were site-specific and caries-state-specific. Among microbiota from different hosts, a prominent functional core, but not an organismal core, was identified. Each microbiota exhibited functional redundancy where dominant genomes tend to encode more functional diversity yet without necessarily contributing to dominant functions. Furthermore, genetic polymorphisms of hosts were also unraveled from salivary DNA without apparent physical or sequence bias in human chromosomes.ConclusionsThe microbial functional sensitivity to disease, links to specific functions, and permission of simultaneous genotyping of hosts and microbiota suggested sequencing salivary DNA might be an advantageous venue in uncovering both human and microbial basis of oral infections.Electronic supplementary materialThe online version of this article (doi:10.1186/s40064-016-3728-6) contains supplementary material, which is available to authorized users.

Evolution of the Oral Microbiome and Dental Caries

“…They found the metagenome of the healthy individuals to be enriched with genes involved in anti-bacterial functions relative to that of the caries-affected individuals. This difference in the health and caries metagenome was also found in a study of four individuals [35]. These metagenomic studies, due to their small sample size, cannot determine the degree of inter-individual variation, nor predict whether it will be large, as seen in16S analyses.…”

“…Recent genetic research of the oral microbiome has indicated that the 'what are they doing?' approach of assessing functional differences between health and caries may be more clinically relevant [34,35]. The function of the oral microbiome can be assessed by directly sequencing the majority of DNA present in a sample, capturing the vast array of different genes from the different bacterial species.…”

“…Identification of the captured genes can be used to predict the functional ability of the oral microbiome sample being assessed. To date, only a few small-scale studies have been performed to assess the metagenomic difference between health and caries [34,35], due to the order of magnitude greater cost of metagenomic sequencing compared to NGS of the 16S gene. However, these limited numbers of studies have revealed promising results.…”

Effect of silver fluoride on micro-ecology of plaque from extensive caries of primary teeth - in vitro study

“…The collected plaque was put into a 1.5 ml centrifuge tube containing 1 ml PBS solution. Saliva was collected using method described by Fang Yang et al [26], an amount of 2.5-3 ml saliva was collected. All collected samples were immediately stored in a refrigerator at -20℃ before laboratory analysis.…”

Effect of silver diammine fluoride on micro-ecology of plaque from extensive caries of deciduous teeth - in vitro study

“…The collected plaque was put into a 1.5 ml centrifuge tube containing 1ml PBS solution. Saliva in the amount of 2.5-3 ml was collected using the spitting method described by Fang Yang et al [26]. All collected samples were immediately stored in a freezer at -20℃ before laboratory analysis.…”