Metagenomic Approach Studying The Taxonomic And Functional Diversity Of The Oral Microbiota In Caries Children

Dental caries constitutes the most prevalent chronic oral disease worldwide.Previous studies,including those based on 16S ribosomal RNA(rRNA),have revealed that the oral microbiome plays a prominent role in development of the disease.However,the present study is mostly limited to the structure of oral microbial group and lack of overall functional genes expression in oral micro-ecological in caries disease.The aim of this report is to use metagenomic analyses to investigate the complex relationship between the oral microbiome and caries in preschool children.Twenty-five children with severe early childhood caries(ECC)and 19 caries-free preschoolers were recruited for this study.MethodsSaliva samples were collected and bacterial genomic DNA was extracted.A total of 44 oral samples were sequenced using a HiSeq 2000 instrument by 100-bp pair-end sequencing.Results1 Oral gene catalogue in healthy and the ECC groupAn average of 3.08 Gb of clean data were generated for each of the 44 samples,from which a non-redundant oral gene set containing 2,200,443 genes was constructed.To our knowledge,this is the first gene catalogue for the human oral microbiome.2 Phylogenetic profiles of saliva microbiome at the phylum levelIn both groups,Proteobacteria was the most abundant phylum,followed by Firmicutes,Bacteroidetes,Actinobacteria and Fusobacteria.These five phyla contributed 99%of the microbial genomic data.The healthy group displayed a higher abundance of Proteobacteria and a lower abundance of Bacteroidetes and Firmiucutes than those of the ECC group.3 Phylogenetic profiles of saliva microbiome at the genus levelAt the genus level,Neisseria,Prevotella,Rothia,Streptococcus,Veillonella and Haemophilus were dominant in both groups.Subsequent analysis of relative abundance revealed that nine genera,including Prevotella,were more abundant in the ECC group than in the healthy group,whereas three genera,including Neisseria,were enriched in the healthy group.4 Phylogenetic profiles of saliva microbiome at the species levelAt the species level,29 microbes(P<0.01),including Streptococcus mutans,Dialister invisus,3 Veillonella spp.(e.g.,V.parvula)and 8 Prevotella spp.(e.g.,P.nigrescens,P.oris,P.oulorum)were enriched in ECC group,whereas Neisseria lactamica,Candidatus Nitrospira defluvii,Erysipelotrichaceae bacterium 5 2 54FAA and Streptococcus australis were enriched in healthy subjects.These differences suggested dysbiosis of the oral microbiome in the ECC group.5 Functional gene analysesMoreover,functional analyses using gene profile,KEGG orthology profile,and eggNOG showed enormous differences at the functional level between the caries and healthy groups,particularly in sugar and amino acid metabolism.Caries-enriched metabolic categories included the AI-2(autoinducer-2)transport system,PTS(phosphoenolpyruvate-dependent sugar phosphotransferase system),glucitol/sorbitol-specific ? component and gluconeogenesis and nucleotide sugar biosynthesis,as well as the glucosyltransferase(GTF)gene.Together,these findings indicate that dental caries are associated with extraordinary alterations of oral microbial communities at various levels.According to the functional genes increased in caries group,we proposed the possible mechanisms of caries.Conclusions1 A microbiome gene catalogue from children with caries was constructed for the first time.2 Preschool children with dental caries and their healthy counterparts exhibited tremendous differences in the oral microbiomes and functional profiles.3 The result is proving that caries is the result of dysbiosis of the oral microbiome and their imbalance at the functional gene level particularly in sugar and amino acid metabolic activities.