Species-level core oral bacteriome identified by 16S rRNA pyrosequencing in a healthy young Arab population

摘要

Background:ReportsonthecompositionoforalbacteriomeinArabsarelacking.Inaddition,themajorityofpreviousstudiesonotherethnicgroupshavebeenlimitedbylow-resolutiontaxonomicassignmentofnext-generationsequencingreads.Furthermore,therehasbeenaconflictabouttheexistenceofa‘core’bacteriome.Objective:TheobjectiveofthisstudywastocharacterizethehealthycoreoralbacteriomeinayoungArabpopulationatthespecieslevel.Methods:OralrinseDNAsamplesobtainedfrom12stringentlyselectedhealthyyoungsubjectsofAraboriginwerepyrosequenced(454’sFLXchemistry)forthebacterial16SV1–V3hypervariableregionatanaveragedepthof11,500reads.High-quality,non-chimericreads≥380bpwereclassifiedtothespecieslevelusingtherecentlydescribed,prioritized,multistageassignmentalgorithm.Acorebacteriomewasdefinedastaxapresentinatleast11samples.TheChao2,abundance-basedcoverageestimator(ACE),andShannonindiceswerecomputedtoassessspeciesrichnessanddiversity.Results:Overall,557species-leveltaxa(211±42persubject)wereidentified,representing122generaand13phyla.Thecorebacteriomecomprised55species-leveltaxabelongingto30generaand7phyla,namelyFirmicutes,Proteobacteria,Actinobacteria,Bacteroidetes,Fusobacteria,Saccharibacteria,andSR1.Thecorespeciesconstitutedbetween67and87%oftheindividualbacteriomes.However,theabundancesdifferedbyuptothreeordersofmagnitudeamongthestudysubjects.Onaverage,Streptococcusmitis,Rothiamucilaginosa,Haemophilusparainfluenzae,Neisseriaflavescence/subflavagroup,Prevotellamelaninogenica,andVeillonellaparvulagroupwerethemostabundant.Streptococcussp.C300,ataxonneverreportedintheoralcavity,wasidentifiedasacorespecies.Speciesrichnesswasestimatedat586(Chao2)and614(ACE)species,whereasdiversity(Shannonindex)averagedat3.99.Conclusions:Aspecies-levelcoreoralbacteriomerepresentingthemajorityofreadswasidentified,whichcanserveasareferenceforcomparisonwithoralbacteriomesofotherpopulationsaswellasthoseassociatedwithdisease.Keywords:core;human;high-throughputnucleotidesequencing;microbiome;mouth;pyrosequencing(Published:17May2016)Citation:JournalofOralMicrobiology2016,8:31444-http://dx.doi.org/10.3402/jom.v8.31444