The Archaea domain was recognized as a separate phylogenetic lineage in the tree of life nearly 3 decades ago. It is now known as part of the human microbiome; however, given that its roles in oral sites are still poorly understood, this review aimed to establish the current level of evidence regarding archaea in the oral cavity to guide future research, providing insights on the present knowledge about the human oral archaeome. A scoping review was conducted with the PRISMA Extension for Scoping Reviews checklist. Five electronic databases were searched, as well as gray literature. Two independent reviewers performed the selection and characterization of the studies. Clinical studies were included when the target population consisted of humans of any age who were donors of samples from the oral cavity. A qualitative analysis was performed, based on the type of oral site and by considering the methods employed for archaeal identification and taxonomy, including the DNA extraction protocols, primers, and probes used. Fifty articles were included in the final scoping review, published from 1987 to 2019. Most studies sampled periodontal sites. Methanogens were the most abundant archaea in those sites, and their presence could be associated with other periodontal pathogens. No consistent relationship with different disease conditions was observed in studies that evaluated the microbiota surviving in endodontic sites. Few articles analyzed the presence of archaea in dental caries, saliva, or tongue microbiota, as well as in archaeologic samples, also showing a relationship with healthy microbiota. Archaea have been detected in different oral niches of individuals from diverse geographic locations and clinical conditions, suggesting potential roles in oral diseases. Methodological limitations may hamper our current knowledge about archaeal diversity and prevalence in oral samples, and future research with diversified methodological approaches may lead to a better comprehension of the human oral archaeome.
AndersonACHellwigEVespermannRWittmerASchmidMKarygianniLAl-AhmadA.2012. Comprehensive analysis of secondary dental root canal infections: a combination of culture and culture-independent approaches reveals new insights. PLoS One. 7(11):e49576.
2.
AshokNWaradSSinghVPChaudhariHNarayananARodriguesJ.2013. Prevalence of archaea in chronic periodontitis patients in an Indian population. Indian J Dent Res. 24(3):289–293.
3.
BalchWEFoxGEMagrumLJWoeseCRWolfeRS. 1979. Methanogens: reevaluation of a unique biological group. Microbiol Rev. 43(2):260–296.
4.
BarkerHA.1936. Studies upon the methane-producing bacteria. Archiv für Mikrobiologie. 7(1–5):420–438.
5.
BelayNJohnsonRRajagopalBSConwaydeMacarioEDanielsL.1988. Methanogenic bacteria from human dental plaque. Appl Environ Microbiol. 54(2):600–603.
6.
BelkacemiSMazelATardivoDTavitianPStephanGBiancaGTerrerEDrancourtMAboudharamG.2018. Peri-implantitis-associated methanogens: a preliminary report. Sci Rep. 8(1):9447.
7.
BringuierAKhelaifiaSRichetHAboudharamGDrancourtM.2013. Real-time PCR quantification of Methanobrevibacter oralis in periodontitis. J Clin Microbiol. 51(3):993–994.
8.
BrockTDBrockKMBellyRTWeissRL. 1972. Sulfolobus: a new genus of sulfur-oxidizing bacteria living at low pH and high temperature. Arch Mikrobiol. 84(1):54–68.
9.
BrusaTCanziEAllieviLDel PuppoEFerrariA.1993. Methanogens in the human intestinal tract and oral cavity. Curr Microbiol. 27(5):261–265.
10.
BrusaTConcaRFerraraAFerrariAPecchioniA.1987. The presence of methanobacteria in human subgingival plaque. J Clin Periodontol. 14(8):470–471.
11.
Brzezińska-BłaszczykEPawłowskaEPłoszajTWitasHGodzikUAgierJ.2018. Presence of archaea and selected bacteria in infected root canal systems. Can J Microbiol. 64(5):317–326.
12.
Dame-TeixeiraNde CenaJACôrtesDABelmokADos Anjos BorgesLGMarconattoLGiongoAKyawCM. 2020. Presence of Archaea in dental caries biofilms. Arch Oral Biol. 110:104606.
13.
DeLongEF. 1998. Everything in moderation: archaea as “non-extremophiles.”Curr Opin Genet Dev. 8(6):649–654.
14.
DengZLSzafrańskiSPJarekMBhujuSWagner-DöblerI.2017. Dysbiosis in chronic periodontitis: key microbial players and interactions with the human host. Sci Rep. 7(1):3703.
FerrariABrusaTRutillACanziEBiavatiB.1994. Isolation and characterization of Methanobrevibacter oralis sp. nov. Curr Microbiol. 29:7–12.
17.
FaveriMGoncalvesLFFeresMFigueiredoLCGouveiaLAShibliJAMayerMP. 2011. Prevalence and microbiological diversity of archaea in peri-implantitis subjects by 16S ribosomal RNA clonal analysis.J Periodontal Res. 46(3):338–344.
18.
FischerMAGüllertSNeulingerSCStreitWRSchmitzRA.2016. Evaluation of 16S rRNA gene primer pairs for monitoring microbial community structures showed high reproducibility within and low comparability between datasets generated with multiple archaeal and bacterial primer pairs. Front Microbiol. 7:1297.
19.
GöhlerAHetzerAHoltfreterBGeiselMHSchmidtCOSteinmetzIKocherT.2014. Quantitative molecular detection of putative periodontal pathogens in clinically healthy and periodontally diseased subjects. PLoS One. 9(7):e99244.
20.
GöhlerASamietzSSchmidtCOKocherTSteinmetzIHoltfreterB.2018. Comparison of oral microbe quantities from tongue samples and subgingival pockets. Int J Dent. 2018:2048390. Erratum in: Int J Dent. 2018:5615780.
21.
GrineGTerrerEBoualamMAAboudharamGChaudetHRuimyRDrancourtM.2018. Tobacco-smoking-related prevalence of methanogens in the oral fluid microbiota. Sci Rep. 8(1):9197.
22.
GuindoCOTerrerEChabrièreEAboudharamGDrancourtMGrineG.2019. Culture of salivary methanogens assisted by chemically produced hydrogen. Anaerobe. 61:102128.
23.
HorzHPConradsG.2011. Methanogenic archaea and oral infections—ways to unravel the black box. J Oral Microbiol. 3. doi:10.3402/jom.v3i0.5940.
24.
HorzHPRobertzNViannaMEHenneKConradsG.2015. Relationship between methanogenic archaea and subgingival microbial complexes in human periodontitis. Anaerobe. 35 Pt A:10–12.
25.
HorzHPSeyfarthIConradsG.2012. McrA and 16S rRNA gene analysis suggests a novel lineage of archaea phylogenetically affiliated with thermoplasmatales in human subgingival plaque. Anaerobe. 18(3):373–377.
HuynhHTNkamgaVDSignoliMTzortzisSPinguetRAudolyGAboudharamGDrancourtM.2016. Restricted diversity of dental calculus methanogens over five centuries, France. Sci Rep. 6:25775.
28.
HuynhHTTPignolyMDrancourtMAboudharamG.2017. A new methanogen “Methanobrevibacter massiliense” isolated in a case of severe periodontitis. BMC Res Notes. 10(1):657.
29.
HuynhHTTPignolyMNkamgaVDDrancourtMAboudharamG.2015. The repertoire of archaea cultivated from severe periodontitis. PLoS One. 10(4):e0121565.
30.
JiangYTXiaWWLiCLJiangWLiangJP. 2009. Preliminary study of the presence and association of bacteria and archaea in teeth with apical periodontitis. Int Endod J. 42(12):1096–1103.
31.
KhelaifiaSLagierJCNkamgaVDGuilhotEDrancourtMRaoultD.2016. Aerobic culture of methanogenic archaea without an external source of hydrogen. Eur J Clin Microbiol Infect Dis. 35(6):985–991.
32.
KilianMChappleIHannigMMarshPMeuricVPedersenATonettiMWadeWZauraE.2016. The oral microbiome—an update for oral healthcare professionals. Br Dent J. 221(10):657–666.
33.
KoskinenKPausanMRPerrasAKBeckMBangCMoraMSchilhabelASchmitzRMoissl-EichingerC.2017. First insights into the diverse human archaeome: specific detection of archaea in the gastrointestinal tract, lung, and nose and on skin. mBio. 8(6):e00824-17.
34.
KulikEMSandmeierHHinniKMeyerJ.2001. Identification of archaeal rDNA from subgingival dental plaque by PCR amplification and sequence analysis. FEMS Microbiol Lett. 196(2):129–133.
35.
LaurenceMHatzisCBrashDE. 2014. Common contaminants in next-generation sequencing that hinder discovery of low-abundance microbes. PLoS One. 9(5):e97876.
36.
LeppPWBrinigMMOuverneyCCPalmKArmitageGCRelmanDA. 2004. Methanogenic archaea and human periodontal disease. Proc Natl Acad Sci U S A. 101(16):6176–6181.
37.
LiCLJiangYTLiuDLQianJLiangJPShuR.2014. Prevalence and quantification of the uncommon archaea phylotype Thermoplasmata in chronic periodontitis. Arch Oral Biol. 59(8):822–828.
38.
LiCLLiuDLJiangYTZhouYBZhangMZJiangWLiuBLiangJP. 2009. Prevalence and molecular diversity of archaea in subgingival pockets of periodontitis patients. Oral Microbiol Immunol. 24(4):343–346.
39.
LiraEARamiroFSChiarelliFMDiasRRFeresMFigueiredoLCFaveriM.2013. Reduction in prevalence of archaea after periodontal therapy in subjects with generalized aggressive periodontitis. Aust Dent J. 58(4):442–447.
40.
LutonPEWayneJMSharpRJRileyPW. 2002. The mcrA gene as an alternative to 16S rRNA in the phylogenetic analysis of methanogen populations in landfill. Microbiology. 148:3521–3530.
41.
MansfieldJMCampbellJHBhandariARJesionowskiAMVickermanMM. 2012. Molecular analysis of 16S rRNA genes identifies potentially periodontal pathogenic bacteria and archaea in the plaque of partially erupted third molars. J Oral Maxillofac Surg. 70(7):1507–14.e1-6.
42.
MarshPD.2005. Dental plaque: biological significance of a biofilm and community life-style. J Clin Periodontol. 32 Suppl6:7–15.
43.
MatarazzoFRibeiroACFaveriMTaddeiCMartinezMBMayerMP. 2012. The domain archaea in human mucosal surfaces. Clin Microbiol Infect. 18(9):834–840.
44.
MatarazzoFRibeiroACFeresMFaveriMMayerMP. 2011. Diversity and quantitative analysis of archaea in aggressive periodontitis and periodontally healthy subjects. J Clin Periodontol. 38(7):621–627.
45.
MillerTLWolinMJ. 1985. Methanosphaera stadtmaniae gen. nov., sp. nov.: a species that forms methane by reducing methanol with hydrogen. Arch Microbiol. 141(2):116–122.
46.
Moissl-EichingerCProbstAJBirardaGAuerbachAKoskinenKWolfPHolmanHN. 2017. Human age and skin physiology shape diversity and abundance of archaea on skin. Sci Rep. 7(1):4039.
47.
NkamgaVDHuynhHTTAboudharamGRuimyRDrancourtM.2015. Diversity of human-associated Methanobrevibacter smithii isolates revealed by multispacer sequence typing. Curr Microbiol. 70(6):810–815.
48.
NottinghamPMHungateRE. 1968. Isolation of methanogenic bacteria from feces of man. J Bacteriol. 96(6):2178–2179.
49.
OzokARPersoonIFHuseSMKeijserBJWesselinkPRCrielaardWZauraE.2012. Ecology of the microbiome of the infected root canal system: a comparison between apical and coronal root segments. Int Endod J. 45(6):530–541.
50.
PaivaSSSiqueiraJFRôçasINCarmoFLFerreiraDCCurveloJASoaresRMRosadoAS. 2012. Supplementing the antimicrobial effects of chemomechanical debridement with either passive ultrasonic irrigation or a final rinse with chlorhexidine: a clinical study. J Endod. 38(9):1202–1206.
51.
PhilipsAStolarekIKuczkowskaBJurasAHandschuhLPiontekJKozlowskiPFiglerowiczM.2017. Comprehensive analysis of microorganisms accompanying human archaeological remains. Gigascience. 6(7):1–13.
52.
RaymannKMoellerAHGoodmanALOchmanH.2017. Unexplored archaeal diversity in the great ape gut microbiome. mSphere. 2(1):e00026-17.
53.
RobichauxMHowellMBoopathyR.2003a. Growth and activities of sulfate-reducing and methanogenic bacteria in human oral cavity. Curr Microbiol. 47(1):12–16.
54.
RobichauxMHowellMBoopathyR.2003b. Methanogenic activity in human periodontal pocket. Curr Microbiol. 46(1):53–58.
55.
SchlaferSMeyerRL. 2017. Confocal microscopy imaging of the biofilm matrix. J Microbiol Methods. 138:50–59.
56.
SeedorfHDreisbachAHedderichRShimaSThauerRK. 2004. F420H2 oxidase (FprA) from Methanobrevibacter arboriphilus, a coenzyme F420-dependent enzyme involved in O2 detoxification. Arch Microbiol. 182(2–3):126–137.
57.
SimonHMDodsworthJAGoodmanRM. 2000. Crenarchaeota colonize terrestrial plant roots. Environ Microbiol. 2(5):495–505.
58.
SiqueiraJFJrRôçasINBaumgartnerJCXiaT.2005. Searching for archaea in infections of endodontic origin. J Endod. 31(10):719–722.
59.
SlatonKHufferMWikEZhangJMorrowCRodesSEleazerP.2017. 16S ribosomal RNA gene sequencing to evaluate the effects of 6 commonly prescribed antibiotics. J Endod. 43(12):1984–1989.
60.
SogodogoEDoumboOAboudharamGKouribaBDiawaraOKoitaHTogoraSDrancourtM.2019. First characterization of methanogens in oral cavity in Malian patients with oral cavity pathologies. BMC Oral Health. 19(1):232.
61.
TriccoACLillieEZarinWO’BrienKKColquhounHLevacDMoherDPetersMDJHorsleyTWeeksL, et al. 2018. Prisma Extension for Scoping Reviews (PRISMA-SCR): checklist and explanation. Ann Intern Med. 169(7):467–473.
62.
van HoekAHvan AlenTASprakelVSLeunissenJABriggeTVogelsGDHacksteinJH. 2000. Multiple acquisition of methanogenic archaeal symbionts by anaerobic ciliates. Mol Biol Evol. 17(2):251–258.
63.
ViannaMEConradsGGomesBPHorzHP. 2006. Identification and quantification of archaea involved in primary endodontic infections. J Clin Microbiol. 44(4):1274–1282.
64.
ViannaMEConradsGGomesBPHorzHP. 2009. T-RFLP-based mcrA gene analysis of methanogenic archaea in association with oral infections and evidence of a novel Methanobrevibacter phylotype. Oral Microbiol Immunol. 24(5):417–422.
65.
ViannaMEHoltgraeweSSeyfarthIConradsGHorzHP. 2008. Quantitative analysis of three hydrogenotrophic microbial groups, methanogenic archaea, sulfate-reducing bacteria, and acetogenic bacteria, within plaque biofilms associated with human periodontal disease. J Bacteriol. 190(10):3779–3785.
66.
VickermanMMBrossardKAFunkDBJesionowskiAMGillSR. 2007. Phylogenetic analysis of bacterial and archaeal species in symptomatic and asymptomatic endodontic infections. J Med Microbiol. 56 Pt1:110–118.
67.
VissersEWBodelierPLMuyzerGLaanbroekHJ. 2009. A nested PCR approach for improved recovery of archaeal 16S rRNA gene fragments from freshwater samples. FEMS Microbiol Lett. 298(2):193–198.
68.
WadeWG.2013. The oral microbiome in health and disease. Pharmacol Res. 69(1):137–143.
69.
WarinnerCRodriguesJFVyasRTrachselCShvedNGrossmannJRadiniAHancockYTitoRYFiddymentS, et al. 2014. Pathogens and host immunity in the ancient human oral cavity. Nat Genet. 46(4):336–344.
70.
WeyrichLSDucheneSSoubrierJArriolaLLlamasBBreenJMorrisAGAltKWCaramelliDDreselyV, et al. 2017. Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus. Nature. 544(7650):357–361.
71.
WoeseCRKandlerOWheelisML. 1990. Towards a natural system of organisms: proposal for the domains archaea, bacteria, and eucarya. Proc Natl Acad Sci U S A. 87(12):4576–4579.
WolfAMoissl-EichingerCPerrasAKoskinenKTomazicPVThurnherD.2017. The salivary microbiome as an indicator of carcinogenesis in patients with oropharyngeal squamous cell carcinoma: a pilot study. Sci Rep. 7(1):5867.
74.
YamabeKMaedaHKokeguchiSSogaYMeguroMNaruishiKAsakawaSTakashibaS.2010. Antigenic group II chaperonin in Methanobrevibacter oralis may cross-react with human chaperonin CCT. Mol Oral Microbiol. 25(2):112–122.
75.
YamabeKMaedaHKokeguchiSTanimotoISonoiNAsakawaSTakashibaS.2008. Distribution of archaea in Japanese patients with periodontitis and humoral immune response to the components. FEMS Microbiol Lett. 287(1):69–75.
ZhangFPitaLErwinPMAbaidSLópez-LegentilSHillRT. 2014. Symbiotic archaea in marine sponges show stability and host specificity in community structure and ammonia oxidation functionality. FEMS Microbiol Ecol. 90(3):699–707.
78.
ZiesemerKAMannAESankaranarayananKSchroederHOzgaATBrandtBWZauraEWaters-RistAHooglandMSalazar-GarciaDC, et al. 2015. Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification. Sci Rep. 5:16498.
79.
ZiganshinaEEMohammedWSShagimardanovaEIVankovPYGogolevaNEZiganshinAM. 2018. Fungal, bacterial, and archaeal diversity in the digestive tract of several beetle larvae (Coleoptera). Biomed Res Int. 2018:6765438.
Supplementary Material
Please find the following supplemental material available below.
For Open Access articles published under a Creative Commons License, all supplemental material carries the same license as the article it is associated with.
For non-Open Access articles published, all supplemental material carries a non-exclusive license, and permission requests for re-use of supplemental material or any part of supplemental material shall be sent directly to the copyright owner as specified in the copyright notice associated with the article.
