Abstract
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.
Introduction
Recognized as a separate phylogenetic lineage in the tree of life nearly 3 decades ago (Woese et al. 1990), the Archaea domain comprises microorganisms with unique structural, physiologic, and genetic features. The first organisms identified as belonging to this domain of life were isolated from hostile habitats, such as geo- and hydrothermal systems (Zeikus and Wolfe 1972; Woese et al. 1978), sulfurous acidic springs (Brock et al. 1972), salt lakes, and paddy fields (Balch et al. 1979). It drove the idea that archaea were restricted to extreme environments. However, the use of 16S rRNA genes to identify microorganisms in natural environments has revealed that archaea are a ubiquitous organism (DeLong 1998; Vissers et al. 2009), with essential roles in global biogeochemical cycles.
The association of archaea and other organisms has also been recognized, such as plant root colonizers (Simon et al. 2000), endosymbionts of amoeba and ciliates (van Hoek et al. 2000), members of the microbiota of marine sponges (Zhang et al. 2014), and habitants of the gastrointestinal tract of animals (Raymann et al. 2017; Ziganshina et al. 2018). Archaea members are also present in the human microbiome, first reported in the human gut long before their recognition as a separate domain of life (Nottingham and Hungate 1968). These organisms have also been detected in various human body sites, including skin, respiratory tract, vagina, and oral cavity (Matarazzo et al. 2012; Koskinen et al. 2017; Moissl-Eichinger et al. 2017).
The human oral cavity comprises an abundant microbiota (Kilian et al. 2016), with heterogeneous oral sites (teeth, gingival sulcus, gum, tongue, cheek, lip, and palate) providing conditions for extremely diverse ecologic systems (Schlafer and Meyer 2017). The first members of Archaea detected on the oral cavity were methanogenic organisms, retrieved from subgingival plaque (Brusa et al. 1987). Afterward, the knowledge on the composition and function of the oral archaeome in oral sites has been expanded, despite the small number of studies dedicated to its identification and physiologic characterization.
Based on the need to establish the current level of evidence regarding archaea in the oral cavity to guide future research on the field, this study aimed to provide insights on the present knowledge about the human oral archaeome. This scoping review therefore set out to summarize what has been published about the presence and taxonomy of Archaea in human oral sites, as well as the methodological procedures that have been employed so far to detect archaeal cells or DNA in oral samples.
Methods
Study Design
We conducted a scoping review using the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) Extension for Scoping Reviews checklist (Tricco et al. 2018).
Search Strategy
A wide-open systematic search of the literature was conducted in electronic databases (MEDLINE/PubMed, Cochrane Library, Scopus, LILACS, Livivo) as well as the gray literature (Google Scholar and OpenGrey). General controlled vocabulary (MeSH terms) and keywords were chosen, and the searches had no language, year, or publication type restriction. Terms included “archaebacteria” to identify older papers when the term “archaea” was not employed yet.
Eligibility Criteria and Selection of the Manuscripts
Studies were included if they satisfied all the following criteria: clinical studies in which the target population consisted of humans of any age who were donors of samples from the oral cavity. Studies were excluded if they 1) had clinical outcomes without microbiology analysis, 2) were not original research, 3) were conference abstracts, or 4) were written in non-Latin alphabet. Two reviewers (A.B. and J.A.C.) independently screened the eligibility of all identified titles and abstracts for inclusion in the full-text review. Both also evaluated full-text articles for inclusion using the same eligibility criteria. The conflicts were resolved by a consensus with the main supervisor (N.D.T.). The reference lists of the selected articles were analyzed manually to identify manuscripts that could have been lost during searches in the electronic database and other gray literature.
Data Extraction and Synthesis
Two reviewers (A.B. and J.A.C.) independently extracted the data in 2 steps. Initially, descriptive data were extracted from the selected studies by type of oral site (periodontal sites, endodontic sites, saliva, ancient dental calculus, and other sites) and with consideration of the publication year, the country in which the study was conducted, and the methods employed for archaeal identification, including DNA extraction protocols, primers sets, probes, sequencing, and cultivation strategies. Second, one reviewer (A.B.) reanalyzed each selected study and critically reviewed the main findings.
Results
The literature search resulted in 390 manuscripts, and after the removal of duplicates and those that did not meet the eligibility criteria (n = 336), 54 were considered for the full-text review. After full-text reading, 4 articles were excluded since they involved nonhuman oral cavity samples (n = 2) or were written in non-Latin alphabet (n = 2). Figure 1 presents a PRISMA flow diagram outlining the study selection process.
Flow diagram for study selection according to the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines.
Figure 2 shows the geographic distribution and proportion of studies of archaea in oral samples, highlighting the investigated oral sites and methodology employed, evidencing that most studies were developed in Brazil and Europe, and indicating the investigated oral sites and general methods used. When the articles were grouped according to oral sites, it became clear that periodontal niches were the most representative ones (n = 26), followed by endodontic sites (n = 10; Fig. 2). The presence of archaeal DNA sequences in supragingival biofilms, tongue, saliva, carious dentine, and dental calculus from archaeological samples has also been reported. Some studies included the identification of archaea after treatment for periodontitis and endodontic infection (Paiva et al. 2012; Brzezińska-Błaszczyk et al. 2018).
Geographic map indicates the distribution and proportion of studies that describe the presence of archaea in human oral samples. Tags in the GoogleMaps tool point out the countries in which the included studies were conducted. Different colors indicate the percentage of studies performed in each location (n = 50), as shown in the caption on the left. The pie chart on the bottom left shows the proportion of studies employing culture-based, culture-independent, or both approaches. The distribution of studies among investigated oral sites is depicted on the pie chart on the bottom right. Four studies evaluated >1 oral site.
Figure 3 shows the temporal distribution of experimental studies about archaea in the oral cavity. The first study was published in 1987, describing the enrichment culture of methanogenic “bacteria” retrieved from subgingival plaque. Until 2003, most articles employed culture-based methods, and in 2004, culture-independent methodologies became popular, such as the sequencing of 16S rRNA genes. After 2012, the number of studies increased substantially, most of them based on culture-independent methods, such as fluorescence in situ hybridization, quantitative polymerase chain reaction (PCR), metagenomics, and metatranscriptomics (Fig. 2, Table 1).
Distribution of studies on oral archaeome over the years.
Culture-Independent Methods Used in 35 Studies to Identify Archaea on Oral Samples.
Some studies used >1 method for archaea identification.
FISH, fluorescence in situ hybridization; PCR, polymerase chain reaction; qPCR, quantitative polymerase chain reaction; RT-PCR, reverse transcription polymerase chain reaction; sqRT-PCR, semiquantitative reverse transcription polymerase chain reaction; T-RFLP, terminal restriction fragment length polymorphism.
Although the studies based on PCR report the use of several pairs of primers directed to archaeal 16S rRNA genes, primers targeting other housekeeping genes were also used, such as mcrA (methyl-coenzyme M reductase) found in methanogens and cnp60 (heat shock chaperone 60) from Methanobrevibacter oralis. The archaeal primer pair SDArch0333aS15/SDArch 0958aA19 (Lepp et al. 2004) was the most frequently used, followed by A109f/A934r. Universal primers designed to amplify prokaryotic 16S rRNA gene fragments were also used to investigate saliva and archaeologic dental calculus samples.
Tables 2 and 3 summarize the general features of the included articles, regarding contemporary and archaeological samples, respectively. The results obtained in the different oral sites investigated to date, in health or disease conditions, are discussed in turn.
Qualitative Data Synthesis of the Included Studies on Oral Archaeome From Contemporary Samples (n = 46).
FISH, fluorescence in situ hybridization; OTU, operational taxonomic unit; PCR, polymerase chain reaction; qPCR, quantitative polymerase chain reaction; RT-PCR, reverse transcription polymerase chain reaction; RT-qPCR, quantitative reverse transcription polymerase chain reaction; sqRT-PCR, semiquantitative reverse transcription polymerase chain reaction; SRB, sulfate-reducing bacteria; SSU, small subunit; T-RFLP, terminal restriction fragment length polymorphism.
M. massiliense, Methanobrevibacter massiliense; M. oralis, Methanobrevibacter oralis; M. smithii, Methanobrevibacter smithii; P. gingivalis, Porphyromonas gingivalis; P. intermedia, Prevotella intermedia; T. denticola, Treponema denticola; T. forsythia, Tannerella forsythia
Oral sites: 1 = periodontal sites; 2 = endodontic sites; 3 = saliva; 4 = tongue; 5 = more than 1 oral site evaluated; 6 = dental caries.
Qualitative Data Synthesis of the Included Studies on Oral Archaeome from Ancient Human Samples (n = 4).
FISH, fluorescence in situ hybridization; OTU, operational taxonomic unit; PCR, polymerase chain reaction.
Oral site: 3 = saliva.
Archaea in Periodontal Sites
The first studies that described the presence of archaeal cells on the oral cavity were published in 1987 and 1988, when enrichment cultures of methanogenic “bacteria” were obtained from subgingival (Brusa et al. 1987) and supragingival (Belay et al. 1988) biofilms from healthy individuals, as well as subjects with different severities of periodontal disease. Later, a study investigating subgingival biofilms from healthy individuals resulted in a pure culture of a new methanogenic species, M. oralis (Ferrari et al. 1994), which is now considered the most abundant and frequently found archaea in periodontal sites.
With the advent of PCR and different methods of DNA sequencing, studies regarding the prevalence of archaea in periodontal sites have increased exponentially. Even though some studies from Japan, China, and Germany could not detect archaeal DNA in subgingival biofilm from healthy subjects (Yamabe et al. 2008; Li et al. 2009; Horz et al. 2015), further investigations described archaea in samples from individuals without periodontitis (Brusa et al. 1993; Faveri et al. 2011; Ashok et al. 2013; Göhler et al. 2014; Li et al. 2014; Grine et al. 2018). Although ethnic and dietary aspects have been suggested to influence archaeal abundance (Brusa et al. 1993), current data indicate that archaea are ordinary members of subgingival biofilms, regardless of the geographic location of sampling. Furthermore, Faveri et al. (2011) reported a higher frequency of Methanobrevibacter and Methanobacterium in dental implants with peri-implantitis from Brazilian individuals. However, no differences were observed in the prevalence of methanogens between peri-implantitis and control samples from French subjects (Belkacemi et al. 2018). Archaea were detected exclusively in subgingival plaque from pericoronaritis molars when compared with healthy erupting molars (Mansfield et al. 2012).
Belay and collaborators (1988) were the first to suggest a probable connection between higher proportions of methanogenic archaea and severity of periodontal disease. These findings were corroborated by other studies (Vianna et al. 2008; Ashok et al. 2013; Bringuier et al. 2013; Göhler et al. 2018). Kulik et al. (2001) detected archaeal rDNA in 77% of subgingival plaque samples from 48 patients experiencing varying degrees of periodontitis. The detection frequency of archaea in Japanese patients with aggressive periodontitis was significantly higher than in healthy controls (Yamabe et al. 2008). Although similar prevalence rates were observed in samples from Brazilian patients presenting generalized aggressive periodontitis and periodontally healthy individuals, the proportions of archaea within total prokaryotes were significantly lower in the control group (Matarazzo et al. 2011).
Furthermore, reductions in archaea abundance after periodontal treatment have been described. A significant decrease in the relative abundance of archaea was observed in samples from patients with chronic periodontitis who received scaling and root-planing treatments in comparison with the same sites before treatment (Lepp et al. 2004). The first randomized clinical trial aiming to evaluate changes in the prevalence of archaea after different periodontal therapies for generalized aggressive periodontitis revealed that scaling and root-planing therapy alone or combined with antibiotics were equally effective in reducing the prevalence of archaea 6 mo after treatment (Lira et al. 2013).
The co-occurrence of archaea and other microorganisms in periodontal sites has also been investigated. Robichaux et al. (2003a) reported the concomitant presence of sulfate-reducing bacteria and methanogenic archaea in the oral cavity of subjects with periodontal disease. Later, the co-occurrence of these organisms was shown to be rare in periodontitis subgingival biofilms, being detected in only 3.9% of samples (Vianna et al. 2008). A positive correlation between levels of archaea and Porphyromonas gingivalis as well as Tannerella forsythia was observed in subgingival biofilms of chronic periodontitis (Matarazzo et al. 2012), and the abundance of M. oralis was reported to be at least 10 times higher in patients who also harbored Prevotella intermedia (Horz et al. 2015). Conversely, large proportions of Treponema populations were found at periodontal sites lacking methanogenic archaea (Lepp et al. 2004). Göhler et al. (2014) showed that moderate archaeal abundances on the tongue were associated with a healthy periodontal status, whereas higher abundances correlated with periodontal disease. Those results suggest that archaea can be indirectly linked to periodontal sites in dysbiosis.
In addition to methanogenic archaea, 16S rDNA sequences affiliated to Thermoplasmata were identified in a Chinese patient with periodontitis, suggesting that other types of archaea can colonize periodontal sulcus (Li et al. 2009). When primers directed to Thermoplasmatales 16S rRNA genes were employed, several DNA sequences were retrieved from subgingival biofilms of German adults with different degrees of periodontitis (Horz et al. 2012). A study that evaluated the metatranscriptome of subgingival biofilms revealed that archaeal sequences accounted for 0.22% of the total putative mRNA reads, comprising 0.11% of periodontitis transcripts and 0.27% of healthy subjects’ transcripts. Sequences affiliated to Methanosarcina vacuolata were the most abundant, encountered in periodontitis and health conditions, but only 5 of the 10 detected archaeal sequences were affiliated to methanogenic classes (Deng et al. 2017).
Archaea in Endodontic Sites
Studies evaluating the presence of archaea in endodontic sites have included samples from asymptomatic chronic periradicular lesions and acute periradicular abscesses (Siqueira et al. 2005), necrotic root canals from teeth with apical periodontitis before and after different treatments (Vianna et al. 2006; Paiva et al. 2012; Slaton et al. 2017), infected root canals from symptomatic and asymptomatic patients (Vickerman et al. 2007; Ozok et al. 2012), pulpitis (Efenberger et al. 2015), as well as necrotic root canal samples with primary and after-treatment infections (Jiang et al. 2009; Anderson et al. 2012; Brzezińska-Błaszczyk et al. 2018). Of the 11 studies involving endodontic sites, only 2 reported negative results for the presence of archaea (Siqueira et al. 2005; Anderson et al. 2012). However, after retesting the archaeal primers used by Siqueira et al. (2005), Vianna et al. (2006) observed that M. oralis and Methanobrevibacter smithii were not amplifiable by these primers, suggesting that archaeal sequences could have been overlooked in endodontic samples. Using a different set of primers directed to the 16S rRNA and mcrA genes, these authors were able to detect archaea in endodontic sites from 5 necrotic root canals (Vianna et al. 2006). It has been suggested that the low prevalence and abundance of archaea in root canal systems indicate that these may be not the preferred niches for these microorganisms (Ozok et al. 2012).
A higher prevalence of archaea in persisting or secondary endodontic infections has been reported (Jiang et al. 2009; Brzezińska-Błaszczyk et al. 2018). Given that it is unknown how archaea respond to classical endodontic disinfectants (Horz and Conrads 2011), their presence in endodontic infections could increase the risk of treatment failure.
Other studies have shown that methanogenic archaea are present in inflamed pulp tissues and may participate in the development of endodontic infection (Vianna et al. 2009). Although M. oralis and M. smithii were the most prevalent archaeal species observed in root canals (Vianna et al. 2006; Vickerman et al. 2007; Brzezińska-Błaszczyk et al. 2018), evidence of different methanogens associated with oral infections was found (Efenberger et al. 2015). Furthermore, a positive association between methanogens and Synergistes spp. has been reported in endodontic sites (Efenberger et al. 2015; Brzezińska-Błaszczyk et al. 2018).
Studies suggest that a diverse community, including archaea, might be related to these disorders (Brzezińska-Błaszczyk et al. 2018), although no consistent correlations could be established so far. Given that residual organisms after endodontic treatments may cause persistent infections, the determination of archaea prevalence and roles in these oral sites is of utmost importance, especially in terms of their resistance to the antibiotics and endodontic disinfectants currently used in the treatment of these infections.
Other Oral Sites
Some articles explored the presence of archaea in different niches, such as saliva, tongue, dental caries, and supragingival biofilms. Göhler et al. (2014) compared tongue biofilm from periodontally diseased and healthy subjects, and the results suggested that moderate archaeal abundances in tongue scrapings were associated with a healthy periodontal status, while high archaeal abundances correlated with periodontal disease effects. In a subsequent study comprising tongue scrapings and subgingival pocket samples, archaeal sequences were found 4 times more often in the former in comparison with the latter, with a negative correlation between archaeal relative abundances in tongue samples and mean pocket depths (Göhler et al. 2018). More recently, 16S rDNA sequences affiliated to phylum Thaumarchaeota were detected in carious and healthy-related supragingival biofilms (Dame-Teixeira et al. 2020). A highly significant correlation between the presence of methanogens and tobacco smoking was observed, suggesting that M. oralis and M. smithii were residents of the saliva microbiota and not mere contamination of the investigated samples (Grine et al. 2018).
The detection of methanogenic archaea from aerobic niches may seem controversial, given that these organisms are usually described as strictly anaerobic and extremely oxygen sensitive (Miller and Wolin 1985; Ferrari et al. 1994). However, interactions with aerobic microorganisms may promote a protective effect and allow methanogens to thrive in aerobic sites, with the aerobic cultivation of oral methanogens in the presence of aerobic hydrogen-producing bacteria having been reported (Khelaifia et al. 2016). Furthermore, it has been observed that some Methanobrevibacter species can thrive under microoxic conditions (Seedorf et al. 2004).
Ancient Dental Calculus Samples
In our search, 4 studies that analyzed the presence of archaea in human archaeologic samples were also found (Table 3). DNA sequences from methanogenic archaea were first detected in ancient dental calculus by shotgun sequencing, although in very low relative proportions (Warinner et al. 2014). Later, Ziesemer et al. (2015) analyzed temporally and geographically diverse archaeological dental calculus specimens by 2 approaches: an amplicon metataxonomic analysis targeting the V3 region of prokaryotic 16S rRNA genes and metagenomic shotgun sequencing. The 16S rRNA amplification approach revealed an exceptionally high frequency of Methanobrevibacter sequences when compared with the shotgun approach or amplifications of modern controls. Due to the high-degraded nature of ancient DNA and the fact that M. oralis is the oral taxon with the shortest V3 region, differential PCR amplifications led to extremely high detections of this archaea species in ancient data sets targeting this 16S rRNA gene variable region, which was termed the “Archaea effect” (Ziesemer et al. 2015). A subsequent metagenomic approach by Philips et al. (2017) revealed a higher archaeal diversity in 161 ancient tooth samples from 7 archaeologic sites, including 4 archaeal classes (Methanobacteria, Methanococci, Halobacteria, Thaumarchaeota).
In a study investigating methanogens in dental calculus dated from the 14th to 19th centuries in France, sequences of Methanobrevibacter massiliense (N13) were the most prevalent, followed by M. oralis, a Methanomassiliicoccus luminyensis–like phylotype and Methanoculleus bourgensis (Huynh et al. 2016). Comparisons of M. oralis in these ancient samples with that of modern-day ones indicated that the prevalence of these archaea was lower in ancient populations than in modern populations, while diversity of methanogens in dental calculus seemed to decrease significantly over the course of the past 7 centuries (Huynh et al. 2016). Although little is know about archaea and oral diseases in ancient humans, high proportions of an archaeal species were detected in dental calculus from a Neanderthal specimen with indications of oral diseases (Weyrich et al. 2017), suggesting their putative role in oral infections of our closest hominin relatives. Analyses revealed that the Neanderthal-associated archaeon is a subspecies of the modern human–associated M. oralis and that divergences between these strains may indicate a transfer between the hosts during subsequent interactions (Weyrich et al. 2017).
Discussion
This scoping review aimed to establish the current level of evidence regarding the presence and potential roles of archaea in different sites of the human oral cavity. So far, information regarding these microorganisms and their involvement in oral diseases is still scarce. There are indications that archaea are part of the indigenous microbiota in various oral sites, such as periodontal and endodontic niches, carious dentine, saliva, and tongue, with current data suggesting that abundance of methanogens rises with increasing periodontitis severity. However, many issues concerning archaeal prevalence and diversity in the oral cavity, potential pathogenicity, and interactions with other oral microbial species remain elusive.
It is well established that the diversity of bacterial species and their metabolisms in different oral niches, as well as the abundance of specific groups, conserves the homeostasis within oral biofilms, which can be disrupted by environmental changes and lead to the enrichment of certain species to the detriment of others and eventually the progression of oral diseases (Marsh 2005). The discovery of archaeal cells in oral sites brought another variable that must be considered in oral disorder investigations, since now it is quite clear that archaea are common inhabitants of many oral niches and may be actively involved in the polymicrobial infection process (Grine et al. 2018). Methanogenic archaea interact syntrophically with fermentative bacteria in anaerobic oral biofilms through interspecies hydrogen transfer and therefore could indirectly promote periodontal disease by serving as hydrogen sinks and enable the proliferation of pathogenic bacteria (Lepp et al. 2004). Data regarding the presence of methanogens, sulfate-reducing bacteria, and members of genus Treponema in severe cases of periodontitis suggest antagonistic interactions, as these microorganisms were found to the exclusion of one another in most of the analyzed samples, indicating niche exclusion of methanogens by other hydrogen-metabolizing microbes (Lepp et al. 2004; Vianna et al. 2008).
Even though some aspects regarding archaea in the oral cavity have already been elucidated, 1) the lower abundance and diversity of these microorganisms when compared with oral bacteria and 2) the current difficulties related to archaea identification and cultivation continue to hamper our understanding of this organism’s roles on oral ecosystems. Archaea cultivation is a fastidious process, with few species having been isolated in the laboratory so far. Although methods for the cultivation of methanogens have been developed since the 1930s (Barker 1936), isolation of these organisms, as well as other archaeal groups, is still laborious, expensive, and time-consuming, limiting our access to their diversity and countless biological aspects. The employment of recently proposed improvements for cultivation procedures (Khelaifia et al. 2016; Guindo et al. 2019) with a broader utilization of high-throughput molecular methods may lead to a better characterization of archaea species residing in the oral cavity and their roles.
It is worth mentioning that some of the studies retrieved in this review did not focus on Archaea, using general methodologies for microbial characterization in oral samples and marginally detecting members of this domain (Ozok et al. 2012; Paiva et al. 2012; Wolf et al. 2017). Other works aimed for the detection of single methanogenic species, such as M. oralis, or methanogenic groups, targeting molecular markers or employing culture conditions appropriate for these organisms (Table 1; Vianna et al. 2008; Yamabe et al. 2010; Faveri et al. 2011, Horz and Conrads 2011; Huynh, Nkamga, et al. 2015). Although archaeal diversity in the oral cavity has been suggested to be limited to methanogens (Wade 2013), detections of DNA sequences phylogenetically affiliated to nonmethanogenic archaea have been reported (Li et al. 2009; Dame-Teixeira et al. 2020), indicating that other archaea can colonize oral niches. Thus, given the still low number of studies on the subject and the approaches used to investigate some oral conditions, it is possible that archaeal diversity in the oral cavity could be currently overlooked.
Another point to be considered is the potential methodological biases involved in archaeal identification. Although a predominance of methanogens in the oral cavity, especially from the genus Methanobrevibacter, is inferred from the data available so far, generalizations should be taken with caution. The majority of investigations regarding archaea in oral sites to date were performed through the amplification of archaeal genes with specific primers, especially those targeting 16S rRNA genes. Primer bias is a recognized problem of PCR-based approaches, and it has been pointed out for widely used universal archaeal primers (Fischer et al. 2016). Issues involving DNA extraction protocols, primer selection, and sequence data processing pipelines have also been shown to interfere significantly with archaea detection in human samples (Koskinen et al. 2017). Furthermore, it was observed that 16S rRNA amplicon data sets were not representative of the biodiversity revealed by shotgun sequencing in human and Neanderthal dental calculus samples (Ziesemer et al. 2015; Weyrich et al. 2017). Even though not void of their limitations—such as dismiss of data related to low-abundance microorganisms misinterpreted as contaminations or artifacts (Laurence et al. 2014)—metagenomic analyses, as well as other “omics” approaches, may help to overcome many of the difficulties mentioned here. In this sense, future research employing diversified methodological approaches could significantly improve our comprehension about the human oral archaeome in health and disease conditions.
In conclusion, archaea are common members of the human oral microbiome, inhabiting different oral niches. Although considerably less abundant and diverse than bacteria, archaea and their potential involvements in oral disorders are being increasingly acknowledged. However, due to methodological limitations and the vast employment of approaches preferable to methanogens, archaeal diversity and prevalence in oral samples may be currently underestimated. Future studies focusing on archaeal characterization with diversified methodological approaches are necessary to a better comprehension of the presence, diversity, and functions of this domain of life in different oral sites and conditions.
Author Contributions
A. Belmok, J.A. de Cena, N. Damé-Teixeira, contributed to conception, design, and data analysis, drafted and critically revised the manuscript; C.M. Kyaw, contributed to data analysis, critically revised the manuscript. All authors gave final approval and agree to be accountable for all aspects of the work.
Supplemental Material
DS_10.1177_0022034520910435 – Supplemental material for The Oral Archaeome: A Scoping Review
Supplemental material, DS_10.1177_0022034520910435 for The Oral Archaeome: A Scoping Review by A. Belmok, J.A. de Cena, C.M. Kyaw and N. Damé-Teixeira in Journal of Dental Research
Footnotes
Acknowledgements
The authors thank the University of Brasilia. Débora Azevedo Côrtes is acknowledged for her assistance. A.B. and J.A.C. acknowledge a fellowship from CNPq.
A supplemental appendix to this article is available online.
The authors received no financial support and declare no potential conflicts of interest with respect to the authorship and/or publication of this article.
References
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