The Oral Archaeome: A Scoping Review

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.

Oral Phenotype and Salivary Microbiome of Individuals With Papillon–Lefèvre Syndrome

“…Our study is the first report on the presence of high abundance of Archaea in the human salivary microbiome. Although mostly methanogen Archaea has been detected at the oral cavity so far ( Belmok et al., 2020 ), and other signs of archaeal presence in oral samples were associated with samples contamination, the high abundance of Caldivirga and Sulfophobococcus represents evidence of the importance of those organisms (or their taxonomic-related), possibly associated with dysbiotic sites. Crenarchaeota was already detected in human fecal samples, suggesting their presence in the microbiota of the human digestive ecosystem ( Rieu-Lesme et al., 2005 ).…”

Arqueas y virus en la enfermedad periodontal. Revisión de la literatura

“…En un principio se impulsó la idea de que las arqueas estaban restringidas a ambientes extremos (extremofilos) 6 . Sin embargo, el uso de genes 16S rRNA para identificar microorganismos en ambientes naturales ha revelado que las arqueas son organismos ubicuos con roles esenciales en los ciclos biogeoquímicos globales 7 .…”

“…Se ha considerado que la cavidad bucal posee la segunda microbiota más compleja del cuerpo humano, precedida por la del colón, y proliferan en el intestino desde el período neonatal como entidad comensal 1,6 . Los miembros arqueas, fueron reportados por primera vez en el intestino mucho antes de su reconocimiento como dominio 7 . Estos organismos también se han detectado en varios sitios del cuerpo humano como piel, vías respiratorias, vagina y cavidad bucal 6 .…”

“…Por su parte, Methanobrevibacter massiliense es uno de esos metanógenos aún no cultivados que se detecta al estudiar muestras de biopelícula dental subgingival y se ha aislado en pacientes con periodontitis. También, se ha informado presencia de estos microorganismos en biopelículas supragingivales, lengua, saliva, dentina cariada y calculo dental 7,9 .…”

“…Se ha demostrado que la presencia de arqueas en la lengua está asociada a salud, mientras que una mayor cantidad de los microrganismos se correlaciona con enfermedad periodontal. Esto sugiere que las arqueas pueden estar indirectamente vinculadas a sitios periodontales en la disbiosis 7 .…”