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OBJECTIVE: The complete picture of how the human microbiome interacts with its host is still largely unknown, particularly concerning microorganisms beyond bacteria. Although existing in very low abundance and not directly linked to causing diseases, archaea have been detected in various sites of the human body, including the gastrointestinal tract, oral cavity, skin, eyes, respiratory and urinary systems. But what exactly are these microorganisms? In the early 1990 s, archaea were classified as a distinct domain of life, sharing a more recent common ancestor with eukaryotes than with bacteria. While archaea's presence and potential significance in Dentistry remain under-recognized, there are concerns that they may contribute to oral dysbiosis. However, detecting archaea in oral samples presents challenges, including difficulties in culturing, the selection of DNA extraction methods, primer design, bioinformatic analysis, and databases. DESIGN: This is a comprehensive review on the oral archaeome, presenting an in-depth in silico analysis of various primers commonly used for detecting archaea in human body sites. RESULTS: Among several primer pairs used for detecting archaea in human samples across the literature, only one specifically designed for detecting methanogenic archaea in stool samples, exhibited exceptional coverage levels for the domain and various archaea phyla. CONCLUSIONS: Our in silico analysis underscores the need for designing new primers targeting not only methanogenic archaea but also nanoarchaeal and thaumarchaeota groups to gain a comprehensive understanding of the archaeal oral community. By doing so, researchers can pave the way for further advancements in the field of oral archaeome research.
Assuntos
Archaea , Microbiota , Humanos , Archaea/genética , Bactérias , Boca , Odontologia , FilogeniaRESUMO
INTRODUCTION: The controversial issue of whether the Archaea domain plays a role in endodontic infections is the focus of this systematic review with meta-analysis. The aim is to emphasize the significance of minority microbial domains in oral dysbiosis by evaluating the prevalence of archaea in root canals and its association with clinical parameters such as symptomatology and type of endodontic infection. METHODS: The search strategy involved researching 6 databases and the gray literature. Publications were accepted in any year or language that identified archaea in samples from endodontic canals. A 2-step selection process narrowed the final choice to 16 articles. The methodological quality of the studies was evaluated using tools from the Joanna Briggs Institute, and the certainty of evidence was assessed using the Grading of Recommendations, Assessment, Development, and Evaluation (GRADE) approach. RESULTS: The results showed that archaea were present in 20% (95% [confidence interval] CI = 8%-32%) of individuals with endodontic samples analyzed. The samples were about twice as likely to be archaeal-positive if collected from individuals with primary vs. persistent/secondary infection (odds ratio = 2.33; 95% CI = 1.31-4.14; I2 = 0%), or individuals with self-reported vs. symptom-free infections (odds ratio = 2.67; 95% CI = 1.47-4.85; I2 = 0%). Methanogenic archaea were reported in 66% of the included studies. Representative members of phyla Thaumarchaeota and Crenarchaeota were also identified. CONCLUSIONS: Archaea are present in about one-fifth of the infected root canals. Recognized biases in experimental approaches for researching archaea must be addressed to understand the prevalence and roles of archaea in endodontic infections, and to determine whether the decontamination process should include the elimination or neutralization of archaea from root canals (International Prospective Register of Systematic Reviews protocol = CRD42021264308).
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Recently, we have published a scoping review on the oral archaeome, showing that these microorganisms inhabit various oral niches, including periodontal sites. In order to reinforce the importance of the Archaea domain and alert the scientific community about the importance of inter-domain relationships in oral dysbiosis, we have performed meta-analyses evaluating the prevalence of archaea in periodontal diseases (PROSPERO protocol: CRD42020213109). A systematic search in the literature was conducted in several databases and in grey literature, retrieving 30 reports on periodontal archaeome, published from 1980 to 2020. The methodological quality of included studies and the certainty of evidence were evaluated by using validated tools. Most studies focused on the detection of methanogens, revealing that the diversity of the periodontal archaeome is currently underestimated. Two meta-analyses concluded that individuals with periodontitis are prone to have archaeal-positive subgingival biofilms when compared to periodontally healthy individuals (OR 6.68, 95% CI 4.74-9.41 for 16S rRNA gene analysis and OR 9.42, 95% CI 2.54-34.91 for mcrA gene analysis). Despite the archaeal enrichment in sites with periodontitis, less than half of the individuals with periodontitis tested positive for archaeal DNA (general estimative of 46%; 95% CI 36-56%). Conventional treatment for periodontitis reduced the archaeal population, but systemic antibiotics used as adjunctive therapy did not increase its effectiveness. Hence, it could conceivably be hypothesised that archaea are secondary colonizers of areas with dysbiosis, probably flourishing in the inflammatory environment. Due to their lower prevalence, archaeal cells are probably underestimated by the current detection protocols. It may also be speculated that archaea do not have a single central role in the infection, with bacterial cells directly involved in that role. New studies are necessary, with different methodological approaches, to explore the underestimated diversity of the oral archaeome.