Presence of Archaea in dental caries biofilms

Damé‐Teixeira, Nailê; Cena, Jéssica Alves de; Côrtes, Débora Azevedo; Belmok, Aline; Borges, Luiz Gustavo dos Anjos; Marconatto, Letícia; Giongo, Adriana; Kyaw, Cynthia Maria

doi:10.1016/j.archoralbio.2019.104606

Cited by 21 publications

(14 citation statements)

References 45 publications

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“…The low abundance related to these domains in other studies may be linked to the sample collection method, detection probe, pair of primers used, sequencing technique, and low number of sequences registered in current databases (Ghannoum et al, 2010;Heisel et al, 2015;Dame-Teixeira et al, 2020). Furthermore, the study of the microbial community through the use of 16S rRNA sequencing and shotgun metagenomic methods allows analysis of the composition and genetic capabilities of the microbiota, but not the particularities of the role of low abundance in the microbial community, and of microbial community interactions (Centanni et al, 2018).…”

Section: Low-abundance Of Other Organismsmentioning

confidence: 99%

Low-Abundant Microorganisms: The Human Microbiome’s Dark Matter, a Scoping Review

Cena

Zhang

Deng

et al. 2021

Front. Cell. Infect. Microbiol.

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Research on the human microbiome has mainly been restricted to the identification of most abundant microbiota associated with health or disease. Their abundance may reflect their capacity to exploit their niche, however, metabolic functions exerted by low-abundant microrganisms can impact the dysbiotic signature of local microbial habitats. This scoping review aims to map the literature regarding the management of low-abundant microorganisms in studies investigating human microbiome samples. A systematic literature search was performed in 5 electronic databases, as well as grey literature. We selected clinical microbiome studies targeting human participants of any age, from any body site. We also included studies with secondary data which originated from human biofilm samples. All of the papers used next-generation sequencing (NGS) techniques in their methodology. A total of 826 manuscripts were retrieved, of which 42 were included in this review and 22 reported low-abundant bacteria (LB) in samples taken from 7 body sites (breast, gut, oral cavity, skin, stomach, upper respiratory tract (URT), and vagina). Four studies reported microbes at abundance levels between 5 and 20%, 8 studies reported between 1 and 5%, and 18 studies reported below 1%. Fifteen papers mentioned fungi and/or archaea, and from those only 4 (fungi) and 2 (archaea) produced data regarding the abundance of these domains. While most studies were directed towards describing the taxonomy, diversity and abundance of the highly abundant species, low-abundant species have largely been overlooked. Indeed, most studies select a cut-off value at <1% for low-abundant organisms to be excluded in their analyses. This practice may compromise the true diversity and influence of all members of the human microbiota. Despite their low abundance and signature in biofilms, they may generate important markers contributing to dysbiosis, in a sort of ‘butterfly effect’. A detailed snapshot of the physiological, biological mechanisms at play, including virulence determinants in the context of a dysbiotic community, may help better understand the health-disease transition.

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Section: Low-abundance Of Other Organismsmentioning

confidence: 99%

Low-Abundant Microorganisms: The Human Microbiome’s Dark Matter, a Scoping Review

Cena

Zhang

Deng

et al. 2021

Front. Cell. Infect. Microbiol.

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“…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 andConrads 2011;. 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.…”

Section: Discussionmentioning

confidence: 99%

“…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 healthyrelated 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).…”

Section: Other Oral Sitesmentioning

confidence: 93%

The Oral Archaeome: A Scoping Review

et al. 2020

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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.

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“…However, these microbial species are largely under-represented when compared to the larger diversity of bacterial taxa. Methanobrevibacter oralis thrives in various niches within the oral cavity 26 .…”

Section: Fungimentioning

confidence: 99%

Importance of Interkingdom Interactions Among Oral Microbiome Towards Caries Development – A Review

Balakrishnan¹,

Sivanesan²,

Mohan³

et al. 2021

J Immunol Sci

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The human microbiome plays a crucial role in health and disease conditions. These microbiomes constitute a structured, coordinated microbial network throughout the human body. The oral cavity harbors one of the extensively diverse bacteria in the human system. Although many studies emphasize bacteriome and its interaction with the host system, very little attention is given to candidate phyla radiation (CPR), fungal components, and its interkingdom interaction in the oral microecology even with advanced techniques. The interkingdom interactions among caries causing microbes trigger the pathogenesis of bacterial diseases and cause ecological shifts and affect the host system. Studying the complex relations among the diverse oral microbiome and its host, especially CPR phyla and fungi, would give a holistic view of the caries etiology. This review provides evidence on the interkingdom interaction that establishes a complex community that could help predict future oral and systemic diseases.

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Presence of Archaea in dental caries biofilms

Cited by 21 publications

References 45 publications

Low-Abundant Microorganisms: The Human Microbiome’s Dark Matter, a Scoping Review

Low-Abundant Microorganisms: The Human Microbiome’s Dark Matter, a Scoping Review

The Oral Archaeome: A Scoping Review

Importance of Interkingdom Interactions Among Oral Microbiome Towards Caries Development – A Review

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