Reduction in prevalence of Archaea after periodontal therapy in subjects with generalized aggressive periodontitis

New putative periodontopathogens and periodontal health-associated species: A systematic review and meta-analysis

To investigate the existence of any association between new putative periodontal pathogens and periodontitis. Two independent reviewers conducted electronic literature searches in the MEDLINE (PubMed), EMBASE, DOSS and Google Scholar databases as well as a manual search to identify eligible clinical studies prior to November 2022. Studies comparing the prevalence of microorganisms other than the already-known periodontal pathogens in subgingival plaque and/or saliva samples between subjects with periodontitis and subject with periodontal health were included. Meta-analyses were performed on data provided by the included studies. Fifty studies including a total of 2739 periodontitis subjects and 1747 subjects with periodontal health were included. The Archaea domain and 25 bacterial species (Anaeroglobus geminatus, Bacteroidales [G-2] bacterium HMT 274, Desulfobulbus sp. HMT 041, Dialister invisus, Dialister pneumosintes, Eubacterium brachy, Enterococcus faecalis, Eubacterium nodatum, Eubacterium saphenum, Filifactor alocis, Fretibacterium sp. HMT 360, Fretibacterium sp. HMT 362, Mogibacterium timidum, Peptoniphilaceae sp. HMT 113, Peptostreptococcus stomatis, Porphyromonas endodontalis, Slackia exigua, Streptococcus gordonii, Selenomonas sputigena, Treponema amylovorum, Treponema lecithinolyticum, Treponema maltophilum, Treponema medium, Treponema parvum and Treponema socranskii) were found to be statistically significantly associated with periodontitis. Network studies should be conducted to investigate the role of these newly identified periodontitis-associated microorganisms through interspecies interaction and host-microbe crosstalk analyses.

Bacteria and Methanogens in the Human Microbiome: a Review of Syntrophic Interactions

Methanogens are microorganisms belonging to the Archaea domain and represent the primary source of biotic methane. Methanogens encode a series of enzymes which can convert secondary substrates into methane following three major methanogenesis pathways. Initially recognized as environmental microorganisms, methanogens have more recently been acknowledged as host-associated microorganisms after their detection and initial isolation in ruminants in the 1950s. Methanogens have also been co-detected with bacteria in various pathological situations, bringing their role as pathogens into question. Here, we review reported associations between methanogens and bacteria in physiological and pathological situations in order to understand the metabolic interactions explaining these associations. To do so, we describe the origin of the metabolites used for methanogenesis and highlight the central role of methanogens in the syntrophic process during carbon cycling. We then focus on the metabolic abilities of co-detected bacterial species described in the literature and infer from their genomes the probable mechanisms of their association with methanogens. The syntrophic interactions between bacteria and methanogens are paramount to gut homeostasis. Therefore, any dysbiosis affecting methanogens might impact human health. Thus, the monitoring of methanogens may be used as a bio-indicator of dysbiosis. Moreover, new therapeutic approaches can be developed based on their administration as probiotics. We thus insist on the importance of investigating methanogens in clinical microbiology.

Probing periodontal microbial dark matter using metataxonomics and metagenomics

Our view of the periodontal microbial community has been shaped by a century or more of cultivation-based and microscopic investigations. While these studies firmly established the infection-mediated etiology of periodontal diseases, it was apparent from the very early days that periodontal microbiology suffered from what Staley and Konopka described as the "great plate count anomaly", in that these culturable bacteria were only a minor part of what was visible under the microscope. For nearly a century, much effort has been devoted to finding the right tools to investigate this uncultivated majority, also known as "microbial dark matter". The discovery that DNA was an effective tool to "see" microbial dark matter was a significant breakthrough in environmental microbiology, and oral microbiologists were among the earliest to capitalize on these advances. By identifying the order in which nucleotides are arranged in a stretch of DNA (DNA sequencing) and creating a repository of these sequences, sequence databases were created. Computational tools that used probability-driven analysis of these sequences enabled the discovery of new and unsuspected species and ascribed novel functions to these species. This review will trace the development of DNA sequencing as a quantitative, open-ended, comprehensive approach to characterize microbial communities in their native environments, and explore how this technology has shifted traditional dogmas on how the oral microbiome promotes health and its role in disease causation and perpetuation.

Methanogenic Archaea: Emerging Partners in the Field of Allergic Diseases

Archaea, which form one of four domains of life alongside Eukarya, Bacteria, and giant viruses, have long been neglected as components of the human microbiota and potential opportunistic infectious pathogens. In this review, we focus on methanogenic Archaea, which rely on hydrogen for their metabolism and growth. On one hand, methanogenic Archaea in the gut are functional associates of the fermentative digestion of dietary fibers, favoring the production of beneficial short-chain fatty acids and likely contributing to the weaning reaction during the neonatal window of opportunity. On the other hand, methanogenic Archaea trigger the activation of innate and adaptive responses and the generation of specific T and B cells in animals and humans. In mouse models, lung hypersensitivity reactions can be induced by inhaled methanogenic Archaea mimicking human professional exposure to organic dust. Changes in methanogenic Archaea of the microbiota are detected in an array of dysimmune conditions comprising inflammatory bowel disease, obesity, malnutrition, anorexia, colorectal cancer, and diverticulosis. At the subcellular level, methanogenic Archaea are activators of the TLR8-dependent NLRP3 inflammasome, modulate the release of antimicrobial peptides and drive the production of proinflammatory, Th-1, Th-2, and Th-17 cytokines. Our objective was to introduce the most recent and major pieces of evidence supporting the involvement of Archaea in the balance between health and dysimmune diseases, with a particular focus on atopic and allergic conditions.

The Oral Archaeome: A Scoping Review

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.

Gingival recession after scaling and root planing with or without systemic metronidazole and amoxicillin: a re-review

BACKGROUND

Gingival recessions inevitably occur during healing after scaling and root planing, but synoptic data on this topic is still lacking. This review compared the recession formation with and without the administration of systemic antibiotics.

OBJECTIVES

To evaluate the formation of recession with and without the administration of antibiotics during the healing after scaling and root planing.

MATERIALS AND METHODS

This study re-analyzed publications that reported clinical attachment levels (CAL) and probing pocket depths (PD) up to January 2019, including the pivotal review by Zandbergen and co-workers (2013). Whereas these studies traditionally focused on PD and CAL, the present analysis compared recession formation (ΔREC) after adjunctive systemic administration of amoxicillin (amx) and metronidazole (met) during scaling and root planing (SRP) and SRP alone. The mean increase in ΔREC, if not reported, was calculated from CAL and PD values and statistically analyzed. Recession formation was compared after 3 and 6 months after therapy. Results were separately reported for chronic periodontitis (CP) as well as aggressive periodontitis (AP) cases.

RESULTS

Recessions increased consistently between baseline and follow-up. In the AP group, median ΔREC was 0.20 mm after 3 months, irrespective of whether antibiotics were administered or not. After 6 months, median ΔREC increased to 0.35 mm after AB and remained stable at 0.20 mm with SRP alone. In the CP group, after 3 months with and without antibiotics, median ΔREC accounted for 0.30 mm and 0.14 mm, respectively. After 6 months, median ΔREC accounted for 0.28 mm (with AB) and 0.20 mm (without AB). The quantitative assessment by meta-analyses also yielded small values (≤ 0.25 mm) for the estimated differences in recession formation between AB and noAB; however, none of them reached statistical significance.

CONCLUSIONS

Although a slight tendency towards higher recession formation after SRP in combination with AB could be observed in many studies, quantitative meta-analyses showed no clinically relevant difference in recession formation due to the administration of AB. In general, the description and discussion of recessions in the literature seems not to be a major focus so far.

CLINICAL RELEVANCE

Since the preservation of gingival tissues is important by preventive and therapeutic means, e.g., when avoiding postoperative root sensitivity or performing regenerative surgery, these aspects should not be neglected. We thus suggest to report REC measurements along with PD and CAL values for more direct recession formation (ΔREC) assessments in the future.

A brief history of periodontics in the United States of America: Pioneers and thought-leaders of the past, and current challenges

This paper summarizes historical events in periodontology in the United States over the past 200 years. The contributions of some of the key thought-leaders of the past are highlighted. Throughout the 20th century, the evolution of thought, leading to the views currently held regarding the pathogenesis and treatment of periodontal diseases, was significantly influenced by: (1) major changes in health-care education; (2) the emergence of periodontics as a specialty of dentistry; (3) the publication of peer-reviewed journals with an emphasis on periodontology; (4) formation of the National Institute of Dental and Craniofacial Research (NIDCR); and (5) expansion of periodontal research programs by the NIDCR. The two major future challenges facing periodontal research are development of a better understanding of the ecological complexities of host-microbial interactions in periodontal health and disease, and identification of the relevant mechanisms involved in the predictable regeneration of damaged periodontal tissues.

Effects of different periodontal treatments in changing the prevalence and levels of Archaea present in the subgingival biofilm of subjects with periodontitis: A secondary analysis from a randomized controlled clinical trial

OBJECTIVE

The aim of this randomized double-blind and placebo-controlled study was to assess if periodontal treatment with or without systemic antibiotic would change the mean level of Archaea.

METHODS

Fifty-nine (59) subjects were randomly assigned to receive scaling and root planing (SRP) alone or combined with metronidazole (MTZ; 400 mg/TID) or either with MTZ and amoxicillin (AMX; 500 mg/TID) for 14 days. Clinical and microbiological examinations were performed at baseline and at 6 months post-SRP. Six subgingival plaque samples per subject were analysed for the presence and levels of Archaea using quantitative polymerase chain reaction.

RESULTS

Scaling and root planing alone or combined with MTZ or MTZ + AMX significantly reduced the prevalence of subjects colonized by Archaea at 6 months post-therapy, without significant differences among groups (P > .05). Both therapies led to a statistically significant decrease in the mean percentage of sites colonized by Archaea (P < .05). The MTZ and MTZ + AMX group had a significantly lower mean number of sites colonized by Archaea and lower levels of these micro-organisms at sites with probing depth ≥5 mm at 6 months compared with SRP group (P < .05).

CONCLUSION

Periodontal treatments including adjunctive MTZ or MTZ + AMX are more effective than mechanical treatment alone in reducing the levels and prevalence of sites colonized by Archaea in subjects with chronic periodontitis.

Presence of archaea and selected bacteria in infected root canal systems

Infections of the root canal have polymicrobial etiology. The main group of microflora in the infected pulp is bacteria. There is limited data that archaea may be present in infected pulp tissue. The aim of this study was to check the prevalence of archaea in necrotic root canal samples obtained from patients with primary or post-treatment infection. The prevalence of selected bacteria species (Prevotella intermedia, Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, Synergistes sp.) in necrotic samples was evaluated as well. Sixty-four samples from root canal were collected for DNA and RNA extraction. A PCR assay based on the 16S rRNA gene was used to determine the presence of archaea and selected bacteria. Of the 64 samples, 6 were analyzed by semiquantitative reverse transcription PCR to estimate expression profiles of 16S rRNA, and another 9 were selected for direct sequencing. Archaea were detected in 48.4% samples. Statistical analysis indicated a negative association in coexistence between archaea and Treponema denticola (P < 0.05; Pearson’s χ2 test). The main representative of the Archaea domain found in infected pulp tissue was Methanobrevibacter oralis. Archaea 16S rRNA gene expression was significantly lower than Synergistes sp., Porphyromonas gingivalis, and Tannerella forsythia (P < 0.05; Student’s t test). Thus, it can be hypothesized that archaea may participate in the endodontic microbial community.

The concomitant administration of systemic amoxicillin and metronidazole compared to scaling and root planing alone in treating periodontitis: =a systematic review=

Background

The treatment of periodontitis begins with a non-surgical phase that includes scaling and root planing(SRP) and on occasion the use of systemic antibiotics. The goal was to systematically evaluate in systemic healthy adults the effect of the concomitant administration of amoxicillin (amx) and metronidazole (met) adjunctive to SRP compared to SRP alone.

Methods

The PubMed-MEDLINE, Cochrane-CENTRAL and EMBASE databases were searched up to November 2014 to identify appropriate studies. Probing Pocket Depth (PD), Clinical Attachment Level (CAL), Bleeding on Pocket Probing(BOP) and Plaque Indices(PI) were selected as outcome variables. Based on the extracted data a meta-analysis was conducted.

Results

A total of 526 unique articles were found, 20 studies met the eligibility criteria. A meta-analysis showed that SRP + amx + met provided significantly better effects overall and more pronounced PD reduction in periodontal pockets initially measuring ≥6 mm (DiffM:-0.86 mm, p < 0.00001) and gain in CAL(DiffM:+0.75 mm, p = 0.0001). The meta-analysis for the secondary inflammatory parameter BOP showed that SRP + amx + met provided full mouth significantly greater reduction in BOP than SRP alone (DiffM:-6.98 %, p = 0.0001).

Conclusion

Adjunctive systemic amoxicillin and metronidazole medication to SRP significantly improved the clinical outcomes with respect to mean PD, CAL and BOP compared to SRP alone. There is moderate to strong evidence in support of the recommendation that adjunctive amx + met therapy to SRP significantly improves the clinical outcomes, with respect to mean PD and CAL compared to SRP alone especially in initially deep (≥6 mm) pockets. No major side effects associated with the intake of amx + met were reported. This treatment regimen is an efficacious, minimally invasive, practical and inexpensive approach for periodontitis therapy. The key components are mechanical tooth and pocket debridement, supportive treatment of the disease with systemic antibiotics and attention to proper self-care.

Electronic supplementary material

The online version of this article (doi:10.1186/s12903-015-0123-6) contains supplementary material, which is available to authorized users.

Archaea and the human gut: New beginning of an old story

Methanogenic archaea are known as human gut inhabitants since more than 30 years ago through the detection of methane in the breath and isolation of two methanogenic species belonging to the order Methanobacteriales, Methanobrevibacter smithii and Methanosphaera stadtmanae. During the last decade, diversity of archaea encountered in the human gastrointestinal tract (GIT) has been extended by sequence identification and culturing of new strains. Here we provide an updated census of the archaeal diversity associated with the human GIT and their possible role in the gut physiology and health. We particularly focus on the still poorly characterized 7^th order of methanogens, the Methanomassiliicoccales, associated to aged population. While also largely distributed in non-GIT environments, our actual knowledge on this novel order of methanogens has been mainly revealed through GIT inhabitants. They enlarge the number of final electron acceptors of the gut metabolites to mono- di- and trimethylamine. Trimethylamine is exclusively a microbiota-derived product of nutrients (lecithin, choline, TMAO, L-carnitine) from normal diet, from which seems originate two diseases, trimethylaminuria (or Fish-Odor Syndrome) and cardiovascular disease through the proatherogenic property of its oxidized liver-derived form. This therefore supports interest on these methanogenic species and its use as archaebiotics, a term coined from the notion of archaea-derived probiotics.

The oral microbiome diversity and its relation to human diseases

As one of the most clinically relevant human habitats, the human mouth is colonized by a set of microorganisms, including bacteria, archaea, fungi, and viruses. Increasing evidence has supported that these microbiota contribute to the two commonest oral diseases of man (dental caries and periodontal diseases), presenting significant risk factors to human health conditions, such as tumor, diabetes mellitus, cardiovascular diseases, bacteremia, preterm birth, and low birth weight in infants. It is widely accepted that oral microorganisms cause diseases mainly by a synergistic or cooperative way, and the interspecies interactions within the oral community play a crucial role in determining whether oral microbiota elicit diseases or not. Since a comprehensive understanding of the complex interspecies interactions within a community needs the knowledge of its endogenous residents, a plenty of research have been carried out to explore the oral microbial diversity. In this review, we focus on the recent progress in this field, including the oral microbiome composition and its association with human diseases.