Prevalence and microbiological diversity of Archaea in peri-implantitis subjects by 16S ribosomal RNA clonal analysis

Symbiosis Between the Oral Microbiome and the Human Host: Microbial Homeostasis and Stability of the Host

The oral cavity presents a highly diverse microbial composition. All the three domains of life, Bacteria, Eukarya, and Archaea, as well as viruses constitute the oral microbiome. Bacteria are among the most abundant microorganisms in the oral cavity, followed by viruses, fungi, and Archaea. These microorganisms tend to live in harmony with each other and with the host by preventing the colonization of oral sites by exogenous microorganisms. Interactions between the host and its microbiota are crucial for keeping ecological stability in the oral cavity and a condition compatible with oral health. This chapter focuses on describing the oral microbiota in healthy individuals based on both targeted and nontargeted genome sequencing methods and the functional activity played by those microorganisms based on metagenomic, metatranscriptomic, metaproteomic, and metabolomic analyses. Additionally, this chapter explores mutualistic and antagonistic microbe-microbe relationships. These interactions are mediated by complex mechanisms like cross-feeding networks, production of bacteriocins and secondary metabolites, synthesis of pH-buffering compounds, and the use of universal signaling molecules. At last, the role played by host-microbe interactions on colonization resistance and immune tolerance will help provide a better understanding about the harmonious and peaceful coexistence among host and microbial cells under oral health-related conditions.

Methanobrevibacter oralis: a comprehensive review

Methanobrevibacter oralis (M. oralis) has predominated human oral microbiota methanogenic archaea as far back as the Palaeolithic era in Neanderthal populations and gained dominance from the 18th century onwards. M. oralis was initially isolated from dental plaque samples collected from two apparently healthy individuals allowing its first characterization. The culture of M. oralis is fastidious and has been the subject of several studies to improve its laboratory growth. Various PCR methods are used to identify M. oralis, targeting either the 16S rRNA gene or the mcrA gene. However, only one RTQ-PCR system, based on a chaperonin gene, offers specificity, and allows for microbial load quantification. Next-generation sequencing contributed five draft genomes, each approximately 2.08 Mb (±0.052 Mb) with a 27.82 (±0.104) average GC%, and two ancient metagenomic assembled genomes. M. oralis was then detected in various oral cavity sites in healthy individuals and those diagnosed with oral pathologies, notably periodontal diseases, and endodontic infections. Transmission pathways, possibly involving maternal milk and breastfeeding, remain to be clarified. M. oralis was further detected in brain abscesses and respiratory tract samples, bringing its clinical significance into question. This review summarizes the current knowledge about M. oralis, emphasizing its prevalence, associations with dysbiosis and pathologies in oral and extra-oral situations, and symbiotic relationships, with the aim of paving the way for further investigations.

Polyphasic molecular approach to the characterization of methanogens in the saliva of Tunisian adults

OBJECTIVES

Methanogenic archaea are a minor component of human oral microbiota. Due to their relatively low abundance, the detection of these neglected microorganisms is challenging. This study concerns the presence of methanogens in salivary samples collected from Tunisian adults to evaluate their prevalence and burden using a polyphasic molecular approach.

METHODS

A total of 43 saliva samples were included. Metagenomic and standard 16S rRNA sequencing were performed as an initial screening to detect the presence of methanogens in the oral microbiota of Tunisian adults. Further investigations were performed using specific quantitative real-time PCR targeting Methanobrevibacter oralis and Methanobrevibacter smithii.

RESULTS

Methanobrevibacter was detected in 5/43 (11.62 %) saliva samples after metagenomic 16S rRNA data analysis. The presence of M. oralis was confirmed in 6/43 samples by standard 16S rRNA sequencing. Using real-time PCR, methanogens were detected in 35/43 (81.39 %) samples, including 62.79 % positive for M. oralis and 76.74 % positive for M. smithii. These findings reflect the high prevalence of both methanogens, revealed by the high sensitivity of the real-time PCR approach. Interestingly, we also noted a significant statistical association between the detection of M. smithii and poor adherence to a Mediterranean diet, indicating the impact of diet on M. smithii prevalence.

CONCLUSION

Our study showed the presence of methanogens in the oral microbiota of Tunisian adults with an unprecedented relatively high prevalence. Choice of methodology is also central to picturing the real prevalence and diversity of such minor taxa in the oral microbiota.

Methanobrevibacter massiliense and Pyramidobacter piscolens Co-Culture Illustrates Transkingdom Symbiosis

Among oral microbiota methanogens, Methanobrevibacter massiliense (M. massiliense) has remained less studied than the well-characterised and cultivated methanogens Methanobrevibacter oralis and Methanobrevibacter smithii. M. massiliense has been associated with different oral pathologies and was co-isolated with the Synergistetes bacterium Pyramidobacter piscolens (P. piscolens) in one case of severe periodontitis. Here, reporting on two additional necrotic pulp cases yielded the opportunity to characterise two co-cultivated M. massiliense isolates, both with P. piscolens, as non-motile, 1-2-µm-long and 0.6-0.8-µm-wide Gram-positive coccobacilli which were autofluorescent at 420 nm. The two whole genome sequences featured a 31.3% GC content, gapless 1,834,388-base-pair chromosome exhibiting an 85.9% coding ratio, encoding a formate dehydrogenase promoting M. massiliense growth without hydrogen in GG medium. These data pave the way to understanding a symbiotic, transkingdom association with P. piscolens and its role in oral pathologies.

Human associated Archaea: a neglected microbiome worth investigating

The majority of research in the field of human microbiota has predominantly focused on bacterial and fungal communities. Conversely, the human archaeome has received scant attention and remains poorly studied, despite its potential role in human diseases. Archaea have the capability to colonize various human body sites, including the gastrointestinal tract, skin, vagina, breast milk, colostrum, urinary tract, lungs, nasal and oral cavities. This colonization can occur through vertical transmission, facilitated by the transfer of breast milk or colostrum from mother to child, as well as through the consumption of dairy products, organic produce, salty foods, and fermented items. The involvement of these microorganisms in diseases, such as periodontitis, might be attributed to their production of toxic compounds and the detoxification of growth inhibitors for pathogens. However, the precise mechanisms through which these contributions occur remain incompletely understood, necessitating further studies to assess their impact on human health.

Presence of methanogenic archaea in necrotic root canals of patients with or without type 2 diabetes mellitus

Theoretically, a necrotic root canal fulfils all requirements as a niche for methanogens to inhabit. However, their presence in it and its implication in apical periodontitis (AP) is controversial. Therefore, to contribute to ending the controversy, this study aimed to detect and compare methanogens' presence in two distinct niches with supposedly different microenvironments; both were necrotic root canals associated with AP but one from patients with type 2 diabetes mellitus (T2DM) while the other from non-diabetic patients. A clinical examination was performed on 65 T2DM patients and 73 non-diabetic controls. Samples from necrotic root canals were obtained, and methanogens were identified. The presence of methanogens was three times higher (27.6%) in the T2DM group than in non-diabetic patients (8.2%). In addition, methanogens' presence was associated with a higher prevalence of periapical symptoms.

The Microbiome of Peri-Implantitis: A Systematic Review of Next-Generation Sequencing Studies

(1) Introduction: Current evidence shows that mechanical debridement augmented with systemic and topical antibiotics may be beneficial for the treatment of peri-implantitis. The microbial profile of peri-implantitis plays a key role in identifying the most suitable antibiotics to be used for the treatment and prevention of peri-implantitis. This systematic review aimed to summarize and critically analyze the methodology and findings of studies which have utilized sequencing techniques to elucidate the microbial profiles of peri-implantitis. (2) Results: Fusobacterium, Treponema, and Porphyromonas sp. are associated with peri-implantitis. Veillonella sp. are associated with healthy implant sites and exhibit a reduced prevalence in deeper pockets and with greater severity of disease progression. Streptococcus sp. have been identified both in diseased and healthy sites. Neisseria sp. have been associated with healthy implants and negatively correlate with the probing depth. Methanogens and AAGPRs were also detected in peri-implantitis sites. (3) Methods: The study was registered with the International Prospective Register of Systematic Reviews (PROSPERO) (CRD42023459266). The PRISMA criteria were used to select articles retrieved from a systematic search of the Scopus, Cochrane, and Medline databases until 1 August 2023. Title and abstract screening was followed by a full-text review of the included articles. Thirty-two articles were included in the final qualitative analysis. (4) Conclusions: A distinct microbial profile could not be identified from studies employing sequencing techniques to identify the microbiome. Further studies are needed with more standardization to allow a comparison of findings. A universal clinical parameter for the diagnosis of peri-implantitis should be implemented in all future studies to minimize confounding factors. The subject pool should also be more diverse and larger to compensate for individual differences, and perhaps a distinct microbial profile can be seen with a larger sample size.

In-vitro polymicrobial oral biofilm model represents clinical microbial profile and disease progression during implant-related infections

AIM

Clinically relevant in-vitro biofilm models are essential and valuable tools for mechanistically dissecting the etiopathogenesis of infectious diseases and test new antimicrobial therapies. Thus, the aim of this study was to develop and test a clinically relevant in-vitro oral polymicrobial biofilm model that mimics implant-related infections in terms of microbial profile.

METHODS AND RESULTS

For this purpose, 24-well plate system was used to model oral biofilms, using three different microbial inoculums to grow in-vitro biofilms: (1) human saliva from periodontally healthy patients; (2) saliva as in inoculum 1 + Porphyromonas gingivalis strain; and (3) supra and subgingival biofilm collected from peri-implant sites of patients diagnosed with peri-implantitis. Biofilms were grown to represent the dynamic transition from an aerobic to anaerobic community profile. Subsequently, biofilms were collected after each phase and evaluated for microbiological composition, microbial counts, biofilm biomass, structure, and susceptibility to chlorhexidine (CHX). Results showed higher live cell count (P < .05) for biofilms developed from patients' biofilm inoculum, but biomass volume, dry weight, and microbiological composition were similar among groups (P > .05). Interestingly, according to the checkerboard DNA-DNA hybridization results, the biofilm developed from stimulated human saliva exhibited a microbial composition more similar to the clinical subgingival biofilm of patients with peri-implantitis, with proportions of the main pathogens closer to those found in the disease. In addition, biofilm developed using saliva as inoculum was shown to be susceptible to CHX with significant reduction in bacteria compared with biofilms without exposure to CHX (P < .05).

CONCLUSION

The findings suggested that the in-vitro polymicrobial biofilm developed from human saliva as inoculum is a suitable model and clinically relevant tool for mimicking the microbial composition of implant-related infections.

The Underrated Gut Microbiota Helminths, Bacteriophages, Fungi, and Archaea

The microbiota inhabits the gastrointestinal tract, providing essential capacities to the host. The microbiota is a crucial factor in intestinal health and regulates intestinal physiology. However, microbiota disturbances, named dysbiosis, can disrupt intestinal homeostasis, leading to the development of diseases. Classically, the microbiota has been referred to as bacteria, though other organisms form this complex group, including viruses, archaea, and eukaryotes such as fungi and protozoa. This review aims to clarify the role of helminths, bacteriophages, fungi, and archaea in intestinal homeostasis and diseases, their interaction with bacteria, and their use as therapeutic targets in intestinal maladies.

Culturing the Human Oral Microbiota, Updating Methodologies and Cultivation Techniques

Recent years have been marked by a paradigm shift in the study of the human microbiota, with a re-emergence of culture-dependent approaches. Numerous studies have been devoted to the human microbiota, while studies on the oral microbiota still remain limited. Indeed, various techniques described in the literature may enable an exhaustive study of the microbial composition of a complex ecosystem. In this article, we report different methodologies and culture media described in the literature that can be applied to study the oral microbiota by culture. We report on specific methodologies for targeted culture and specific culture techniques and selection methodologies for cultivating members of the three kingdoms of life commonly found in the human oral cavity, namely, eukaryota, bacteria and archaea. This bibliographic review aims to bring together the various techniques described in the literature, enabling a comprehensive study of the oral microbiota in order to demonstrate its involvement in oral health and diseases.

Functional biomes beyond the bacteriome in the oral ecosystem

Selective constraint and pressures upon the host tissues often signifies a beneficial microbiome in any species. In the context of oral microbiome this displays a healthy microbial cosmos resisting the colonization and helps in rendering protection. This review highlights the endeavors of the oral microbiome beyond the bacteriome encompassing virome, mycobiome, protozoa and archaeomes in maintaining the oral homeostasis in health and disease. Scientific data based on the peer-reviewed publications on the microbial communities of the oral microbiome were selected and collated from the scientific database collection sites of web of science (WOS), pubmed central, Inspec etc., from 2010 to 2021 using the search key words like oral microbiome, oral microbiota, oral virome, oral bacteriome, oral mycobiome and oral archaeome. Data excluded were from conference proceedings, abstracts and book chapters. The oral homeostasis in both the health and disease conditions, mostly is balanced by the unrevealed virome, mycobiome, oral protozoa and archaeome. The review documents the need to comprehend the diversity that prevails among the kingdoms in order to determine the specific role played by each domain. Oral microbiome is also a novel research arena to develop drug and targeted therapies to treat various oro-dental infections.

Oral Microbiome and Dental Caries Development

Dental caries remains the most prevalent oral disease worldwide. The development of dental caries is highly associated with the microbiota in the oral cavity. Microbiological research of dental caries has been conducted for over a century, with conventional culture-based methods and targeted molecular methods being used in order to identify the microorganisms related to dental caries. These methods' major limitation is that they can identify only part of the culturable microorganisms in the oral cavity. Introducing sequencing-based technology and bioinformatics analysis has boosted oral microbiome research and greatly expanded the understanding of complex oral microbiology. With the continuing revolution of molecular technologies and the accumulated sequence data of the oral microbiome, researchers have realized that microbial composition alone may be insufficient to uncover the relationship between caries and the microbiome. Most updated evidence has coupled metagenomics with transcriptomics and metabolomics techniques in order to comprehensively understand the microbial contribution to dental caries. Therefore, the objective of this article is to give an overview of the research of the oral microbiome and the development of dental caries. This article reviews the classical concepts of the microbiological aspect of dental caries and updates the knowledge of caries microbiology with the results of current studies on the oral microbiome. This paper also provides an update on the caries etiological theory, the microorganisms related to caries development, and the shifts in the microbiome in dental caries development.

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.

The oralome and its dysbiosis: New insights into oral microbiome-host interactions

The oralome is the summary of the dynamic interactions orchestrated between the ecological community of oral microorganisms (comprised of up to approximately 1000 species of bacteria, fungi, viruses, archaea and protozoa - the oral microbiome) that live in the oral cavity and the host. These microorganisms form a complex ecosystem that thrive in the dynamic oral environment in a symbiotic relationship with the human host. However, the microbial composition is significantly affected by interspecies and host-microbial interactions, which in turn, can impact the health and disease status of the host. In this review, we discuss the composition of the oralome and inter-species and host-microbial interactions that take place in the oral cavity and examine how these interactions change from healthy (eubiotic) to disease (dysbiotic) states. We further discuss the dysbiotic signatures associated with periodontitis and caries and their sequalae, (e.g., tooth/bone loss and pulpitis), and the systemic diseases associated with these oral diseases, such as infective endocarditis, atherosclerosis, diabetes, Alzheimer's disease and head and neck/oral cancer. We then discuss current computational techniques to assess dysbiotic oral microbiome changes. Lastly, we discuss current and novel techniques for modulation of the dysbiotic oral microbiome that may help in disease prevention and treatment, including standard hygiene methods, prebiotics, probiotics, use of nano-sized drug delivery systems (nano-DDS), extracellular polymeric matrix (EPM) disruption, and host response modulators.

Hydrogen-methane breath testing results influenced by oral hygiene

The measurement of hydrogen–methane breath gases is widely used in gastroenterology to evaluate malabsorption syndromes and bacterial overgrowth. Laboratories offering breath testing provide variable guidance regarding oral hygiene practices prior to testing. Given that oral dysbiosis has the potential to cause changes in breath gases, it raises concerns that oral hygiene is not a standard inclusion in current breath testing guidelines. The aim of this study was to determine how a pre-test mouthwash may impact hydrogen–methane breath test results. Participants presenting for breath testing who had elevated baseline gases were given a chlorhexidine mouthwash. If a substantial reduction in expired hydrogen or methane occurred after the mouthwash, breath samples were collected before and after a mouthwash at all breath sample collection points for the duration of testing. Data were evaluated to determine how the mouthwash might influence test results and diagnostic status. In 388 consecutive hydrogen–methane breath tests, modifiable elevations occurred in 24.7%. Administration of a chlorhexidine mouthwash resulted in significantly (p ≤ 0.05) reduced breath hydrogen in 67% and/or methane gas in 93% of those consenting to inclusion. In some cases, this modified the diagnosis. Mean total gas concentrations pre- and post-mouthwash were 221.0 ppm and 152.1 ppm (p < 0.0001) for hydrogen, and 368.9 ppm and 249.8 ppm (p < 0.0001) for methane. Data suggest that a single mouthwash at baseline has a high probability of returning a false positive diagnosis. Variations in gas production due to oral hygiene practices has significant impacts on test interpretation and the subsequent diagnosis. The role of oral dysbiosis in causing gastrointestinal symptoms also demands exploration as it may be an underlying factor in the presenting condition that was the basis for the referral.

Diversity of Methanogens in Animals' Gut

Methanogens are members of anaerobe microbiota of the digestive tract of mammals, including humans. However, the sources, modes of acquisition, and dynamics of digestive tract methanogens remain poorly investigated. In this study, we aimed to expand the spectrum of animals that could be sources of methanogens for humans by exploring methanogen carriage in animals. We used real-time PCR, PCR-sequencing, and multispacer sequence typing to investigate the presence of methanogens in 407 fecal specimens collected from nine different mammalian species investigated here. While all the negative controls remained negative, we obtained by PCR-sequencing seven different species of methanogens, of which three (Methanobrevibacter smithii, Methanobrevibacter millerae and Methanomassiliicoccus luminyensis) are known to be part of the methanogens present in the human digestive tract. M. smithii was found in 24 cases, including 12/24 (50%) in pigs, 6/24 (25%) in dogs, 4/24 (16.66%) in cats, and 1/24 (4.16%) in both sheep and horses. Genotyping these 24 M. smithii revealed five different genotypes, all known in humans. Our results are fairly representative of the methanogen community present in the digestive tract of certain animals domesticated by humans, and other future studies must be done to try to cultivate methanogens here detected by molecular biology to better understand the dynamics of methanogens in animals and also the likely acquisition of methanogens in humans through direct contact with these animals or through consumption of the meat and/or milk of certain animals, in particular cows.

Strong oral plaque microbiome signatures for dental implant diseases identified by strain-resolution metagenomics

Dental implants are installed in an increasing number of patients. Mucositis and peri-implantitis are common microbial-biofilm-associated diseases affecting the tissues that surround the dental implant and are a major medical and socioeconomic burden. By metagenomic sequencing of the plaque microbiome in different peri-implant health and disease conditions (113 samples from 72 individuals), we found microbial signatures for peri-implantitis and mucositis and defined the peri-implantitis-related complex (PiRC) composed by the 7 most discriminative bacteria. The peri-implantitis microbiome is site specific as contralateral healthy sites resembled more the microbiome of healthy implants, while mucositis was specifically enriched for Fusobacterium nucleatum acting as a keystone colonizer. Microbiome-based machine learning showed high diagnostic and prognostic power for peri-implant diseases and strain-level profiling identified a previously uncharacterized subspecies of F. nucleatum to be particularly associated with disease. Altogether, we associated the plaque microbiome with peri-implant diseases and identified microbial signatures of disease severity.

Microbiological Profile and Human Immune Response Associated with Peri-Implantitis: A Systematic Review

PURPOSE

To evaluate and synthesize the existing evidence on the microbiological and human immune response associated with peri-implantitis in comparison to healthy implants.

MATERIALS AND METHODS

Three electronic databases (MEDLINE, Embase, and Cochrane Library) were searched in October 2019 to identify clinical studies evaluating the microbiota and the immune response associated with peri-implantitis. Two reviewers independently screened the studies and used the full text to extract the data. A qualitative synthesis was performed on the extracted data and summary tables were prepared. Due to clinical and methodological heterogeneity among included studies, no meta-analysis was performed.

RESULTS

Forty studies were included in this review. Of these, 20 studies compared the microbiological profile of peri-implantitis with healthy implants. Nineteen studies focused on the immune response associated with peri-implantitis in comparison to healthy implants. Three studies focus on gene polymorphism associated with peri-implantitis. The most commonly reported bacteria associated with peri-implantitis were obligate anaerobe Gram-negative bacteria (OAGNB), asaccharolytic anaerobic Gram-positive rods (AAGPRs), and other Gram-positive species. In regard to immune response, the most frequently reported pro-inflammatory mediators associated with peri-implantitis were IL-1β, IL-6, IL-17, TNF-α. Osteolytic mediator, e.g., RANK, RANKL, Wnt5a and proteinase enzymes, MMP-2, MMP-9, and Cathepsin-K were also expressed at higher level in peri-implantitis sites compared to control.

CONCLUSIONS

Peri-implantitis is associated with complex and different microbiota than healthy implants including bacteria, archaea, fungi, and virus. This difference in the microbiota could provoke higher inflammatory response and osteolytic activity. All of this could contribute to the physiopathology of peri-implantitis.

Digestive tract methanodrome: Physiological roles of human microbiota-associated methanogens

Methanogens are the archaea most commonly found in humans, in particular in the digestive tract and are an integral part of the digestive microbiota. They are present in humans from the earliest moments of life and represent the only known source of methane production to date. They are notably detected in humans by microscopy, fluorescent in situ hybridization, molecular biology including PCR-sequencing, metagenomics, matrix-assisted laser desorption ionization time-of-flight mass spectrometry and culture. Methanogens present in the human digestive tract play major roles, in particular the use of hydrogen from the fermentation products of bacteria, thus promoting digestion. They are also involved in the transformation of heavy metals and in the use of trimethylamine produced by intestinal bacteria, thus preventing major health problems, in particular cardiovascular diseases. Several pieces of evidence suggest their close physical contacts with bacteria support symbiotic metabolism. Their imbalance during dysbiosis is associated with many pathologies in humans, particularly digestive tract diseases such as Crohn's disease, ulcerative colitis, diverticulosis, inflammatory bowel disease, irritable bowel syndrome, colonic polyposis, and colorectal cancer. There is a huge deficit of knowledge and partially contradictory information concerning human methanogens, so much remains to be done to fully understand their physiological role in humans. It is necessary to develop new methods for the identification and culture of methanogens from clinical samples. This will permit to isolate new methanogens species as well as their phenotypic characterization, to explore their genome by sequencing and to study the population dynamics of methanogens by specifying in particular their exact role within the complex flora associated with the mucous microbiota of human.

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.

The Microbiome of Peri-Implantitis: A Systematic Review and Meta-Analysis

This review aimed to systematically compare microbial profiles of peri-implantitis to those of periodontitis and healthy implants. Therefore, an electronic search in five databases was conducted. For inclusion, studies assessing the microbiome of peri-implantitis in otherwise healthy patients were considered. Literature was assessed for consistent evidence of exclusive or predominant peri-implantitis microbiota. Of 158 potentially eligible articles, data of 64 studies on 3730 samples from peri-implant sites were included in this study. Different assessment methods were described in the studies, namely bacterial culture, PCR-based assessment, hybridization techniques, pyrosequencing, and transcriptomic analyses. After analysis of 13 selected culture-dependent studies, no microbial species were found to be specific for peri-implantitis. After assessment of 28 studies using PCR-based methods and a meta-analysis on 19 studies, a higher prevalence of Aggregatibacter actinomycetemcomitans and Prevotella intermedia (log-odds ratio 4.04 and 2.28, respectively) was detected in peri-implantitis biofilms compared with healthy implants. Actinomyces spp., Porphyromonas spp. and Rothia spp. were found in all five pyrosequencing studies in healthy-, periodontitis-, and peri-implantitis samples. In conclusion, the body of evidence does not show a consistent specific profile. Future studies should focus on the assessment of sites with different diagnosis for the same patient, and investigate the complex host-biofilm interaction.

First characterization of methanogens in oral cavity in Malian patients with oral cavity pathologies

BACKGROUND

The oral cavity of humans is inhabited by several hundreds of bacterial species and other microorganisms such as fungi and archaeal methanogens. Regarding methanogens, data have been obtained from oral cavity samples collected in Europe, America and Asia. There is no study published on the presence of methanogens in the oral cavity in persons living in Africa. The objective of our study was to bring new knowledge on the distribution of oral methanogens in persons living in Mali, Africa.

METHODS

A total of 31 patients were included in the study during a 15-day collection period in September. Bacterial investigations consisted in culturing the bacteria in 5% sheep blood-enriched Columbia agar and PolyViteX agar plates. For archaeal research, we used various methods including culture, molecular biology and fluorescent in situ hybridization (FISH).

RESULTS

Eight of 31 (26%) oral samples collected in eight patients consulting for stomatology diseases tested positive in polymerase chain-reaction (PCR)-based assays for methanogens including five cases of Methanobrevibacter oralis and one case each of Methanobrevibacter smithii, Methanobrevibacter massiliense and co-infection Methanobrevibacter oralis and Methanobrevibacter massiliense.

CONCLUSIONS

In this pilot study, we are reporting here the first characterization of methanogens in the oral cavity in eight patients in Mali. These methanogen species have already been documented in oral specimens collected from individuals in Europe, Asia, North America and Brazil.

A common vaginal microbiota composition among breeds of Bos taurus indicus (Gyr and Nellore)

Describing the bovine vaginal microbiota is essential to better understand its physiology and its impact on health maintenance. Despite the economic importance of reproduction of these animals, bovine vaginal microbial community is still poorly described in comparison with rumen microbiome. Previous studies of our group described the vaginal microbiota of Nellore, an important Bos taurus indicus breed, using metagenomics. In order to better understand this microbiota, the present work aims to investigate another important breed, Gyr. Results have shown bacterial dominance over Archaea and Fungi was observed, with the most abundant bacterial phylum (Firmicutes) representing 40-50% of bacterial population, followed by Bacteroidetes, Proteobacteria, and Actinobacteria. The Fungi kingdom had the Mycosphaerella genus as its main representative, followed by Cladosporium. Archaea were observed at a very low abundance in all animals, with a high relative abundance of Methanobrevibacter genus. These results demonstrate a high microbial diversity on vaginal tract of Gyr, as demonstrated for Nellore and different from the previously described for other species. Our results indicate a great similarity between vaginal microbiota of Nellore and Gyr despite the differences in animal handling and genetic improvement. As observed for both breeds, individual variation is the largest source of microbial diversity between animals.

Archaeal biofilm formation

Biofilms are structured and organized communities of microorganisms that represent one of the most successful forms of life on Earth. Bacterial biofilms have been studied in great detail, and many molecular details are known about the processes that govern bacterial biofilm formation, however, archaea are ubiquitous in almost all habitats on Earth and can also form biofilms. In recent years, insights have been gained into the development of archaeal biofilms, how archaea communicate to form biofilms and how the switch from a free-living lifestyle to a sessile lifestyle is regulated. In this Review, we explore the different stages of archaeal biofilm development and highlight similarities and differences between archaea and bacteria on a molecular level. We also consider the role of archaeal biofilms in industry and their use in different industrial processes.

Co-culture of Methanobrevibacter smithii with enterobacteria during urinary infection

BACKGROUND

Urinary tract infections are known to be caused by bacteria, but the potential implications of archaea have never been studied in this context.

METHODS

In two different university hospital centres we used specific laboratory methods for the detection and culture of archaeal methanogens in 383 urine specimens prospectively collected for diagnosing urinary tract infection (UTI).

FINDINGS

Methanobrevibacter smithii was detected by quantitative PCR and sequencing in 34 (9%) of the specimens collected from 34 patients. Escherichia coli, Klebsiella pneumoniae, Enterobacter sp., Enterococcus faecium and mixed cultures were detected along with M. smithii in eighteen, six, three, one and six urine samples, respectively. Interestingly, using our specific culture method for methanogens, we also isolated M. smithii in 31 (91%) of the 34 PCR positive urine samples. Genotyping the 31 isolates using multispacer sequence typing revealed three different genotypes which have been previously reported in intestinal microbiota. Antibiotic susceptibility testing found the 31 isolates to be in vitro susceptible to metronidazole (MIC: 1 mg/L) but resistant to fosfomycin, sulfamethoxazole-trimethoprim, amoxicillin-clavulanate and ofloxacin, commonly used to treat bacterial UTI. Finally, 19 (54%) of the 34 patients in whose urine samples M. smithii was detected were diagnosed with UTIs, including cystitis, pyelonephritis and prostatitis.

INTERPRETATION

Our results show that M. smithii is part of the urinary microbiota of some individuals and could play a role in community-acquired UTI in association with enteric bacteria. FUND: This study was supported by IHU Méditerranée Infection, Marseille, France.

Efficacy of virginiamycin for the control of periodontal disease in calves

ABSTRACT: Periodontal diseases are multifactorial infectious processes caused by complexes of microorganisms, with damage to health, production, and animal welfare. The aim of the present study was to evaluate the efficacy of virginiamycin in the prevention and control of two early forms of periodontal disease: gingivitis and necrotizing gingivitis. Ten weaned calves, aged four to six months, were permanently kept in a single lot under the same rotational grazing regime in a newly reformed area of Panicum maximum. Five of the calves were orally administered 340mg of virginiamycin (Virginiamycin Group) daily for a period of 18 weeks, while the remaining five calves (Control Group) remained under the same food management but did not receive virginiamycin. During this period, animals underwent 18 weekly evaluations regarding periodontal health, with monitoring and recording of clinical parameters of the eight deciduous incisor teeth on the labial and lingual faces. At approximately two-week intervals, nine collections of subgingival sulcus material from five sites of the four right incisor teeth of each animal were performed and subjected to microbiological evaluation using polymerase chain reaction with primers of 25 microorganisms considered potentially pathogenic. After 1440 periodontal clinical evaluations of incisor teeth of the 10 calves, a total of 395 episodes of gingivitis were recorded, of which 267 occurred in the Control Group and 128 in the Virginiamycin Group. Similarly, 89 episodes of necrotizing gingivitis were recorded; 58 in the Control Group and 31 in the Virginiamycin Group. Comparison of between-group means found significant differences for teeth with gingivitis and necrotizing gingivitis (t test; p<0.05). The total number of teeth with gingivitis (p<0.01) and necrotizing gingivitis (p<0.01) in Control Group was significantly higher than that of gingivitis (p<0.01) and necrotizing gingivitis (p<0.05) in the Virginiamycin Group. There was a positive correlation between total occurrence of gingivitis and necrotizing gingivitis in the Virginiamycin Group by Pearson’s test. Virginiamycin had a protective effect on treated animals compared with the Control Group (OR = 0.36: CI (95%) = 0.27-0.43). In the Control Group, Actinomyces israelli (4.74%), domain Archaea (1.58%), Eikenella corrodens (1.05%), Fusobacterium nucleatum (27.37%), class Mollicutes (5.26%); Porphyromonas endodontalis(5.26%); Porphyromonas gulae(0.53%), Prevotella buccae (6.32%), Prevotella loescheii (3.68%), Prevotella nigrescens (8.42%), Prevotella oralis (1.58%), Tannerella forsythia (0.53%), and Treponema denticola (4.21%) were detected at healthy sites, and gingivitis or necrotizing gingivitis samples. In the Virginiamycin Group, A. israelli (3.41%), domain Archaea (0.98%), F. nucleatum (9.27%), class Mollicutes(4.39%), P. endodontalis (4.39%), P. gulae (0.49%), P. buccae (8.29%), P. loescheii (6.83%), P. nigrescens (15.61%), P. oralis (1.46%), Selenomonas sputigena (0.49%), T. forsythia (0.49%), and T. denticola (2.44%) were detected. In conclusion, virginiamycin administered at a dosage of 340mg/animal/day significantly reduced the occurrence of gingivitis and necrotizing gingivitis in cattle maintained on reformed pastures, and was revealed to have action against periodontal bacterial microbiota considered to be potentially pathogenic.

Peri-implantitis-associated methanogens: a preliminary report

Methanogens have already been described in periodontitis but not in peri-implantitis. Thirty peri-implantitis samples and 28 control samples were collected in 28 consenting peri-implantitis patients. PCR-sequencing of the 16S rRNA gene was used as a broad-spectrum screening method and results were further confirmed by real-time quantitative PCR targeting the mcrA genes. Results showed a methanogen community dominated by Methanobrevibacter oralis in 31/58 (51%) samples including 16/28 (57%) control samples and 15/30 (50%) peri-implantitis samples. Methanobrevibacter massiliense was detected in 5/58 (8.6%) samples including 3/28 (1%) control samples and 2/30 (6.7%) peri-implantitis samples. The prevalence of M. oralis or M. massiliense did not significantly differ in peri-implantitis and control samples (exact Fisher test, P = 0.61 and P = 0.67, respectively). Further ponderation of the methanogen load by the real-time quantitative PCR for actin human gene again indicated non-significant difference (Wilcoxon-Mann-Whitney test, P = 0.48 and P = 0.40, respectively). These data show that the prevalence of methanogens does not differ in peri-implantitis lesions and healthy sites, when individuals are their own control. These data do not allow assigning a specific pathogenic role to methanogens in peri-implantitis; methanogens rather are part of the commensal and normal flora of the oral cavity.

Tobacco-smoking-related prevalence of methanogens in the oral fluid microbiota

The oral fluid microbiome comprises an important bacterial diversity, yet the presence of archaea has not been reported so far. In order to quest for the presence of methanogenic archaea (methanogens) in oral fluid, we used a polyphasic approach including PCR-sequencing detection, microscopic observation by fluorescence in-situ hybridization, isolation and culture, molecular identification and genotyping of methanogens in 200 oral fluid specimens. In the presence of negative controls, 64/200 (32%) prospectively analysed oral fluid specimens were PCR-positive for methanogens, all identified as Methanobrevibacter oralis by sequencing. Further, fluorescence in-situ hybridization detected methanogens in 19/48 (39.6%) investigated specimens; with morphology suggesting M. oralis in 10 cases and co-infecting Methanobrevibacter smithii in nine cases. M. oralis was cultured from 46/64 (71.8%) PCR-positive specimens and none of PCR-negative specimens; and one M. smithii isolate was co-cultured with M. oralis in one specimen. Multispacer Sequence Typing found one M. oralis genotype per specimen and a total of five different genotypes with 19/46 (41%) of isolates all belonging to spacer-type four. Statistical analyses showed a significant correlation between the PCR-detection of methanogens in oral fluid and tobacco smoking. These data indicate that M. oralis and M. smithii are oral fluid-borne methanogens in tobacco smokers. Both methanogens could be transmitted during intimate contacts such as mother-to-child contacts and kissing.

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.

Microbial Profiles and Detection Techniques in Peri-Implant Diseases: a Systematic Review

Objectives

To describe the microbial profiles of peri-implant diseases and the main detection methods.

Material and Methods

A literature search was performed in MEDLINE via PubMed database to identify studies on microbial composition of peri-implant surfaces in humans published in the last 5 years. Studies had to have clear implant status definition for health, peri-implant mucositis and/or peri-implantitis and specifically study microbial composition of the peri-implant sulcus.

Results

A total of 194 studies were screened and 47 included. Peri-implant sites are reported to be different microbial ecosystems compared to periodontal sites. However, differences between periodontal and peri-implant health and disease are not consistent across all studies, possibly due to the bias introduced by the microbial detection technique. New methods non species-oriented are being used to find ‘unexpected’ microbiota not previously described in these scenarios.

Conclusions

Microbial profile of peri-implant diseases usually includes classic periodontopathogens. However, correlation between studies is difficult, particularly because of the use of different detection methods. New metagenomic techniques should be promoted for future studies to avoid detection bias.

Restricted diversity of dental calculus methanogens over five centuries, France

Methanogens are acknowledged archaeal members of modern dental calculus microbiota and dental pathogen complexes. Their repertoire in ancient dental calculus is poorly known. We therefore investigated archaea in one hundred dental calculus specimens collected from individuals recovered from six archaeological sites in France dated from the 14(th) to 19(th) centuries AD. Dental calculus was demonstrated by macroscopic and cone-beam observations. In 56 calculus specimens free of PCR inhibition, PCR sequencing identified Candidatus Methanobrevibacter sp. N13 in 44.6%, Methanobrevibacter oralis in 19.6%, a new Methanomassiliicoccus luminyensis-like methanogen in 12.5%, a Candidatus Nitrososphaera evergladensis-like in one and Methanoculleus bourgensis in one specimen, respectively. One Candidatus Methanobrevibacter sp. N13 dental calculus was further documented by fluorescent in situ hybridization. The prevalence of dental calculus M. oralis was significantly lower in past populations than in modern populations (P = 0.03, Chi-square test). This investigation revealed a previously unknown repertoire of archaea found in the oral cavity of past French populations as reflected in preserved dental calculus.

Vaginal Microbiome Characterization of Nellore Cattle Using Metagenomic Analysis

Understanding of microbial communities inhabiting cattle vaginal tract may lead to a better comprehension of bovine physiology and reproductive health being of great economic interest. Up to date, studies involving cattle microbiota are focused on the gastrointestinal tract, and little is known about the vaginal microbiota. This study aimed to investigate the vaginal microbiome in Nellore cattle, heifers and cows, pregnant and non-pregnant, using a culture independent approach. The main bacterial phyla found were Firmicutes (~40–50%), Bacteroidetes (~15–25%) and Proteobacteria (~5–25%), in addition to ~10–20% of non-classified bacteria. 45–55% of the samples were represented by only ten OTUs: Aeribacillus, Bacteroides, Clostridium, Ruminococcus, Rikenella, Alistipes, Bacillus, Eubacterium, Prevotella and non-classified bacteria. Interestingly, microbiota from all 20 animals could be grouped according to the respiratory metabolism of the main OTUs found, creating three groups of vaginal microbiota in cattle. Archaeal samples were dominated by the Methanobrevibacter genus (Euryarchaeota, ~55–70%). Ascomycota was the main fungal phylum (~80–95%) and Mycosphaerella the most abundant genus (~70–85%). Hormonal influence was not clear, but a tendency for the reduction of bacterial and increase of archaeal populations in pregnant animals was observed. Eukaryotes did not vary significantly between pregnant and non-pregnant animals, but tended to be more abundant on cows than on heifers. The present work describes a great microbial variability in the vaginal community among the evaluated animals and groups (heifers and cows, pregnant and non-pregnant), which is significantly different from the findings previously reported using culture dependent methods, pointing out the need for further studies on this issue. The microbiome found also indicates that the vaginal colonization appears to be influenced by the gastrointestinal community.

Archaea prevalence in inflamed pulp tissues

Archaea have been detected in several ecological niches of the human body such as the large intestine, skin, vagina as well as the oral cavity. At present, archaea are recognized as nonpathogenic microorganisms. However, some data indicate that they may be involved in the etiopathogenesis of several diseases, including intestinal diseases as well as oral diseases: periodontitis, peri-implantitis and endodontitis. In this study, on the basis of 16S rRNA gene sequence analysis, we examined whether archaea might be present in inflamed pulp tissues and contribute to the development of endodontic infection. In comparison, we also determined selected bacterial species associated with endodontitis. We detected archaea in 85% of infected endodontic samples. In addition, Prevotella intermedia, Porphyromonas gingivalis, Tannerella forsythia and Treponema denticola were present in inflamed pulp tissue samples and Treponema denticola occurred with the highest frequency (70%). Further analysis revealed the presence of methanogenic archaea in analyzed samples. Direct sequencing of archaeal 16S rRNA gene PCR products indicated the occurrence of methanogenic archaea in inflamed pulp tissues; phylogenetically most similar were Methanobrevibacter oralis and Methanobrevibacter smithii. Therefore, our results show that methanogenic archaea are present in inflamed pulp tissues and may participate in the development of endodontic infection.

The repertoire of archaea cultivated from severe periodontitis

In previous studies, the abundance and diversity of methanogenic archaea in the dental microbiota have been analysed by the detection of specific DNA sequences by PCR-based investigations and metagenomic studies. Few data issued regarding methanogens actually living in dental plaque. We collected dental plaque specimens in 15 control individuals and 65 periodontitis patients. Dental plaque specimens were cultured in an anoxic liquid medium for methanogens in the presence of negative control tubes. Dental plaque methanogens were cultured from 1/15 (6.67%) control and 36/65 (55.38%) periodontitis patient samples (p<0.001). The cultures yielded Methanobrevibacter oralis in one control and thirty-one patients, Methanobrevibacter smithii in two patients and a potential new species named Methanobrevibacter sp. strain N13 in three patients with severe periodontitis. Our observations of living methanogens, strengthen previous observations made on DNA-based studies regarding the role of methanogens, in periodontitis.

Intraindividual variation in core microbiota in peri-implantitis and periodontitis

The oral microbiota change dramatically with each part of the oral cavity, even within the same mouth. Nevertheless, the microbiota associated with peri-implantitis and periodontitis have been considered the same. To improve our knowledge of the different communities of complex oral microbiota, we compared the microbial features between peri-implantitis and periodontitis in 20 patients with both diseases. Although the clinical symptoms of peri-implantitis were similar to those of periodontitis, the core microbiota of the diseases differed. Correlation analysis revealed the specific microbial co-occurrence patterns and found some of the species were associated with the clinical parameters in a disease-specific manner. The proportion of Prevotella nigrescens was significantly higher in peri-implantitis than in periodontitis, while the proportions of Peptostreptococcaceae sp. and Desulfomicrobium orale were significantly higher in periodontitis than in peri-implantitis. The severity of the peri-implantitis was also species-associated, including with an uncultured Treponema sp. that correlated to 4 clinical parameters. These results indicate that peri-implantitis and periodontitis are both polymicrobial infections with different causative pathogens. Our study provides a framework for the ecologically different bacterial communities between peri-implantitis and periodontitis, and it will be useful for further studies to understand the complex microbiota and pathogenic mechanisms of oral polymicrobial diseases.

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.

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

BACKGROUND

There is evidence of a possible relationship between Archaea and periodontal disease; however, to date few studies have assessed the changes in prevalence of this domain after periodontal therapy. 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 prevalence of Archaea after periodontal therapy.

METHODS

Thirty subjects were randomly assigned to receive scaling and root planing (SRP) alone or combined with metronidazole (MTZ) + amoxicillin (AMX) for 14 days. Clinical and microbiological examinations were performed at baseline and at six months post-SRP. Nine subgingival plaque samples per subject were analysed for the presence of Archaea.

RESULTS

SRP alone or combined with MTZ + AMX significantly reduced the prevalence of subjects colonized by Archaea at six months post-therapy. However, no significant differences between treatment groups were observed (p > 0.05). Both therapies led to a statistically significant decrease in the mean percentage of sites colonized by Archaea (p < 0.05). A negative Spearman correlation was observed between the presence of Archaea and the mean clinical attachment gain at six months post-therapy (r(2) = -0.61; 95% CI -0.80- -0.31; p = 0.003).

CONCLUSIONS

SRP alone or combined with MTZ + AMX provides a similar reduction in the prevalence of Archaea in the subgingival biofilm of subjects with generalized aggressive periodontitis.

Microbiological diversity of peri-implantitis biofilm by Sanger sequencing

BACKGROUND AND OBJECTIVE

To examine the microbial diversity associated with implants with or without peri-implantitis and to identify differences between the bacterial communities in these clinical conditions.

MATERIAL AND METHODS

Twenty subjects were assigned to a Control group consisting of subjects with healthy implants and a Test group consisting of subjects with peri-implantitis sites, as well as a healthy implant site (n = 10/group). In the Test group, subgingival biofilm samples were taken from the deepest sites of the diseased implant. In both groups, samples were collected from one site around a healthy implant. DNA was extracted and the 16S rRNA gene was amplified and sequenced, and the phylotypes were identified by comparison with known 16S rRNA sequences.

RESULTS

The phylogenetic identity of 1387 16S rRNA gene clones was determined. Healthy implants demonstrated higher proportions of Actinomyces, Atopobium, Gemella, Kingella and Rothia and lower levels of Campylobacter, Desulfobulbus, Dialister, Eubacterium, Filifactor, Mitsukella, Porphyromonas and Pseudoramibacter (Mann-Whitney U-test; P < 0.05). Fusobacterium nucleatum, Dialister invisus, Streptococcus sp. human oral taxon (HOT) 064, Filifactor alocis and Mitsuokella sp. HOT 131 presented a higher mean proportion, while Veillonella dispar, Actinomyces meyeri, Granulicatella adiacens showed lower mean proportions in the peri-implantitis sites when compared with healthy implants in both the Control and Test groups (Mann-Whitney U-test; P < 0.05).

CONCLUSION

Marked differences were observed in the composition of the subgingival biofilm between healthy and diseased implants. The biofilm associated with peri-implantitis harbored more pathogenic bacterial species from the orange complex and other "unusual" putative pathogens, such as F. alocis, D. invisus and Mitsuokella sp. HOT 131.

Archaeal biofilms: the great unexplored

Biofilms are currently viewed as the most common form in which microorganisms exist in nature. Bacterial biofilms play important roles in disease and industrial applications, and they have been studied in great detail. Although it is well accepted that archaea are not only the extremists they were thought to be as they occupy nearly every habitat where also bacteria are found, it is surprising how little molecular details are known about archaeal biofilm formation. Therefore, we aim to highlight the available information and indicate open questions in this field.

Antibiotic resistance in human peri-implantitis microbiota

OBJECTIVES

Because antimicrobial therapy is often employed in the treatment of infectious dental implant complications, this study determined the occurrence of in vitro antibiotic resistance among putative peri-implantitis bacterial pathogens.

METHODS

Submucosal biofilm specimens were cultured from 160 dental implants with peri-implantitis in 120 adults, with isolated putative pathogens identified to species level, and tested in vitro for susceptibility to 4 mg/l of doxycycline, 8 mg/l of amoxicillin, 16 mg/l of metronidazole, and 4 mg/l of clindamycin. Findings for amoxicillin and metronidazole were combined post-hoc to identify peri-implantitis species resistant to both antibiotics. Gram-negative enteric rods/pseudomonads were subjected to ciprofloxacin disk diffusion testing.

RESULTS

One or more cultivable submucosal bacterial pathogens, most often Prevotella intermedia/nigrescens or Streptococcus constellatus, were resistant in vitro to clindamycin, amoxicillin, doxycycline, or metronidazole in 46.7%, 39.2%, 25%, and 21.7% of the peri-implantitis subjects, respectively. Only 6.7% subjects revealed submucosal test species resistant in vitro to both amoxicillin and metronidazole, which were either S. constellatus (one subject) or ciprofloxacin-susceptible strains of gram-negative enteric rods/pseudomonads (seven subjects). Overall, 71.7% of the 120 peri-implantitis subjects exhibited submucosal bacterial pathogens resistant in vitro to one or more of the tested antibiotics.

CONCLUSIONS

Peri-implantitis patients frequently yielded submucosal bacterial pathogens resistant in vitro to individual therapeutic concentrations of clindamycin, amoxicillin, doxycycline, or metronidazole, but only rarely to both amoxicillin and metronidazole. Due to the wide variation in observed drug resistance patterns, antibiotic susceptibility testing of cultivable submucosal bacterial pathogens may aid in the selection of antimicrobial therapy for peri-implantitis patients.