PrimerEvalPy: a tool for in-silico evaluation of primers for targeting the microbiome.

BACKGROUND: The selection of primer pairs in sequencing-based research can greatly influence the results, highlighting the need for a tool capable of analysing their performance in-silico prior to the sequencing process. We therefore propose PrimerEvalPy, a Python-based package designed to test the performance of any primer or primer pair against any sequencing database. The package calculates a coverage metric and returns the amplicon sequences found, along with information such as their average start and end positions. It also allows the analysis of coverage for different taxonomic levels. RESULTS: As a case study, PrimerEvalPy was used to test the most commonly used primers in the literature against two oral 16S rRNA gene databases containing bacteria and archaea. The results showed that the most commonly used primer pairs in the oral cavity did not match those with the highest coverage. The best performing primer pairs were found for the detection of oral bacteria and archaea. CONCLUSIONS: This demonstrates the importance of a coverage analysis tool such as PrimerEvalPy to find the best primer pairs for specific niches. The software is available under the MIT licence at https://gitlab.citius.usc.es/lara.vazquez/PrimerEvalPy .

Critical review of 16S rRNA gene sequencing workflow in microbiome studies: From primer selection to advanced data analysis.

The multi-batch reanalysis approach of jointly reevaluating gene/genome sequences from different works has gained particular relevance in the literature in recent years. The large amount of 16S ribosomal ribonucleic acid (rRNA) gene sequence data stored in public repositories and information in taxonomic databases of the same gene far exceeds that related to complete genomes. This review is intended to guide researchers new to studying microbiota, particularly the oral microbiota, using 16S rRNA gene sequencing and those who want to expand and update their knowledge to optimise their decision-making and improve their research results. First, we describe the advantages and disadvantages of using the 16S rRNA gene as a phylogenetic marker and the latest findings on the impact of primer pair selection on diversity and taxonomic assignment outcomes in oral microbiome studies. Strategies for primer selection based on these results are introduced. Second, we identified the key factors to consider in selecting the sequencing technology and platform. The process and particularities of the main steps for processing 16S rRNA gene-derived data are described in detail to enable researchers to choose the most appropriate bioinformatics pipeline and analysis methods based on the available evidence. We then produce an overview of the different types of advanced analyses, both the most widely used in the literature and the most recent approaches. Several indices, metrics and software for studying microbial communities are included, highlighting their advantages and disadvantages. Considering the principles of clinical metagenomics, we conclude that future research should focus on rigorous analytical approaches, such as developing predictive models to identify microbiome-based biomarkers to classify health and disease states. Finally, we address the batch effect concept and the microbiome-specific methods for accounting for or correcting them.

Biomarkers for diagnosis of stage III, grade C with molar incisor pattern periodontitis in children and young adults: a systematic review and meta-analysis.

AIM: To explore the existing salivary, gingival crevicular fluid (GCF), blood, and serum biomarkers associated with grade C molar-incisor pattern (C/MIP) periodontitis in systemically healthy children and young adults. MATERIALS AND METHODS: Cross-sectional, case-control, and cohort studies on stage III grade C periodontitis or former equivalent diagnosis with analysis of molecular biomarkers in saliva, GCF, blood, or serum were retrieved from six databases and screened based on the eligibility criteria. The risk of bias in included studies was evaluated. Meta-analysis was planned for biomarkers assessed using the same detection methods and sample type in at least two papers. RESULTS: Out of 5621 studies identified at initial screening, 28 papers were included in the qualitative analysis of which 2 were eligible for meta-analysis for IgG in serum samples. Eighty-seven biomarkers were assessed with the majority being higher in cases than in controls. Only the meta-analysis of total serum IgG with low heterogeneity value revealed a significant increase in its levels in C/MIPs compared to controls (standardised mean difference: 1.08; 95% CI: 0.76, 1.40). CONCLUSION: There is a paucity of data on biomarkers associated with molar-incisor pattern periodontitis. Although serum IgG levels are raised, other more specific biomarkers in saliva, GCF, and blood/serum may be promising but require further investigation.

A systematic overview of dental methods for age assessment in living individuals: from traditional to artificial intelligence-based approaches.

Dental radiographies have been used for many decades for estimating the chronological age, with a view to forensic identification, migration flow control, or assessment of dental development, among others. This study aims to analyse the current application of chronological age estimation methods from dental X-ray images in the last 6 years, involving a search for works in the Scopus and PubMed databases. Exclusion criteria were applied to discard off-topic studies and experiments which are not compliant with a minimum quality standard. The studies were grouped according to the applied methodology, the estimation target, and the age cohort used to evaluate the estimation performance. A set of performance metrics was used to ensure good comparability between the different proposed methodologies. A total of 613 unique studies were retrieved, of which 286 were selected according to the inclusion criteria. Notable tendencies to overestimation and underestimation were observed in some manual approaches for numeric age estimation, being especially notable in the case of Demirjian (overestimation) and Cameriere (underestimation). On the other hand, the automatic approaches based on deep learning techniques are scarcer, with only 17 studies published in this regard, but they showed a more balanced behaviour, with no tendency to overestimation or underestimation. From the analysis of the results, it can be concluded that traditional methods have been evaluated in a wide variety of population samples, ensuring good applicability in different ethnicities. On the other hand, fully automated methods were a turning point in terms of performance, cost, and adaptability to new populations.

In silico evaluation and selection of the best 16S rRNA gene primers for use in next-generation sequencing to detect oral bacteria and archaea.

BACKGROUND: Sequencing has been widely used to study the composition of the oral microbiome present in various health conditions. The extent of the coverage of the 16S rRNA gene primers employed for this purpose has not, however, been evaluated in silico using oral-specific databases. This paper analyses these primers using two databases containing 16S rRNA sequences from bacteria and archaea found in the human mouth and describes some of the best primers for each domain. RESULTS: A total of 369 distinct individual primers were identified from sequencing studies of the oral microbiome and other ecosystems. These were evaluated against a database reported in the literature of 16S rRNA sequences obtained from oral bacteria, which was modified by our group, and a self-created oral archaea database. Both databases contained the genomic variants detected for each included species. Primers were evaluated at the variant and species levels, and those with a species coverage (SC) ≥75.00% were selected for the pair analyses. All possible combinations of the forward and reverse primers were identified, with the resulting 4638 primer pairs also evaluated using the two databases. The best bacteria-specific pairs targeted the 3-4, 4-7, and 3-7 16S rRNA gene regions, with SC levels of 98.83-97.14%; meanwhile, the optimum archaea-specific primer pairs amplified regions 5-6, 3-6, and 3-6, with SC estimates of 95.88%. Finally, the best pairs for detecting both domains targeted regions 4-5, 3-5, and 5-9, and produced SC values of 95.71-94.54% and 99.48-96.91% for bacteria and archaea, respectively. CONCLUSIONS: Given the three amplicon length categories (100-300, 301-600, and >600 base pairs), the primer pairs with the best coverage values for detecting oral bacteria were as follows: KP_F048-OP_R043 (region 3-4; primer pair position for Escherichia coli J01859.1: 342-529), KP_F051-OP_R030 (4-7; 514-1079), and KP_F048-OP_R030 (3-7; 342-1079). For detecting oral archaea, these were as follows: OP_F066-KP_R013 (5-6; 784-undefined), KP_F020-KP_R013 (3-6; 518-undefined), and OP_F114-KP_R013 (3-6; 340-undefined). Lastly, for detecting both domains jointly they were KP_F020-KP_R032 (4-5; 518-801), OP_F114-KP_R031 (3-5; 340-801), and OP_F066-OP_R121 (5-9; 784-1405). The primer pairs with the best coverage identified herein are not among those described most widely in the oral microbiome literature. Video Abstract.

Impact of 16S rRNA Gene Redundancy and Primer Pair Selection on the Quantification and Classification of Oral Microbiota in Next-Generation Sequencing.

This study aimed to evaluate the number of 16S rRNA genes in the complete genomes of the bacterial and archaeal species inhabiting the human mouth and to assess how the use of different primer pairs would affect the detection and classification of redundant amplicons and matching amplicons (MAs) from different taxa. A total of 518 oral-bacterial and 191 oral-archaeal complete genomes were downloaded from the NCBI database, and their complete 16S rRNA genes were extracted. The numbers of genes and variants per genome were calculated. Next, 39 primer pairs were used to search for matches in the genomes and obtain amplicons. For each primer, we calculated the number of gene amplicons, variants, genomes, and species detected and the percentage of coverage at the species level with no MAs (SC-NMA). The results showed that 94.09% of oral bacteria and 52.59% of oral archaea had more than one intragenomic 16S rRNA gene. From 1.29% to 46.70% of bacterial species and from 4.65% to 38.89% of archaea detected by the primers had MAs. The best primers were the following (SC-NMA; region; position for Escherichia coli [GenBank version no. J01859.1]): KP_F048-OP_R030 for bacteria (93.55%; V3 to V7; 342 to 1079), KP_F018-KP_R063 for archaea (89.63%; V3 to V9; undefined to 1506), and OP_F114-OP_R121 for both domains (92.52%; V3 to V9; 340 to 1405). In addition to 16S rRNA gene redundancy, the presence of MAs must be controlled to ensure an accurate interpretation of microbial diversity data. The SC-NMA is a more useful parameter than the conventional coverage percentage for selecting the best primer pairs. The pairs used the most in the oral microbiome literature were not among the best performers. IMPORTANCE Hundreds of publications have studied the oral microbiome through 16S rRNA gene sequencing. However, none have assessed the number of 16S rRNA genes in the genomes of oral microbes, or how the use of primer pairs targeting different regions affects the detection of MAs from different taxa. Here, we found that almost all oral bacteria and more than half of oral archaea have more than one intragenomic 16S rRNA gene. The performance of the primer pairs in not detecting MAs increases as the length of the amplicon augments. As none of those most employed in the oral literature were among the best performers, we selected a series of primers to detect bacteria and/or archaea based on their percentage of species detected without MAs. The intragenomic 16S rRNA gene redundancy and the presence of MAs between distinct taxa need to be considered to ensure an accurate interpretation of microbial diversity data.

Adapting Demirjian Standards for Portuguese and Spanish Children and Adolescents.

Estimation of children's chronological age is highly important in human and forensic sciences. The Demirjian method has been reported as accurate for this purpose. The literature review shows some evidence that the accuracy of estimating chronological age via the Demirjian standards is not a straightforward process. The objective of this research is to analyze the reliability of the Demirjian standards in Portuguese and Spanish children and adolescents and adapt it to include sex and group age as contingent factors. METHODS: Orthopantomographs of 574 Portuguese and Spanish male and female children and adolescents were employed to test the reliability of the Demirjian method. After testing for inter-rater consistency and age estimation using the Demirjian standards, multiple regression analysis was performed controlling for sex and age group. RESULTS: The Demirjian standards overestimated chronological age for both sexes, mainly for females. Through the development of regression functions, more detailed dental age estimation was performed. The predictive capacities of the Demirjian method and the significant teeth varied as a function of children's age. The Demirjian global standard predicted over 65% of the variance of the chronological age. Taking a tooth-by-tooth approach, the predictive ability increased by over 70%. CONCLUSIONS: The accuracy of estimating chronological age via the Demirjian method is not as reliable as it might appear, judging from the results found according to age group and according to sex crossed with age group.

XAS: Automatic yet eXplainable Age and Sex determination by combining imprecise per-tooth predictions.

Chronological age and biological sex estimation are two key tasks in a variety of procedures, including human identification and migration control. Issues such as these have led to the development of both semiautomatic and automatic prediction models, but the former are expensive in terms of time and human resources, while the latter lack the interpretability required to be applicable in real-life scenarios. This paper therefore proposes a new, fully automatic methodology for the estimation of age and sex. This first applies a tooth detection by means of a modified CNN with the objective of extracting the oriented bounding boxes of each tooth. Then, it feeds the image features inside the tooth boxes into a second CNN module designed to produce per-tooth age and sex probability distributions. The method then adopts an uncertainty-aware policy to aggregate these estimated distributions. Our approach yielded a lower mean absolute error than any other previously described, at 0.97 years. The accuracy of the sex classification was 91.82%, confirming the suitability of the teeth for this purpose. The proposed model also allows analyses of age and sex estimations on every tooth, enabling experts to identify the most relevant for each task or population cohort or to detect potential developmental problems. In conclusion, the performance of the method in both age and sex predictions is excellent and has a high degree of interpretability, making it suitable for use in a wide range of application scenarios.

Update on the Role of Cytokines as Oral Biomarkers in the Diagnosis of Periodontitis.

Periodontitis is one of the world's most common chronic human diseases and has a significant impact on oral health. Recent evidence has revealed a link between periodontitis and certain severe systemic conditions. Moreover, periodontal patients remain so for life, even following successful therapy, requiring ongoing supportive care to prevent the disease's recurrence. The first challenge in treating the condition is ensuring a timely and accurate diagnosis since the loss of periodontal bone and soft tissue is progressive and largely irreversible. Although current clinical and radiographic parameters are the best available for identifying and monitoring the disease, the scientific community has a particular interest in finding quantifiable biomarkers in oral fluids that can improve early detection rates of periodontitis and evaluations of its severity. It is widely accepted that periodontitis is associated with polymicrobial dysbiosis and a chronic inflammatory immune response in the host. This response causes the generation of mediators like cytokines. Higher concentrations of cytokines are involved in inflammation and disease progression, acting as a network of biological redundancy. Most of the cytokines investigated concerning the periodontitis pathogenesis are proinflammatory. Of all of them, interleukin (IL) 1beta has been studied the most, followed by tumor necrosis factor (TNF) alpha and IL6. In contrast, only a few papers have evaluated antiinflammatory cytokines, with the most researched being IL4 and IL10. Several systemic reviews have concluded that the specific cytokines present in patients with periodontitis have a distinctive profile, which may indicate their possible discriminatory potential. In this chapter, the focus is on analyzing studies that investigate the accuracy of diagnoses of periodontitis based on the cytokines present in gingival crevicular fluid and saliva. The findings of our research group are also described.

Polymicrobial Aggregates in Human Saliva Build the Oral Biofilm.

Biofilm community development has been established as a sequential process starting from the attachment of single cells on a surface. However, microorganisms are often found as aggregates in the environment and in biological fluids. Here, we conduct a comprehensive analysis of the native structure and composition of aggregated microbial assemblages in human saliva and investigate their spatiotemporal attachment and biofilm community development. Using multiscale imaging, cell sorting, and computational approaches combined with sequencing analysis, a diverse mixture of aggregates varying in size, structure, and microbial composition, including bacteria associated with host epithelial cells, can be found in saliva in addition to a few single-cell forms. Phylogenetic analysis reveals a mixture of complex consortia of aerobes and anaerobes in which bacteria traditionally considered early and late colonizers are found mixed together. When individually tracked during colonization and biofilm initiation, aggregates rapidly proliferate and expand tridimensionally, modulating population growth, spatial organization, and community scaffolding. In contrast, most single cells remain static or are incorporated by actively growing aggregates. These results suggest an alternative biofilm development process whereby aggregates containing different species or associated with human cells collectively adhere to the surface as "growth nuclei" to build the biofilm and shape polymicrobial communities at various spatial and taxonomic scales. IMPORTANCE Microbes in biological fluids can be found as aggregates. How these multicellular structures bind to surfaces and initiate the biofilm life cycle remains understudied. Here, we investigate the structural organization of microbial aggregates in human saliva and their role in biofilm formation. We found diverse mixtures of aggregates with different sizes, structures, and compositions in addition to free-living cells. When individually tracked during binding and growth on tooth-like surfaces, most aggregates developed into structured biofilm communities, whereas most single cells remained static or were engulfed by the growing aggregates. Our results reveal that preformed microbial consortia adhere as "buds of growth," governing biofilm initiation without specific taxonomic order or cell-by-cell succession, which provide new insights into spatial and population heterogeneity development in complex ecosystems.

Automated description of the mandible shape by deep learning.

PURPOSE: The shape of the mandible has been analyzed in a variety of fields, whether to diagnose conditions like osteoporosis or osteomyelitis, in forensics, to estimate biological information such as age, gender, and race or in orthognathic surgery. Although the methods employed produce encouraging results, most rely on the dry bone analyses or complex imaging techniques that, ultimately, hamper sample collection and, as a consequence, the development of large-scale studies. Thus, we proposed an objective, repeatable, and fully automatic approach to provide a quantitative description of the mandible in orthopantomographies (OPGs). METHODS: We proposed the use of a deep convolutional neural network (CNN) to localize a set of landmarks of the mandible contour automatically from OPGs. Furthermore, we detailed four different descriptors for the mandible shape to be used for a variety of purposes. This includes a set of linear distances and angles calculated from eight anatomical landmarks of the mandible, the centroid size, the shape variations from the mean shape, and a group of shape parameters extracted with a point distribution model. RESULTS: The fully automatic digitization of the mandible contour was very accurate, with a mean point to the curve error of 0.21 mm and a standard deviation comparable to that of a trained expert. The combination of the CNN and the four shape descriptors was validated in the well-known problems of forensic sex and age estimation, obtaining 87.8% of accuracy and a mean absolute error of 1.57 years, respectively. CONCLUSION: The methodology proposed, including the shape model, can be valuable in any field that requires a quantitative description of the mandible shape and a visual representation of its changes such as clinical practice, surgery management, dental research, or legal medicine.

In-Silico Detection of Oral Prokaryotic Species With Highly Similar 16S rRNA Sequence Segments Using Different Primer Pairs.

Although clustering by operational taxonomic units (OTUs) is widely used in the oral microbial literature, no research has specifically evaluated the extent of the limitations of this sequence clustering-based method in the oral microbiome. Consequently, our objectives were to: 1) evaluate in-silico the coverage of a set of previously selected primer pairs to detect oral species having 16S rRNA sequence segments with ≥97% similarity; 2) describe oral species with highly similar sequence segments and determine whether they belong to distinct genera or other higher taxonomic ranks. Thirty-nine primer pairs were employed to obtain the in-silico amplicons from the complete genomes of 186 bacterial and 135 archaeal species. Each fasta file for the same primer pair was inserted as subject and query in BLASTN for obtaining the similarity percentage between amplicons belonging to different oral species. Amplicons with 100% alignment coverage of the query sequences and with an amplicon similarity value ≥97% (ASI97) were selected. For each primer, the species coverage with no ASI97 (SC-NASI97) was calculated. Based on the SC-NASI97 parameter, the best primer pairs were OP_F053-KP_R020 for bacteria (region V1-V3; primer pair position for Escherichia coli J01859.1: 9-356); KP_F018-KP_R002 for archaea (V4; undefined-532); and OP_F114-KP_R031 for both (V3-V5; 340-801). Around 80% of the oral-bacteria and oral-archaea species analyzed had an ASI97 with at least one other species. These very similar species play different roles in the oral microbiota and belong to bacterial genera such as Campylobacter, Rothia, Streptococcus and Tannerella, and archaeal genera such as Halovivax, Methanosarcina and Methanosalsum. Moreover, ~20% and ~30% of these two-by-two similarity relationships were established between species from different bacterial and archaeal genera, respectively. Even taxa from distinct families, orders, and classes could be grouped in the same possible OTU. Consequently, regardless of the primer pair used, sequence clustering with a 97% similarity provides an inaccurate description of oral-bacterial and oral-archaeal species, which can greatly affect microbial diversity parameters. As a result, OTU clustering conditions the credibility of associations between some oral species and certain health and disease conditions. This significantly limits the comparability of the microbial diversity findings reported in oral microbiome literature.

DenTiUS Plaque, a Web-Based Application for the Quantification of Bacterial Plaque: Development and Usability Study.

BACKGROUND: In the dentistry field, the analysis of dental plaque is vital because it is the main etiological factor in the 2 most prevalent oral diseases: caries and periodontitis. In most of the papers published in the dental literature, the quantification of dental plaque is carried out using traditional, non-automated, and time-consuming indices. Therefore, the development of an automated plaque quantification tool would be of great value to clinicians and researchers. OBJECTIVE: This study aimed to develop a web-based tool called DenTiUS and various clinical indices to evaluate dental plaque levels using image analysis techniques. METHODS: The tool was executed as a web-based application to facilitate its use by researchers. Expert users are free to define experiments, including images from either a single patient (to observe an individual plaque growth pattern) or several patients (to perform a group characterization) at a particular moment or over time. A novel approach for detecting visible plaque has been developed as well as a new concept known as nonvisible plaque. This new term implies the classification of the remaining dental area into 3 subregions according to the risk of accumulating plaque in the near future. New metrics have also been created to describe visible and nonvisible plaque levels. RESULTS: The system generates results tables of the quantitative analysis with absolute averages obtained in each image (indices about visible plaque) and relative measurements (indices about visible and nonvisible plaque) relating to the reference moment. The clinical indices that can be calculated are the following: plaque index of an area per intensity (API index, a value between 0 and 100), area growth index (growth rate of plaque per unit of time in hours; percentage area/hour), and area time index (the time in days needed to achieve a plaque area of 100% concerning the initial area at the same moment). Images and graphics can be obtained for a moment from a patient in addition to a full report presenting all the processing data. Dentistry experts evaluated the DenTiUS Plaque software through a usability test, with the best-scoring questions those related to the workflow efficiency, value of the online help, attractiveness of the user interface, and overall satisfaction. CONCLUSIONS: The DenTiUS Plaque software allows automatic, reliable, and repeatable quantification of dental plaque levels, providing information about area, intensity, and growth pattern. Dentistry experts recognized that this software is suitable for quantification of dental plaque levels. Consequently, its application in the analysis of plaque evolution patterns associated with different oral conditions, as well as to evaluate the effectiveness of various oral hygiene measures, can represent an improvement in the clinical setting and the methodological quality of research studies.

Diagnostic accuracy of IL1ß in saliva: The development of predictive models for estimating the probability of the occurrence of periodontitis in non-smokers and smokers.

AIM: To obtain salivary interleukin (IL) 1ß-based models to predict the probability of the occurrence of periodontitis, differentiating by smoking habit. MATERIALS/METHODS: A total of 141 participants were recruited, 62 periodontally healthy controls and 79 subjects affected by periodontitis. Fifty of the diseased patients were given non-surgical periodontal treatment and showed significant clinical improvement in 2 months. IL1ß was measured in the salivary samples using the Luminex instrument. Binary logistic regression models were obtained to differentiate untreated periodontitis from periodontal health (first modelling) and untreated periodontitis from treated periodontitis (second modelling), distinguishing between non-smokers and smokers. The area under the curve (AUC) and classification measures were calculated. RESULTS: In the first modelling, IL1ß presented AUC values of 0.830 for non-smokers and 0.689 for smokers (accuracy = 77.6% and 70.7%, respectively). In the second, the predictive models revealed AUC values of 0.671 for non-smokers and 0.708 for smokers (accuracy = 70.0% and 75.0%, respectively). CONCLUSION: Salivary IL1ß has an excellent diagnostic capability when it comes to distinguishing systemically healthy patients with untreated periodontitis from those who are periodontally healthy, although this discriminatory potential is reduced in smokers. The diagnostic capacity of salivary IL1ß remains acceptable for differentiating between untreated and treated periodontitis.

Deep Neural Networks for Chronological Age Estimation From OPG Images.

Chronological age estimation is crucial labour in many clinical procedures, where the teeth have proven to be one of the best estimators. Although some methods to estimate the age from tooth measurements in orthopantomogram (OPG) images have been developed, they rely on time-consuming manual processes whose results are affected by the observer subjectivity. Furthermore, all those approaches have been tested only on OPG image sets of good radiological quality without any conditioning dental characteristic. In this work, two fully automatic methods to estimate the chronological age of a subject from the OPG image are proposed. The first (DANet) consists of a sequential Convolutional Neural Network (CNN) path to predict the age, while the second (DASNet) adds a second CNN path to predict the sex and uses sex-specific features with the aim of improving the age prediction performance. Both methods were tested on a set of 2289 OPG images of subjects from 4.5 to 89.2 years old, where both bad radiological quality images and images showing conditioning dental characteristics were not discarded. The results showed that the DASNet outperforms the DANet in every aspect, reducing the median Error (E) and the median Absolute Error (AE) by about 4 months in the entire database. When evaluating the DASNet in the reduced datasets, the AE values decrease as the real age of the subjects decreases, until reaching a median of about 8 months in the subjects younger than 15. The DASNet method was also compared to the state-of-the-art manual age estimation methods, showing significantly less over- or under-estimation problems. Consequently, we conclude that the DASNet can be used to automatically predict the chronological age of a subject accurately, especially in young subjects with developing dentitions.

Accuracy of single molecular biomarkers in saliva for the diagnosis of periodontitis: A systematic review and meta-analysis.

AIM: To analyse, using a meta-analytical approach, the diagnostic accuracy of single molecular biomarkers in saliva for the detection of periodontitis in systemically healthy subjects. MATERIALS AND METHODS: Articles on molecular biomarkers in saliva providing a binary contingency table (or sensitivity and specificity values and group sample sizes) in individuals with clinically diagnosed periodontitis were considered eligible. Searches for candidate articles were conducted in six electronic databases. The methodological quality was assessed through the tool Quality Assessment of Diagnostic Studies. Meta-analyses were performed using the Hierarchical Summary Receiver Operating Characteristic model. RESULTS: Meta-analysis was possible for 5 of the 32 biomarkers studied. The highest values of sensitivity for the diagnosis of periodontitis were obtained for IL1beta (78.7%), followed by MMP8 (72.5%), IL6 and haemoglobin (72.0% for both molecules); the lowest sensitivity value was for MMP9 (70.3%). In terms of specificity estimates, MMP9 had the best result (81.5%), followed by IL1beta (78.0%) and haemoglobin (75.2%); MMP8 had the lowest specificity (70.5%). CONCLUSIONS: MMP8, MMP9, IL1beta, IL6 and Hb were salivary biomarkers with good capability to detect periodontitis in systemically healthy subjects. MMP8 and IL1beta are the most researched biomarkers in the field, both showing clinically fair effectiveness for the diagnosis of periodontitis.

Accuracy of single molecular biomarkers in gingival crevicular fluid for the diagnosis of periodontitis: A systematic review and meta-analysis.

AIM: To analyse, by means of a meta-analytical approach, the diagnostic accuracy of molecular biomarkers in gingival crevicular fluid (GCF) for the detection of periodontitis in systemically healthy subjects. MATERIAL AND METHODS: Studies on GCF molecular biomarkers providing a binary classification table (or sensitivity and specificity values and group sample sizes) in individuals with clinically diagnosed periodontitis were considered eligible. The search was performed using six electronic databases. The methodological quality of studies was assessed through the tool Quality Assessment of Diagnostic Studies. Meta-analyses were performed using the Hierarchical Summary Receiver Operating Characteristic, which adjusts classification data using random effects logistic regression. RESULTS: The included papers identified 36 potential biomarkers for the detection of periodontitis and for four of them meta-analyses were performed. The median sensitivity and specificity were for MMP8, 76.7% and 92.0%; for elastase, 74.6% and 81.1%; for cathepsin, 72.8% and 67.3%, respectively. The worst estimates of sensitivity and specificity were for trypsin (71.3% and 66.1%, respectively). CONCLUSIONS: MMP8 showed good sensitivity and excellent specificity, which resulted in this biomarker being clinically the most useful or effective for the diagnosis of periodontitis in systemically healthy subjects, regardless of smoking condition.

In situ substrate-formed biofilms using IDODS mimic supragingival tooth-formed biofilms.

This study aimed to compare the bacterial viability and diversity of a substrate-formed biofilm (SF-biofilm) in situ to a supragingival tooth-formed biofilm (TF-biofilm) in the same group of individuals. The impact of the device/disc position and toothbrushing during the formation of SF-biofilm was also assessed. Two tests were run. In test 1, 15 volunteers wore two hemi-splints carrying six discs of human enamel, glass, and hydroxyapatite for 2 days, and were instructed to not perform any oral hygiene measure. Biofilm samples were collected from the substrates and the contralateral tooth and were analysed using CLSM. In five volunteers, half of the biofilm present on the discs and their contralateral teeth were scraped and analysed using 16S  pyrosequencing. In test 2, the microscopic analysis was repeated only on the SF-biofilm samples, and the volunteers were allowed to brush their teeth. Multivariate analyses revealed that the donors had a significant effect on the composition of the biofilm, confirming its subject-dependent character. The bacterial composition of the SF-biofilm was similar to the TF-biofilm, with significant differential abundance detected in very few taxa of low abundance. The toothbrushing during the formation of SF-biofilm was the only factor that conditioned the thickness or bacterial viability.

In Situ Antibacterial Activity of Essential Oils with and without Alcohol on Oral Biofilm: A Randomized Clinical Trial.

Currently, there is little evidence on the in situ antibacterial activity of essential oils (EO) without alcohol. This study aimed to evaluate in situ the substantivity and antiplaque effect on the plaque-like biofilm (PL-biofilm) of two solutions, a traditional formulation that contains EO with alcohol (T-EO) and an alcohol-free formulation of EO (Af-EO). Eighteen healthy adults performed a single mouthwash of: T-EO, Af-EO, and sterile water (WATER) after wearing an individualized disk-holding splint for 2 days. The bacterial viability (BV) and thickness of the PL-biofilm were quantified at baseline, 30 s, and 1, 3, 5, and 7 h post-rinsing (Test 1). Subsequently, each volunteer wore the splint for 4 days, applying two daily mouthwashes of: T-EO, Af-EO, and WATER. The BV, thickness, and covering grade (CG) of the PL-biofilm were quantified (Test 2). Samples were analyzed by confocal laser scanning microscopy after staining with the LIVE/DEAD® BacLight™ solution. To conduct the computations of the BV automatically, a Matlab toolbox called Dentius Biofilm was developed. In test 1, both EO antiseptics had a similar antibacterial effect, reducing BV after a single rinse compared to the WATER, and keeping it below baseline levels up to 7 h post-rinse (P < 0.001). The mean thickness of the PL-biofilm after rinsing was not affected by any of the EO formulations and ranged from 18.58 to 20.19 µm. After 4 days, the T-EO and Af-EO solutions were significantly more effective than the WATER, reducing the BV, thickness, and CG of the PL-biofilm (P < 0.001). Although, both EO antiseptics presented a similar bactericidal activity, the Af-EO rinses led to more significant reductions in the thickness and CG of the PL-biofilm than the T-EO rinses (thickness = 7.90 vs. 9.92 µm, P = 0.012; CG = 33.36 vs. 46.61%, P = 0.001). In conclusion, both essential oils antiseptics had very high immediate antibacterial activity and substantivity in situ on the 2-day PL-biofilm after a single mouthwash. In the 4-day PL-biofilm, both essential oils formulations demonstrated a very good antiplaque effect in situ, although the alcohol-free formula performed better at reducing the biofilm thickness and covering grade.