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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 ., (© 2024. The Author(s).)

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., (©Nicolás Vila-Blanco, Vicente Freire, Carlos Balsa-Castro, Inmaculada Tomás, María J Carreira. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 03.09.2020.)

Objectives: The objective of this study is to analyse the correlation of our own design of oral health scale (grades 0 and 1-better oral health vs. grades 2 and 3-poorer oral health) with the salivary microbiota., Patients and Methods: The oral health scale we elaborated was evaluated in 100 adults (25 patients from each global oral health grade). Saliva samples collected from these patients were analysed using microbiological culture techniques, determining the presence/absence and the concentrations of some odontopathogens and periodontopathogens., Results: In comparison with the global oral health grades 0-1, the grades 2-3 presented significantly higher values for the presence of odontopathogens (78 vs. 38 %; Streptococcus mutans, Lactobacillus spp. and Actinomyces spp.) and periodontopathogens (100 vs. 90 %; Aggregatibacter actinomycetemcomitans, Campylobacter spp., Fusobacterium spp. and Prevotella gingivalis). In comparison with the grades 0-1, the grades 2-3 presented significantly higher values for the concentrations (CFU/mL log10) of facultative anaerobes, strict anaerobes, odontopathogens (S. mutans, Lactobacillus spp. and Actinomyces spp.) and periodontopathogens (A. actinomycetemcomitans, Capnocytophaga spp., Campylobacter spp. and Fusobacterium spp.)., Conclusion: Our new global oral health scale shows a positive correlation with the detection and quantification of certain odontopathogens and periodontopathogens present in the saliva, confirming their possible infectious potential., Clinical Relevance: Our own design of oral health scale could be particularly useful for the epidemiological study of different populations, the evaluation of the influence of oral health on the development of certain systemic diseases as well as the analysis of inter- and intra-individual variability of the oral microbiota in relation to the different grades of the oral health scale.

Aim: The aim of this study was to investigate the robustness of the observations on the influence of oral hygiene, gingival and periodontal status on the development of bacteraemia from everyday oral activities ( B-EOA), analysing its prevalence, duration, magnitude and bacterial diversity. Material and Methods: This systematic review/meta-analysis complies with PRISMA reporting guidelines. MEDLINE-PubMed, the Cochrane Library and Embase were explored for detecting studies on B-EOA. Results: There were 290 potentially eligible articles, of which 12 article on B-EOA fulfilled the inclusion criteria and were processed for data extraction (seven on toothbrushing, one on dental flossing and four on chewing). Evaluating the influence of plaque and gingival indices on the prevalence of bacteraemia following toothbrushing, the pooled odds ratios were 2.61 [95% confidence interval ( CI) = 1.45-4.69] and 2.77 (95% CI = 1.50-5.11), respectively. None of five studies on bacteraemia following dental flossing and chewing revealed a statistically significant association between oral hygiene, gingival or periodontal status and the development of bacteraemia. Conclusions: Meta-analysis showed that plaque accumulation and gingival inflammation scores significantly increased the prevalence of bacteraemia following toothbrushing. However, systematic review showed no relationship between oral hygiene, gingival and periodontal status and the development of B-chewing, and there is no evidence that gingival and periodontal health status affects B-flossing. [ABSTRACT FROM AUTHOR]