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      The predictive power of saliva electrolytes exceeds that of saliva microbiomes in diagnosing early childhood caries

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          ABSTRACT

          Early childhood caries (ECC) is one of the most prevalent chronic diseases affecting children worldwide, and thus its etiology, diagnosis, and prognosis are of particular clinical significance. This study aims to test the ability of salivary microbiome and electrolytes in diagnosing ECC, and their interplays within the same population. We here simultaneously profiled salivary microbiome and biochemical components of 331 children (166 caries-free (H group) and 165 caries-active children (C group)) aged 4-6 years. We identified both salivary microbial and biochemical dysbiosis associated with ECC. Remarkably, K +, Cl -, NH 4 +, Na +, SO 4 2-, Ca 2+, Mg 2+, and Br - were enriched while pH and NO 3 - were depleted in ECC. Moreover, the dmft index (ECC severity) positively correlated with Cl -, NH 4 +, Ca 2+, Mg 2+, Br -, while negatively with pH and NO 3 -. Furthermore, machine-learning classification models were constructed based on these biomarkers from saliva microbiota, or electrolytes (and pH). Unexpectedly, the electrolyte-based classifier (AUROC = 0.94) outperformed microbiome-based (AUROC = 0.70) one and the composite-based one (with both microbial and biochemical data; AUC = 0.89) in predicting ECC. Collectively, these findings indicate ECC-associated alterations and interplays in the oral microbiota, electrolytes and pH, underscoring the necessity of developing diagnostic models with predictors from salivary electrolytes.

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          An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

          Reference phylogenies are crucial for providing a taxonomic framework for interpretation of marker gene and metagenomic surveys, which continue to reveal novel species at a remarkable rate. Greengenes is a dedicated full-length 16S rRNA gene database that provides users with a curated taxonomy based on de novo tree inference. We developed a ‘taxonomy to tree' approach for transferring group names from an existing taxonomy to a tree topology, and used it to apply the Greengenes, National Center for Biotechnology Information (NCBI) and cyanoDB (Cyanobacteria only) taxonomies to a de novo tree comprising 408 315 sequences. We also incorporated explicit rank information provided by the NCBI taxonomy to group names (by prefixing rank designations) for better user orientation and classification consistency. The resulting merged taxonomy improved the classification of 75% of the sequences by one or more ranks relative to the original NCBI taxonomy with the most pronounced improvements occurring in under-classified environmental sequences. We also assessed candidate phyla (divisions) currently defined by NCBI and present recommendations for consolidation of 34 redundantly named groups. All intermediate results from the pipeline, which includes tree inference, jackknifing and transfer of a donor taxonomy to a recipient tree (tax2tree) are available for download. The improved Greengenes taxonomy should provide important infrastructure for a wide range of megasequencing projects studying ecosystems on scales ranging from our own bodies (the Human Microbiome Project) to the entire planet (the Earth Microbiome Project). The implementation of the software can be obtained from http://sourceforge.net/projects/tax2tree/.
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            Dental caries.

            Dental caries, otherwise known as tooth decay, is one of the most prevalent chronic diseases of people worldwide; individuals are susceptible to this disease throughout their lifetime. Dental caries forms through a complex interaction over time between acid-producing bacteria and fermentable carbohydrate, and many host factors including teeth and saliva. The disease develops in both the crowns and roots of teeth, and it can arise in early childhood as an aggressive tooth decay that affects the primary teeth of infants and toddlers. Risk for caries includes physical, biological, environmental, behavioural, and lifestyle-related factors such as high numbers of cariogenic bacteria, inadequate salivary flow, insufficient fluoride exposure, poor oral hygiene, inappropriate methods of feeding infants, and poverty. The approach to primary prevention should be based on common risk factors. Secondary prevention and treatment should focus on management of the caries process over time for individual patients, with a minimally invasive, tissue-preserving approach.
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              Demineralization–remineralization dynamics in teeth and bone

              Biomineralization is a dynamic, complex, lifelong process by which living organisms control precipitations of inorganic nanocrystals within organic matrices to form unique hybrid biological tissues, for example, enamel, dentin, cementum, and bone. Understanding the process of mineral deposition is important for the development of treatments for mineralization-related diseases and also for the innovation and development of scaffolds. This review provides a thorough overview of the up-to-date information on the theories describing the possible mechanisms and the factors implicated as agonists and antagonists of mineralization. Then, the role of calcium and phosphate ions in the maintenance of teeth and bone health is described. Throughout the life, teeth and bone are at risk of demineralization, with particular emphasis on teeth, due to their anatomical arrangement and location. Teeth are exposed to food, drink, and the microbiota of the mouth; therefore, they have developed a high resistance to localized demineralization that is unmatched by bone. The mechanisms by which demineralization–remineralization process occurs in both teeth and bone and the new therapies/technologies that reverse demineralization or boost remineralization are also scrupulously discussed. Technologies discussed include composites with nano- and micron-sized inorganic minerals that can mimic mechanical properties of the tooth and bone in addition to promoting more natural repair of surrounding tissues. Turning these new technologies to products and practices would improve health care worldwide.
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                Author and article information

                Journal
                J Oral Microbiol
                J Oral Microbiol
                Journal of Oral Microbiology
                Taylor & Francis
                2000-2297
                13 May 2021
                2021
                : 13
                : 1
                : 1921486
                Affiliations
                [a ]School of Stomatology, Qingdao University; , Qingdao, Shandong, China
                [b ]Single-Cell Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences; , Qingdao, Shandong, China
                [c ]Centre of Microbiome Innovation, Jacobs School of Engineering, University of California; , San Diego, La Jolla, California, 92093, USA
                [d ]UCSD Health Department of Pediatrics, University of California; , San Diego, La Jolla, California, 92093, USA
                [e ]Stomatology Centre; , Qingdao Municipal Hospital, Qingdao, Shandong, 266071 China
                [f ]Department of Stomatology, Tianjin Children’s Hospital; , Tianjin, 300400 China
                [g ]Department of Stomatology, Women & Children’s Health Care Hospital of Linyi; , Linyi, Shandong, 276000 China
                Author notes
                CONTACT Fang Yang yangf82@ 123456sina.com and Fei Teng tengfei@ 123456qibebt.ac.cn School of Stomatology, Qingdao University; , Qingdao, Shandong, 276003, China, and Single-Cell Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences; , Qingdao, Shandong, 266101, China.

                Ying Zhang, Shi Huang, and Songbo Jia, These authors contributed equally to this work

                Author information
                https://orcid.org/0000-0002-7529-2269
                https://orcid.org/0000-0002-8537-8576
                https://orcid.org/0000-0001-8639-5856
                Article
                1921486
                10.1080/20002297.2021.1921486
                8131007
                d2f1248e-4110-48df-9ed5-8c32ca2b861e
                © 2021 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License ( http://creativecommons.org/licenses/by-nc/4.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Page count
                Figures: 5, Tables: 1, References: 81, Pages: 14
                Categories
                Research Article
                Original Article

                Microbiology & Virology
                dental caries,unstimulated saliva,oral microbiome,electrolytes,diagnostic models

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