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Pagnussatti MEL, de Barros Santos HS, Parolo CCF, Hilgert JB, Arthur RA. Oral microbiota: Taxonomic composition and functional profile in caries-free and in caries-affected individuals - A systematic review. Arch Oral Biol 2024; 168:106070. [PMID: 39226678 DOI: 10.1016/j.archoralbio.2024.106070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Revised: 08/18/2024] [Accepted: 08/20/2024] [Indexed: 09/05/2024]
Abstract
OBJECTIVE To compare the oral microbiota among caries-free (CF) with caries-affected (CA) individuals, both at taxonomic and at functional levels. DESIGN This systematic review was conducted following PRISMA guidelines. A structured search was carried out in MEDLINE/PUBMED, Web of Science, EMBASE, LILACS, SciELO, Scopus and Google Scholar databases up to September, 2023. Observational studies, without any restriction on date of publication and using next-generation targeted or untargeted sequencing methods for identification of microbial communities were included. Qualitative synthesis was performed from all included studies. RESULTS 54 studies were included (43 cross-sectional; 11 cohort) comprising more than 3486 participants (at least 1666 CF and 1820 CA) whose saliva and/or dental plaque were used as clinical samples. Methodological quality was graded as "fair" for most of the studies. The abundance of 87 bacterial and 44 fungal genera were statistically different among CF and CA individuals. Atopobium spp., Capnocytophaga spp., Lactobacillus spp., Prevotella spp., Scardovia spp., Selenomonas spp. among others were frequently reported as being more abundant in CA individuals. Several functional patterns, such as lipids, carbohydrate, starch, sucrose, amino sugar metabolisms, among others, were identified as being specifically related to CF or to CA conditions. CONCLUSION In spite of the variability among the included studies and of the predominance of qualitative synthesis, groups of microorganisms as well as specific functional profiles coded by the assessed microbiota are differently abundant among caries-affected and caries-free individuals. These results need to be interpreted with caution considering the limitations inherent to each assessed primary study.
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Affiliation(s)
- Maria Eduarda Lisbôa Pagnussatti
- Preventive and Community Dentistry Department, Dental School, Federal University of Rio Grande do Sul (UFRGS), Ramiro Barcelos, 2492, Porto Alegre 90035-003, Brazil.
| | - Heitor Sales de Barros Santos
- Preventive and Community Dentistry Department, Dental School, Federal University of Rio Grande do Sul (UFRGS), Ramiro Barcelos, 2492, Porto Alegre 90035-003, Brazil.
| | - Clarissa Cavalcanti Fatturi Parolo
- Preventive and Community Dentistry Department, Dental School, Federal University of Rio Grande do Sul (UFRGS), Ramiro Barcelos, 2492, Porto Alegre 90035-003, Brazil.
| | - Juliana Balbinot Hilgert
- Preventive and Community Dentistry Department, Dental School, Federal University of Rio Grande do Sul (UFRGS), Ramiro Barcelos, 2492, Porto Alegre 90035-003, Brazil; National Council for Research and Development (CNPq).
| | - Rodrigo Alex Arthur
- Preventive and Community Dentistry Department, Dental School, Federal University of Rio Grande do Sul (UFRGS), Ramiro Barcelos, 2492, Porto Alegre 90035-003, Brazil.
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Chimileski S, Borisy GG, Dewhirst FE, Mark Welch JL. Tip extension and simultaneous multiple fission in a filamentous bacterium. Proc Natl Acad Sci U S A 2024; 121:e2408654121. [PMID: 39226354 PMCID: PMC11406273 DOI: 10.1073/pnas.2408654121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 07/29/2024] [Indexed: 09/05/2024] Open
Abstract
Organisms display an immense variety of shapes, sizes, and reproductive strategies. At microscopic scales, bacterial cell morphology and growth dynamics are adaptive traits that influence the spatial organization of microbial communities. In one such community-the human dental plaque biofilm-a network of filamentous Corynebacterium matruchotii cells forms the core of bacterial consortia known as hedgehogs, but the processes that generate these structures are unclear. Here, using live-cell time-lapse microscopy and fluorescent D-amino acids to track peptidoglycan biosynthesis, we report an extraordinary example of simultaneous multiple division within the domain Bacteria. We show that C. matruchotii cells elongate at one pole through tip extension, similar to the growth strategy of soil-dwelling Streptomyces bacteria. Filaments elongate rapidly, at rates more than five times greater than other closely related bacterial species. Following elongation, many septa form simultaneously, and each cell divides into 3 to 14 daughter cells, depending on the length of the mother filament. The daughter cells then nucleate outgrowth of new thinner vegetative filaments, generating the classic "whip handle" morphology of this taxon. Our results expand the known diversity of bacterial cell cycles and help explain how this filamentous bacterium can compete for space, access nutrients, and form important interspecies interactions within dental plaque.
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Affiliation(s)
- Scott Chimileski
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543
| | - Gary G Borisy
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543
- Department of Microbiology, American Dental Association Forsyth Institute, Cambridge, MA 02142
| | - Floyd E Dewhirst
- Department of Microbiology, American Dental Association Forsyth Institute, Cambridge, MA 02142
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA 02115
| | - Jessica L Mark Welch
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543
- Department of Microbiology, American Dental Association Forsyth Institute, Cambridge, MA 02142
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Pinheiro ET, Karygianni L, Candeiro GTM, Vilela BG, Dantas LO, Pereira ACC, Gomes BPFA, Attin T, Thurnheer T, Russo G. Metatranscriptome and Resistome of the Endodontic Microbiome. J Endod 2024; 50:1059-1072.e4. [PMID: 38719087 DOI: 10.1016/j.joen.2024.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 02/07/2024] [Accepted: 03/11/2024] [Indexed: 06/07/2024]
Abstract
INTRODUCTION In this study, we used metatranscriptomics for the first time to investigate microbial composition, functional signatures, and antimicrobial resistance gene expression in endodontic infections. METHODS Root canal samples were collected from ten teeth, including five primary and five persistent/secondary endodontic infections. RNA from endodontic samples was extracted, and RNA sequencing was performed on a NovaSeq6000 system (Illumina). Taxonomic analysis was performed using the Kraken2 bacterial database. Then, sequences with a taxonomic classification were annotated against the Universal Protein Knowledgebase for functional annotation and the Comprehensive Antibiotic Resistance Database for AR-like gene identification. RESULTS Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria represented the dominant phyla, whereas Fusobacteria, Spirochetes, and Synergistetes were among the nondominant phyla. The top ten species were mainly represented by obligate (or quasiobligate) anaerobes, including Gram-negative (eg, Capnocytophaga sp. oral taxon 323, Fusobacterium nucleatum, Prevotella intermedia, Prevotella oris, Tannerella forsythia, and Tannerella sp. oral taxon HOT-286) and Gram-positive species (eg, Olsenella uli and Parvimonas micra). Transcripts encoding moonlighting proteins (eg, glycolytic proteins, translational elongation factors, chaperonin, and heat shock proteins) were highly expressed, potentially affecting bacterial adhesion, biofilm formation, host defense evasion, and inflammation induction. Endodontic bacteria expressed genes conferring resistance to antibiotic classes commonly used in dentistry, with a high prevalence and expression of tetracycline and lincosamide resistance genes. Antibiotic efflux and antibiotic target alteration/protection were the main resistance mechanisms. CONCLUSIONS Metatranscriptomics revealed the activity of potential endodontic pathogens, which expressed putative virulence factors and a wide diversity of genes potentially involved in AR.
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Affiliation(s)
- Ericka T Pinheiro
- Department of Dentistry, School of Dentistry, University of São Paulo, São Paulo, Brazil; Clinic of Conservative and Preventive Dentistry, Center of Dental Medicine, University of Zurich, Zürich, Switzerland.
| | - Lamprini Karygianni
- Clinic of Conservative and Preventive Dentistry, Center of Dental Medicine, University of Zurich, Zürich, Switzerland
| | - George T M Candeiro
- Faculty of Dentistry, Christus University Center (Unichristus), Fortaleza, Ceará, Brazil
| | - Bruna G Vilela
- Department of Dentistry, School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Larissa O Dantas
- Department of Dentistry, School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Ana C C Pereira
- Department of Dentistry, School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Brenda P F A Gomes
- Department of Restorative Dentistry, Division of Endodontics, Piracicaba Dental School, State University of Campinas - UNICAMP, Piracicaba, São Paulo, Brazil
| | - Thomas Attin
- Clinic of Conservative and Preventive Dentistry, Center of Dental Medicine, University of Zurich, Zürich, Switzerland
| | - Thomas Thurnheer
- Clinic of Conservative and Preventive Dentistry, Center of Dental Medicine, University of Zurich, Zürich, Switzerland
| | - Giancarlo Russo
- Functional Genomics Center Zurich, ETH-University of Zurich, Zürich, Switzerland (previous affiliation); EMBL Partnership Institute for Genome Editing Technologies, Life Sciences Center, Vilnius University, Vilnius, Lithuania; Institute of Bioscience, Life Sciences Center, Vilnius University, Vilnius, Lithuania
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Held NA, Manhart M. Are microbes colimited by multiple resources? Curr Opin Microbiol 2024; 80:102509. [PMID: 38991468 DOI: 10.1016/j.mib.2024.102509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/03/2024] [Accepted: 06/20/2024] [Indexed: 07/13/2024]
Abstract
Resource colimitation - the dependence of growth on multiple resources simultaneously - has become an important topic in microbiology due both to the development of systems approaches to cell physiology and ecology and to the relevance of colimitation to environmental science, biotechnology, and human health. Empirical tests of colimitation in microbes suggest that it may be common in nature. However, recent theoretical and empirical work has demonstrated the need for systematic measurements across resource conditions, in contrast to the factorial supplementation experiments used in most previous studies. The mechanistic causes of colimitation remain unclear in most cases and are an important challenge for future work, but we identify the alignment of resource consumption with the environment, interactions between resources, and biological and environmental heterogeneity as major factors. On the other hand, the consequences of colimitation are widespread for microbial physiology and ecology, especially the prediction and control of microbial growth, motivating continued consideration of this state in microbiology.
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Affiliation(s)
- Noelle A Held
- Department of Biological Sciences, Marine and Enviornmental Biology Section, University of Southern California, Los Angeles, CA, USA.
| | - Michael Manhart
- Center for Advanced Biotechnology and Medicine and Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, USA.
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Ahmad P, Moussa DG, Siqueira WL. Metabolomics for dental caries diagnosis: Past, present, and future. MASS SPECTROMETRY REVIEWS 2024. [PMID: 38940512 DOI: 10.1002/mas.21896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 05/22/2024] [Accepted: 06/15/2024] [Indexed: 06/29/2024]
Abstract
Dental caries, a prevalent global infectious condition affecting over 95% of adults, remains elusive in its precise etiology. Addressing the complex dynamics of caries demands a thorough exploration of taxonomic, potential, active, and encoded functions within the oral ecosystem. Metabolomic profiling emerges as a crucial tool, offering immediate insights into microecosystem physiology and linking directly to the phenotype. Identified metabolites, indicative of caries status, play a pivotal role in unraveling the metabolic processes underlying the disease. Despite challenges in metabolite variability, the use of metabolomics, particularly via mass spectrometry and nuclear magnetic resonance spectroscopy, holds promise in caries research. This review comprehensively examines metabolomics in caries prevention, diagnosis, and treatment, highlighting distinct metabolite expression patterns and their associations with disease-related bacterial communities. Pioneering in approach, it integrates singular and combinatory metabolomics methodologies, diverse biofluids, and study designs, critically evaluating prior limitations while offering expert insights for future investigations. By synthesizing existing knowledge, this review significantly advances our comprehension of caries, providing a foundation for improved prevention and treatment strategies.
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Affiliation(s)
- Paras Ahmad
- College of Dentistry, University of Saskatchewan, Saskatoon, SK, Canada
| | - Dina G Moussa
- College of Dentistry, University of Saskatchewan, Saskatoon, SK, Canada
| | - Walter L Siqueira
- College of Dentistry, University of Saskatchewan, Saskatoon, SK, Canada
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Stankevic E, Kern T, Borisevich D, Poulsen CS, Madsen AL, Hansen TH, Jonsson A, Schubert M, Nygaard N, Nielsen T, Belstrøm D, Ahluwalia TS, Witte DR, Grarup N, Arumugam M, Pedersen O, Hansen T. Genome-wide association study identifies host genetic variants influencing oral microbiota diversity and metabolic health. Sci Rep 2024; 14:14738. [PMID: 38926497 PMCID: PMC11208528 DOI: 10.1038/s41598-024-65538-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 06/20/2024] [Indexed: 06/28/2024] Open
Abstract
The microbial communities of the oral cavity are important elements of oral and systemic health. With emerging evidence highlighting the heritability of oral bacterial microbiota, this study aimed to identify host genome variants that influence oral microbial traits. Using data from 16S rRNA gene amplicon sequencing, we performed genome-wide association studies with univariate and multivariate traits of the salivary microbiota from 610 unrelated adults from the Danish ADDITION-PRO cohort. We identified six single nucleotide polymorphisms (SNPs) in human genomes that showed associations with abundance of bacterial taxa at different taxonomical tiers (P < 5 × 10-8). Notably, SNP rs17793860 surpassed our study-wide significance threshold (P < 1.19 × 10-9). Additionally, rs4530093 was linked to bacterial beta diversity (P < 5 × 10-8). Out of these seven SNPs identified, six exerted effects on metabolic traits, including glycated hemoglobin A1c, triglyceride and high-density lipoprotein cholesterol levels, the risk of type 2 diabetes and stroke. Our findings highlight the impact of specific host SNPs on the composition and diversity of the oral bacterial community. Importantly, our results indicate an intricate interplay between host genetics, the oral microbiota, and metabolic health. We emphasize the need for integrative approaches considering genetic, microbial, and metabolic factors.
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Affiliation(s)
- Evelina Stankevic
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Timo Kern
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Dmitrii Borisevich
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Casper Sahl Poulsen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anne Lundager Madsen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tue Haldor Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Medical Department, Zealand University Hospital, Koege, Denmark
| | - Anna Jonsson
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel Schubert
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nikoline Nygaard
- Department of Odontology, Section for Clinical Oral Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Trine Nielsen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Medical Department, Zealand University Hospital, Koege, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Daniel Belstrøm
- Department of Odontology, Section for Clinical Oral Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Tarunveer S Ahluwalia
- Steno Diabetes Center Copenhagen, Herlev, Denmark
- The Bioinformatics Center, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Daniel R Witte
- Department of Public Health, Aarhus University, Aarhus, Denmark
- Steno Diabetes Center Aarhus, Aarhus, Denmark
| | - Niels Grarup
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Manimozhiyan Arumugam
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Oluf Pedersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Center for Clinical Metabolic Research, Herlev-Gentofte University Hospital, Copenhagen, Denmark
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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Quiles KR, Shao FZ, Johnson WE, Chen F. EPITHELIAL REMODELING AND MICROBIAL DYSBIOSIS IN THE LOWER RESPIRATORY TRACT OF VITAMIN A-DEFICIENT MOUSE LUNGS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.21.600110. [PMID: 38948802 PMCID: PMC11212965 DOI: 10.1101/2024.06.21.600110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
The World Health Organization identified vitamin A deficiency (VAD) as a major public health issue in low-income communities and developing countries, while additional studies have shown dietary VAD leads to various lung pathologies. Once believed to be sterile, research now shows that transient microbial communities exist within healthy lungs and are often dysregulated in patients suffering from malnourishment, respiratory infections, and disease. The inability to parse vitamin A-mediated mechanisms from other metabolic mechanisms in humans with pathogenic endotypes, as well as the lack of data investigating how VAD affects the lung microbiome, remains a significant gap in the field. To address this unmet need, we compared molecular, metatranscriptomic, and morphometric data to identify how dietary VAD affects the lung as well as the lung microbiome. Our research shows structural and functional alterations in host-microbe-diet interactions in VAD lungs compared to vitamin A-sufficient (VAS) lungs; these changes are associated with epithelial remodeling, a breakdown in mucociliary clearance, microbial imbalance, and altered microbial colonization patterns after 8 weeks of vitamin A deficient diet. These findings confirm vitamin A is critical for lung homeostasis and provide mechanistic insights that could be valuable for the prevention of respiratory infections and disease.
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Affiliation(s)
- Kiloni R Quiles
- Boston University Pulmonary Allergy, Sleep, and Critical Care Center
| | - Feng-Zhi Shao
- Boston University Pulmonary Allergy, Sleep, and Critical Care Center
| | - W Evan Johnson
- Rutgers University, New Jersey Medical School, Division of Infectious Disease, Department of Medicine
- Rutgers University, New Jersey Medical School, Center for Data Science
| | - Felicia Chen
- Boston University Pulmonary Allergy, Sleep, and Critical Care Center
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Salgado-Peralvo ÁO, Kewalramani N, Pérez-Jardón A, Pérez-Sayáns M, Mateos-Moreno MV, Arriba-Fuente L. Antibiotic prescribing patterns in the placement of dental implants in Europe: A systematic review of survey-based studies. Med Oral Patol Oral Cir Bucal 2024; 29:e441-e450. [PMID: 38615255 PMCID: PMC11175579 DOI: 10.4317/medoral.26450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 03/18/2024] [Indexed: 04/15/2024] Open
Abstract
BACKGROUND The present systematic review aims to investigate the guidelines for prescribing Preventive Antibiotic Therapy (PAT) in the placement of dental implants (DIs) without anatomical constraints in healthy patients by clinicians in Europe and to compare them with current recommendations. MATERIAL AND METHODS A search was performed in 4 databases: Medline (via PubMed), Web of Science, Scopus, and LILACS. The criteria employed were those described in the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analysis) declaration (PROSPERO Registration number: CRD42022382278). RESULTS The electronic search identified 10 studies published between 2010 and 2023 that met the established criteria. Overall, 60.8% ± 24.1% of European professionals routinely prescribe PAT, with the most frequent regimen being perioperative (mean= 46.7% ± 24.3%), followed by postoperative PAT only (mean= 20.3% ± 9.7%). CONCLUSIONS The most commonly prescribed antibiotic both pre- and postoperatively is amoxicillin and, in allergic patients, clindamycin. In Europe, more doses of PAT are being prescribed than suggested by current recommendations. For this reason, more PAT education is needed in educational curricula to promote a more rational use of antibiotics to reduce the occurrence of antimicrobial resistance.
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Affiliation(s)
- Á-O Salgado-Peralvo
- Facultad de Odontología Universidad Complutense de Madrid Plaza Ramón y Cajal s/n. 28040 Madrid, Spain
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Dahlquist-Axe G, Standeven FJ, Speller CF, Tedder A, Meehan CJ. Inferring diet, disease and antibiotic resistance from ancient human oral microbiomes. Microb Genom 2024; 10:001251. [PMID: 38739117 PMCID: PMC11165619 DOI: 10.1099/mgen.0.001251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 04/24/2024] [Indexed: 05/14/2024] Open
Abstract
The interaction between a host and its microbiome is an area of intense study. For the human host, it is known that the various body-site-associated microbiomes impact heavily on health and disease states. For instance, the oral microbiome is a source of various pathogens and potential antibiotic resistance gene pools. The effect of historical changes to the human host and environment to the associated microbiome, however, has been less well explored. In this review, we characterize several historical and prehistoric events which are considered to have impacted the oral environment and therefore the bacterial communities residing within it. The link between evolutionary changes to the oral microbiota and the significant societal and behavioural changes occurring during the pre-Neolithic, Agricultural Revolution, Industrial Revolution and Antibiotic Era is outlined. While previous studies suggest the functional profile of these communities may have shifted over the centuries, there is currently a gap in knowledge that needs to be filled. Biomolecular archaeological evidence of innate antimicrobial resistance within the oral microbiome shows an increase in the abundance of antimicrobial resistance genes since the advent and widespread use of antibiotics in the modern era. Nevertheless, a lack of research into the prevalence and evolution of antimicrobial resistance within the oral microbiome throughout history hinders our ability to combat antimicrobial resistance in the modern era.
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Affiliation(s)
- Gwyn Dahlquist-Axe
- School of Chemistry and Biosciences, University of Bradford, Bradford, UK
| | | | - Camilla F. Speller
- Department of Anthropology, University of British Columbia, Vancouver, Canada
| | - Andrew Tedder
- School of Chemistry and Biosciences, University of Bradford, Bradford, UK
| | - Conor J. Meehan
- Department of Biosciences, Nottingham Trent University, Nottingham, UK
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10
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Almeida E, Puri S, Labossiere A, Elangovan S, Kim J, Ramsey M. Bacterial multispecies interaction mechanisms dictate biogeographic arrangement between the oral commensals Corynebacterium matruchotii and Streptococcus mitis. mSystems 2023; 8:e0011523. [PMID: 37610230 PMCID: PMC10654079 DOI: 10.1128/msystems.00115-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 06/27/2023] [Indexed: 08/24/2023] Open
Abstract
IMPORTANCE As the microbiome era matures, the need for mechanistic interaction data between species is crucial to understand how stable microbiomes are preserved, especially in healthy conditions where the microbiota could help resist opportunistic or exogenous pathogens. Here we reveal multiple mechanisms of interaction between two commensals that dictate their biogeographic relationship to each other in previously described structures in human supragingival plaque. Using a novel variation for chemical detection, we observed metabolite exchange between individual bacterial cells in real time validating the ability of these organisms to carry out metabolic crossfeeding at distal and temporal scales observed in vivo. These findings reveal one way by which these interactions are both favorable to the interacting commensals and potentially the host.
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Affiliation(s)
- Eric Almeida
- Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, Rhode Island, USA
| | - Surendra Puri
- Department of Chemistry, The University of Rhode Island, Kingston, Rhode Island, USA
| | - Alex Labossiere
- Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, Rhode Island, USA
| | - Subashini Elangovan
- Department of Chemistry, The University of Rhode Island, Kingston, Rhode Island, USA
| | - Jiyeon Kim
- Department of Chemistry, The University of Rhode Island, Kingston, Rhode Island, USA
| | - Matthew Ramsey
- Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, Rhode Island, USA
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Ghilotti J, Mayorga P, Sanz JL, Forner L, Llena C. Remineralizing Ability of Resin Modified Glass Ionomers (RMGICs): A Systematic Review. J Funct Biomater 2023; 14:421. [PMID: 37623665 PMCID: PMC10455182 DOI: 10.3390/jfb14080421] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 08/09/2023] [Accepted: 08/09/2023] [Indexed: 08/26/2023] Open
Abstract
The selective caries removal approach leads to the need to use materials with the ability to remineralize remaining partially demineralized dentin. Among the materials proposed are resin-modified glass ionomer cements (RMGICs). The aim of this systematic review was to evaluate, based on in vitro experimental studies, whether RMGICs are suitable for remineralizing affected dentin. A systematic literature search was performed in four databases, followed by article selection, data extraction, and quality assessment. Studies assessing the remineralizing potential of RMGICs on dentin were included in our review. Studies which compared such properties between different RMGICs or with other materials were also eligible. The studies report the remineralizing ability of RMGICs, albeit with differences between different commercial products. RMGICs show a similar ability to conventional GICs to remineralize affected dentin, fulfilling the function for which they are designed. Moreover, the incorporation of additives, such as bioactive glass (BAG) or CCP-ACP, improves their remineralizing potential. The results of this review support the use of RMGICs as restorative materials after selective caries removal.
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Affiliation(s)
| | | | - José Luis Sanz
- Department of Stomatology, Faculty of Medicine and Dentistry, Universitat de València, 46010 Valencia, Spain
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12
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Zhang JS, Chen Z, Chu CH, Yu OY. Effect of silver diamine fluoride upon the microbial community of carious lesions: A scoping review. J Dent 2023; 134:104554. [PMID: 37220834 DOI: 10.1016/j.jdent.2023.104554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/03/2023] [Accepted: 05/15/2023] [Indexed: 05/25/2023] Open
Abstract
OBJECTIVES To explore the effects of silver diamine fluoride (SDF) on the microbial community of carious lesions. DATA Original studies evaluating the effect of SDF treatment on the microbial community of human carious lesions were included. SOURCES A systematic search of English-language publications was performed in PubMed, EMBASE, Scopus, and Web of Science. Gray literature was searched in ClinicalTrials.gov and Google Scholar. STUDY SELECTION/RESULTS This review included seven publications reporting the effects of SDF on microbial community of dental plaque or carious dentin, including the microbial biodiversity, relative abundance of microbial taxa, and predicted functional pathways of the microbial community. The studies on microbial community of dental plaque reported that SDF did not have a significant effect on both the within-community species diversity (alpha-diversity) and inter-community microbial compositional dissimilarity (beta-diversity) of the plaque microbial communities. However, SDF changed the relative abundance of 29 bacterial species of plaque community, inhibited carbohydrate transportation and interfered with the metabolic functions of the plaque microbial community. A study on the microbial community in dentin carious lesions reported that SDF affected its beta-diversity and changed the relative abundance of 14 bacterial species. CONCLUSION SDF showed no significant effects on the biodiversity of the plaque microbial community but changed the beta-diversity of the carious dentin microbial community. SDF could change the relative abundance of certain bacterial species in the dental plaque and the carious dentin. SDF could also affect the predicted functional pathways of the microbial community. CLINICAL SIGNIFICANCE This review provided comprehensive evidence on the potential effect of SDF treatment on the microbial community of carious lesions.
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Affiliation(s)
- Josie Shizhen Zhang
- Faculty of Dentistry, The University of Hong Kong, 34 Hospital Road, Hong Kong SAR, China
| | - Zigui Chen
- Faculty of Dentistry, The University of Hong Kong, 34 Hospital Road, Hong Kong SAR, China; Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Chun-Hung Chu
- Faculty of Dentistry, The University of Hong Kong, 34 Hospital Road, Hong Kong SAR, China
| | - Ollie Yiru Yu
- Faculty of Dentistry, The University of Hong Kong, 34 Hospital Road, Hong Kong SAR, China.
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13
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Antibiotic Resistance: The Silent Pandemia (in the COVID-19 Era). Int Dent J 2023; 73:328-329. [PMID: 36737266 PMCID: PMC9834172 DOI: 10.1016/j.identj.2023.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/03/2023] [Accepted: 01/03/2023] [Indexed: 01/13/2023] Open
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14
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Ojala T, Kankuri E, Kankainen M. Understanding human health through metatranscriptomics. Trends Mol Med 2023; 29:376-389. [PMID: 36842848 DOI: 10.1016/j.molmed.2023.02.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 02/02/2023] [Accepted: 02/08/2023] [Indexed: 02/27/2023]
Abstract
Metatranscriptomics has revolutionized our ability to explore and understand transcriptional programs in microbial communities. Moreover, it has enabled us to gain deeper and more specific insight into the microbial activities in human gut, respiratory, oral, and vaginal communities. Perhaps the most important contribution of metatranscriptomics arises, however, from the analyses of disease-associated communities. We review the advantages and disadvantages of metatranscriptomics analyses in understanding human health and disease. We focus on human tissues low in microbial biomass and conditions associated with dysbiotic microbiota. We conclude that a more widespread use of metatranscriptomics and increased knowledge on microbe activities will uncover critical interactions between microbes and host in human health and provide diagnostic basis for culturing-independent, direct functional pathogen identification.
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Affiliation(s)
- Teija Ojala
- Department of Pharmacology, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Laboratory of Genetics, HUS Diagnostic Center, Hospital District of Helsinki and Uusimaa (HUS), Helsinki, Finland
| | - Esko Kankuri
- Department of Pharmacology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Matti Kankainen
- Laboratory of Genetics, HUS Diagnostic Center, Hospital District of Helsinki and Uusimaa (HUS), Helsinki, Finland; Hematology Research Unit Helsinki, University of Helsinki, Helsinki, Finland.
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15
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Chen WA, Dou Y, Fletcher HM, Boskovic DS. Local and Systemic Effects of Porphyromonas gingivalis Infection. Microorganisms 2023; 11:470. [PMID: 36838435 PMCID: PMC9963840 DOI: 10.3390/microorganisms11020470] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/16/2023] Open
Abstract
Porphyromonas gingivalis, a gram-negative anaerobe, is a leading etiological agent in periodontitis. This infectious pathogen can induce a dysbiotic, proinflammatory state within the oral cavity by disrupting commensal interactions between the host and oral microbiota. It is advantageous for P. gingivalis to avoid complete host immunosuppression, as inflammation-induced tissue damage provides essential nutrients necessary for robust bacterial proliferation. In this context, P. gingivalis can gain access to the systemic circulation, where it can promote a prothrombotic state. P. gingivalis expresses a number of virulence factors, which aid this pathogen toward infection of a variety of host cells, evasion of detection by the host immune system, subversion of the host immune responses, and activation of several humoral and cellular hemostatic factors.
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Affiliation(s)
- William A. Chen
- Division of Biochemistry, Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA
| | - Yuetan Dou
- Division of Microbiology and Molecular Genetics, Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA
| | - Hansel M. Fletcher
- Division of Microbiology and Molecular Genetics, Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA
| | - Danilo S. Boskovic
- Division of Biochemistry, Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA
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16
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Baybekov O, Stanishevskiy Y, Sachivkina N, Bobunova A, Zhabo N, Avdonina M. Isolation of Clinical Microbial Isolates during Orthodontic Aligner Therapy and Their Ability to Form Biofilm. Dent J (Basel) 2023; 11:dj11010013. [PMID: 36661550 PMCID: PMC9858208 DOI: 10.3390/dj11010013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/14/2022] [Accepted: 12/19/2022] [Indexed: 01/04/2023] Open
Abstract
The purpose of this study is to calculate microbiological composition of aligners after a day of wearing them. To date, the dental market for orthodontists offers many ways to correct bites. Aligners are transparent and almost invisible from the teeth. They are used for everyday wear to correct the incorrect position of the teeth, which was once considered the prerogative of braces. Scientists worldwide have repeatedly considered questions regarding the interaction between aligners and the oral cavity's microflora; however, the emphasis has mainly shifted toward species composition and antibiotic resistance. The various properties of these microorganisms, including biofilm formation, adhesion to various cells, and the ability to phagocytize, have not been studied so widely. In addition, these characteristics, as well as the microorganisms themselves, have properties that change over time, location, and in certain conditions. In this regard, the problem of biofilm formation in dental practice is always relevant. It requires constant monitoring since high contamination of orthodontic materials can reduce the effectiveness of local anti-inflammatory therapy and cause relapses in caries and inflammatory diseases of the oral cavity. Adhesive properties, one of the key factors in forming the architectonics of biofilms, provide the virulence factors of microorganisms and are characterized by an increase in optical density, determining the duration and retrospectivity of diagnostic studies. This paper focuses on the isolation of clinical microbial isolates during aligner therapy and their ability to form biofilms. In the future, we plan to use the obtained strains of microorganisms to create an effective and safe biofilm-destroying agent. We aimed to study morphometric and densitometric indicators of biofilms of microorganisms persisting on aligners.
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Affiliation(s)
- Oleg Baybekov
- Institute of Biochemical Technology and Nanotechnology, Peoples Friendship University of Russia (RUDN University), 117198 Moscow, Russia
| | - Yaroslav Stanishevskiy
- Institute of Biochemical Technology and Nanotechnology, Peoples Friendship University of Russia (RUDN University), 117198 Moscow, Russia
| | - Nadezhda Sachivkina
- Department of Microbiology V.S. Kiktenko, Peoples Friendship University of Russia (RUDN University), 117198 Moscow, Russia
- Correspondence:
| | - Anna Bobunova
- Department of Foreign Languages, Institute of Medicine, Peoples’ Friendship University of Russia (RUDN University), 117198 Moscow, Russia
| | - Natallia Zhabo
- Department of Foreign Languages, Institute of Medicine, Peoples’ Friendship University of Russia (RUDN University), 117198 Moscow, Russia
| | - Marina Avdonina
- Department of Linguistics and Intercultural Communication, Moscow State Linguistic University, 119034 Moscow, Russia
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Abstract
The oral cavity is an unique ecosystem formed by different structures, tissues, and a complex microbial community formed by hundreds of different species of bacteria, fungi, viruses, phages, and the candidate phyla radiation (CPR) group, all living in symbiosis with healthy individuals. In an opposite state, dental caries is a biofilm-mediated dysbiosis that involves changes in the core microbiome composition and function, which leads to the demineralization of tooth tissues due to the fermentation of dietary carbohydrates, producing acid by select oral bacteria. The cariogenic biofilm is typically characterized by bacterial species with the ability of adhering to the saliva-coated tooth surface, production of exopolysaccharides-rich matrix (which will limit the diffusion of acidic products of carbohydrate fermentation), and the ability of surviving in this acidic environment. Besides years of research and dental treatment, dental caries remains the most common chronic disease in children worldwide. This article aims to bring an insightful discussion about important questions that remain unanswered in the Cariology and Oral Microbiology fields, to move Science forward, characterize the interrelationships of these communities, and understand mechanistic functions between microorganisms and the host, therefore leading to translatable knowledge that benefits the provision of care to our pediatric patients.
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Affiliation(s)
- Apoena Aguiar Ribeiro
- Division of Diagnostic Sciences, Adams School of Dentistry, University of North Carolina, Chapel Hill, USA
- CONTACT Apoena Aguiar Ribeiro Division of Diagnostic Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, 150 Dental Circle, Chapel Hill, CB 7450, USA
| | - Bruce J. Paster
- Department of Microbiology, The Forsyth Institute, Cambridge, Massachusetts, USA
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, USA
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18
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The tongue biofilm metatranscriptome identifies metabolic pathways associated with the presence or absence of halitosis. NPJ Biofilms Microbiomes 2022; 8:100. [PMID: 36535943 PMCID: PMC9763428 DOI: 10.1038/s41522-022-00364-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022] Open
Abstract
Intra-oral halitosis usually results from the production of volatile sulfur compounds, such as methyl mercaptan and hydrogen sulfide, by the tongue microbiota. There are currently no reports on the microbial gene-expression profiles of the tongue microbiota in halitosis. In this study, we performed RNAseq of tongue coating samples from individuals with and without halitosis. The activity of Streptococcus (including S. parasanguinis), Veillonella (including V. dispar) and Rothia (including R. mucilaginosa) was associated with halitosis-free individuals while Prevotella (including P. shahi), Fusobacterium (including F. nucleatum) and Leptotrichia were associated with halitosis. Interestingly, the metatranscriptome of patients that only had halitosis levels of methyl mercaptan was similar to that of halitosis-free individuals. Finally, gene expression profiles showed a significant over-expression of genes involved in L-cysteine and L-homocysteine synthesis, as well as nitrate reduction genes, in halitosis-free individuals and an over-expression of genes responsible for cysteine degradation into hydrogen sulfide in halitosis patients.
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19
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Gómez-García AP, López-Vidal Y, Pinto-Cardoso S, Aguirre-García MM. Overexpression of proinflammatory cytokines in dental pulp tissue and distinct bacterial microbiota in carious teeth of Mexican Individuals. Front Cell Infect Microbiol 2022; 12:958722. [PMID: 36569197 PMCID: PMC9772992 DOI: 10.3389/fcimb.2022.958722] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 11/15/2022] [Indexed: 12/13/2022] Open
Abstract
The prevalence of dental caries in the Mexican adult population aged 20 to 85 years is around 93.3%, and 50% in Mexican children and adolescents. Worldwide, it is the most common non-communicable disease. One of the main etiological factors for dental caries is the oral microbiome and changes in its structure and function, with an expansion of pathogenic bacteria like Streptococcus mutans. The exposed dental pulp tissue triggers an innate immune response to counteract this bacterial invasion. The relation between oral dysbiosis and innate immune responses remains unclear. We aimed to understand the relationship between innate immune response and the oral microbiota by quantifying the expression of Toll-like receptors (TLRs) and proinflammatory markers (cytokines and a chemokine) in dental pulp tissue, either exposed or not to carious dentin, and to correlate this information with the oral microbiome found in healthy teeth and those with moderate caries. RNA was purified from pulp tissue, subjected to RT-qPCR and analysed with the ΔΔCt method. Supragingival dental plaque of non-carious teeth and dentin of carious teeth were subjected to 16S targeted sequencing. Principal coordinate analysis, permutational multivariate ANOVA, and linear discriminant analysis were used to assess differences between non-carious and carious teeth. Correlations were assessed with Spearman´s test and corrected for multiple comparisons using the FDR method. The relative abundance (RA) of Lactobacillus, Actinomyces, Prevotella, and Mitsuokella was increased in carious teeth; while the RA of Haemophilus and Porphyromonas decreased. Olsenella and Parascardovia were only detected in carious teeth. Significant overexpression of interleukin 1 beta (IL1 β), IL6, and CXCL8 was detected in pulp tissue exposed to carious dentin. IL1β correlated positively with TLR2 and Actinomyces; yet negatively with Porphyromonas. These findings suggest that immune response of pulp tissue chronically exposed to cariogenic microbiome is triggered by proinflammatory cytokines IL1β and IL6 and the chemokine CXCL8.
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Affiliation(s)
- Ana Pamela Gómez-García
- Unidad de Investigación UNAM-INC, División de Investigación, Facultad de Medicina, UNAM, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México, México
| | - Yolanda López-Vidal
- Programa de Inmunología Molecular Microbiana, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de Mexico, Ciudad de México, México
| | - Sandra Pinto-Cardoso
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, México
| | - María Magdalena Aguirre-García
- Unidad de Investigación UNAM-INC, División de Investigación, Facultad de Medicina, UNAM, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México, México,*Correspondence: María Magdalena Aguirre-García,
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20
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Zhang JS, Chu CH, Yu OY. Oral Microbiome and Dental Caries Development. Dent J (Basel) 2022; 10:184. [PMID: 36285994 PMCID: PMC9601200 DOI: 10.3390/dj10100184] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 09/25/2022] [Accepted: 09/27/2022] [Indexed: 11/06/2022] Open
Abstract
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.
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Affiliation(s)
| | | | - Ollie Yiru Yu
- Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China
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21
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Sharma MK, Srivastav VK, Joshi CK, Kumar M, Bhat KM. Metagenomic analysis of oral microbiota among oral cancer patients and tobacco chewers in Rajasthan, India. Bioinformation 2022; 18:757-763. [PMID: 37426511 PMCID: PMC10326344 DOI: 10.6026/97320630018757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 09/30/2022] [Accepted: 09/30/2022] [Indexed: 09/28/2024] Open
Abstract
Data on the microbial composition among tobacco chewers and oral cancer patients in Rajasthan, India is of interest. NGS analysis from tobacco chewers and oral cancer comprised the most abundant and core microbial taxa in the oral cavity. It shows that highly pathogenic phylum consisting of 6% Fusobacteria and 9% Firmicutes are observed in oral cancer samples; whereas, 0.6% Treponema, 34% Firmicutes, 0.02% Mollicutes, and 4% Fusobacteria are seen in tobacco chewers. Thus, data shows that the most abundant and core microbial taxa are found in the oral cavity of tobacco chewers and oral cancer patients in Rajasthan, India.
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Affiliation(s)
- Mukesh Kumar Sharma
- Department of Biotechnology, Maharaj Vinayak Global University, Jaipur Rajasthan, India
- Department of Botany, Vishwa Bharti PG College, Sikar, Rajasthan India
| | - Vivek Kumar Srivastav
- Department of Biotechnology, Maharaj Vinayak Global University, Jaipur Rajasthan, India
| | - Chetan Kumar Joshi
- Department of Zoology, Government Science College, Sikar, Rajasthan, India
| | - Mohan Kumar
- Gyan Joyti College of Pharmacy and Nursing School, Hazaribagh, Jharkhand India
| | - K. Manohar Bhat
- Department of Pedodontics and Preventive Dentistry, Jaipur Dental College, Jaipur, Rajasthan India
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22
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Carda-Diéguez M, Moazzez R, Mira A. Functional changes in the oral microbiome after use of fluoride and arginine containing dentifrices: a metagenomic and metatranscriptomic study. MICROBIOME 2022; 10:159. [PMID: 36171634 PMCID: PMC9520947 DOI: 10.1186/s40168-022-01338-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 07/27/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Tooth decay is one of the most prevalent diseases worldwide, and efficient tooth brushing with a fluoride-containing dentifrice is considered fundamental to caries prevention. Fluoride-containing dentifrices have been extensively studied in relation to enamel resistance to demineralization. Arginine (Arg) has also been proposed as a promising prebiotic to promote pH buffering through ammonia production. Here, we present the first metagenomic (DNA sequencing of the whole microbial community) and metatranscriptomic (RNAseq of the same community) analyses of human dental plaque to evaluate the effect of brushing with fluoride (Fl) and a Fl+Arg containing dentifrices on oral microbial composition and activity. Fifty-three patients were enrolled in a longitudinal clinical intervention study with two arms, including 26 caries-active and 27 caries-free adults. After a minimum 1-week washout period, dental plaque samples were collected at this post-washout baseline, 3 months after the use of a 1450-ppm fluoride dentifrice, and after 6 months of using a 1450-ppm fluoride with 1.5% arginine dentifrice. RESULTS There was a shift in both the composition and activity of the plaque microbiome after 3 months of brushing with the fluoride-containing toothpaste compared to the samples collected at the 1-week post-washout period, both for caries-active and caries-free sites. Although several caries-associated bacteria were reduced, there was also an increase in several health- and periodontitis-associated bacteria. Over 400 genes changed proportion in the metagenome, and between 180 and 300 genes changed their expression level depending on whether caries-free or caries-active sites were analyzed. The metagenome and metatranscriptome also changed after the subjects brushed with the Fl+Arg dentifrice. There was a further decrease of both caries- and periodontitis-associated organisms. In both caries-free and caries-active sites, a decrease of genes from the arginine biosynthesis pathway was also observed, in addition to an increase in the expression of genes associated with the arginine deiminase pathway, which catabolizes arginine into ammonia, thereby buffering acidic pH. Bacterial richness and diversity were not affected by either of the two treatments in the two arms of the study. CONCLUSIONS Our data demonstrate that long-term use of both assayed dentifrices changes the bacterial composition and functional profiles of human dental plaque towards a healthier microbial community, both in caries-free and caries-active sites. This observation was especially apparent for the Fl+Arg dentifrice. Thus, we conclude that the preventive benefits of tooth brushing go beyond the physical removal of dental plaque and that the active ingredients formulated within dentifrices have a positive effect not only on enamel chemistry but also on the metabolism of oral microbial populations. Video Abstract.
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Affiliation(s)
| | - Rebecca Moazzez
- Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Alex Mira
- Genomics and Health Department, FISABIO Institute, Valencia, Spain.
- Network of Epidemiology and Public Health, CIBERESP, Madrid, Spain.
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Moussa DG, Sharma AK, Mansour TA, Witthuhn B, Perdigão J, Rudney JD, Aparicio C, Gomez A. Functional signatures of ex-vivo dental caries onset. J Oral Microbiol 2022; 14:2123624. [PMID: 36189437 PMCID: PMC9518263 DOI: 10.1080/20002297.2022.2123624] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/09/2022] [Accepted: 08/18/2022] [Indexed: 11/18/2022] Open
Abstract
Background The etiology of dental caries remains poorly understood. With the advent of next-generation sequencing, a number of studies have focused on the microbial ecology of the disease. However, taxonomic associations with caries have not been consistent. Researchers have also pursued function-centric studies of the caries microbial communities aiming to identify consistently conserved functional pathways. A major question is whether changes in microbiome are a cause or a consequence of the disease. Thus, there is a critical need to define conserved functional signatures at the onset of dental caries. Methods Since it is unethical to induce carious lesions clinically, we developed an innovative longitudinal ex-vivo model integrated with the advanced non-invasive multiphoton second harmonic generation bioimaging to spot the very early signs of dental caries, combined with 16S rRNA short amplicon sequencing and liquid chromatography-mass spectrometry-based targeted metabolomics. Findings For the first time, we induced longitudinally monitored caries lesions validated with the scanning electron microscope. Consequently, we spotted the caries onset and, associated with it, distinguished five differentiating metabolites - Lactate, Pyruvate, Dihydroxyacetone phosphate, Glyceraldehyde 3-phosphate (upregulated) and Fumarate (downregulated). Those metabolites co-occurred with certain bacterial taxa; Streptococcus, Veillonella, Actinomyces, Porphyromonas, Fusobacterium, and Granulicatella, regardless of the abundance of other taxa. Interpretation These findings are crucial for understanding the etiology and dynamics of dental caries, and devising targeted interventions to prevent disease progression.
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Affiliation(s)
- Dina G. Moussa
- Minnesota Dental Research Center for Biomaterials and Biomechanics, Department of Restorative Sciences, School of Dentistry, University of Minnesota, Minneapolis, Minnesota, USA
- Department of Animal Science, College of Food, Agriculture and Natural Resource Sciences, University of Minnesota, St Paul, Minnesota, USA
| | - Ashok K. Sharma
- Department of Animal Science, College of Food, Agriculture and Natural Resource Sciences, University of Minnesota, St Paul, Minnesota, USA
| | - Tamer A Mansour
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA
- Department of Clinical Pathology, School of Medicine, Mansoura University, Mansoura, Egypt
| | - Bruce Witthuhn
- Center for Mass Spectrometry and Proteomics, Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Jorge Perdigão
- Department of Restorative Sciences, School of Dentistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Joel D. Rudney
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Conrado Aparicio
- Minnesota Dental Research Center for Biomaterials and Biomechanics, Department of Restorative Sciences, School of Dentistry, University of Minnesota, Minneapolis, Minnesota, USA
- Department of Restorative Sciences, School of Dentistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Andres Gomez
- Department of Animal Science, College of Food, Agriculture and Natural Resource Sciences, University of Minnesota, St Paul, Minnesota, USA
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24
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Krukiewicz K, Kazek-Kęsik A, Brzychczy-Włoch M, Łos MJ, Ateba CN, Mehrbod P, Ghavami S, Shyntum DY. Recent Advances in the Control of Clinically Important Biofilms. Int J Mol Sci 2022; 23:9526. [PMID: 36076921 PMCID: PMC9455909 DOI: 10.3390/ijms23179526] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 08/17/2022] [Accepted: 08/20/2022] [Indexed: 11/16/2022] Open
Abstract
Biofilms are complex structures formed by bacteria, fungi, or even viruses on biotic and abiotic surfaces, and they can be found in almost any part of the human body. The prevalence of biofilm-associated diseases has increased in recent years, mainly because of the frequent use of indwelling medical devices that create opportunities for clinically important bacteria and fungi to form biofilms either on the device or on the neighboring tissues. As a result of their resistance to antibiotics and host immunity factors, biofilms have been associated with the development or persistence of several clinically important diseases. The inability to completely eradicate biofilms drastically increases the burden of disease on both the patient and the healthcare system. Therefore, it is crucial to develop innovative ways to tackle the growth and development of biofilms. This review focuses on dental- and implant-associated biofilm infections, their prevalence in humans, and potential therapeutic intervention strategies, including the recent advances in pharmacology and biomedical engineering. It lists current strategies used to control the formation of clinically important biofilms, including novel antibiotics and their carriers, antiseptics and disinfectants, small molecule anti-biofilm agents, surface treatment strategies, and nanostructure functionalization, as well as multifunctional coatings particularly suitable for providing antibacterial effects to the surface of implants, to treat either dental- or implant-related bacterial infections.
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Affiliation(s)
- Katarzyna Krukiewicz
- Department of Physical Chemistry and Technology of Polymers, Silesian University of Technology, M. Strzody 9, 44-100 Gliwice, Poland
- Centre for Organic and Nanohybrid Electronics, Silesian University of Technology, Konarskiego 22B, 44-100 Gliwice, Poland
| | - Alicja Kazek-Kęsik
- Department of Inorganic Chemistry, Analytical Chemistry and Electrochemistry, Silesian University of Technology, 44-100 Gliwice, Poland
- Biotechnology Centre, Silesian University of Technology, Krzywoustego 8 Street, 44-100 Gliwice, Poland
| | - Monika Brzychczy-Włoch
- Department of Molecular Medical Microbiology, Chair of Microbiology, Faculty of Medicine, Jagiellonian University Medical College, Czysta 18 Street, 31-121 Krakow, Poland
| | - Marek J. Łos
- Department of Pathology, Pomeranian Medical University, 71-344 Szczecin, Poland
| | - Collins Njie Ateba
- Food Security and Safety Niche Area, North West University, Private Bag X2046, Mahikeng 2735, South Africa
| | - Parvaneh Mehrbod
- Influenza and Respiratory Viruses Department, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Saeid Ghavami
- Faculty of Medicine in Zabrze, University of Technology in Katowice, Academia of Silesia, 41-800 Zabrze, Poland
- Research Institute of Oncology and Hematology, Cancer Care Manitoba-University of Manitoba, Winnipeg, MB R3E 3P5, Canada
- Biology of Breathing Theme, Children Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB R3E 3P5, Canada
- Department of Human Anatomy and Cell Science, University of Manitoba College of Medicine, Winnipeg, MB R3E 3P5, Canada
| | - Divine Yufetar Shyntum
- Biotechnology Centre, Silesian University of Technology, Krzywoustego 8 Street, 44-100 Gliwice, Poland
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Guo M, Zhang Z, Lu J, Wang D, Yan Y, Zhang S, Yu X, Su S, Yuan L, Li Z, Zhang B. Differences in Supragingival Microbiome in Patients with and without Full-Crown Prostheses. Dent J (Basel) 2022; 10:dj10080152. [PMID: 36005250 PMCID: PMC9406617 DOI: 10.3390/dj10080152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/10/2022] [Accepted: 07/14/2022] [Indexed: 11/16/2022] Open
Abstract
Objectives: To characterize the microflora profile of supragingival biofilm in patients with and without full-crown prostheses. Methods: Plaque samples of full-crown prostheses and teeth in patients with porcelain-fused-to-metal crowns, all-ceramic crowns, and no prostheses were collected (three patients per group), using 16S rRNA high-throughput sequencing technology to conduct DNA sequencing on the samples and using Qiime, R, and PICRUSt2 software to perform bioinformatics analyses and functional analyses on sequencing data. Results: In total, 110,209 valid sequences were obtained in the experiment, corresponding to 11 phyla and 120 genera. The predominant species shared by the three groups were phyla Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria, and Proteobacteria and genera Rothia, Porphyromonas, Prevotella, Streptococcus, Veillonella, Leptotrichia, Neisseria, Citrobacter, and Pseudomonas. The species-difference analysis showed that genus Hameophilus significantly increased after the patient wore the dental prosthesis. Compared with the no-prosthesis samples, the functional analysis showed that cell motility increased in the samples from full-crown prostheses, while replication and repair, and translation decreased. Conclusions: This study reveals the changes in the oral microbial community of patients with full-crown prostheses, which could provide insights regarding the safety of materials for long-term use in the oral cavity.
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Affiliation(s)
- Manli Guo
- Key Lab of Oral Diseases of Gansu Province, Northwest Minzu University, Lanzhou 730000, China
| | - Zhidong Zhang
- School of Stomatology, Lanzhou University, Lanzhou 730000, China
| | - Jiyuan Lu
- School of Stomatology, Lanzhou University, Lanzhou 730000, China
| | - Di Wang
- School of Stomatology, Lanzhou University, Lanzhou 730000, China
| | - Yimin Yan
- School of Stomatology, Lanzhou University, Lanzhou 730000, China
| | - Shen Zhang
- School of Stomatology, Lanzhou University, Lanzhou 730000, China
| | - Xin Yu
- School of Stomatology, Lanzhou University, Lanzhou 730000, China
| | - Songhua Su
- School of Stomatology, Lanzhou University, Lanzhou 730000, China
| | - Lu Yuan
- School of Stomatology, Lanzhou University, Lanzhou 730000, China
| | - Zhige Li
- School of Stomatology, Lanzhou University, Lanzhou 730000, China
- Hospital of Stomatology Lanzhou University, Lanzhou 730000, China
| | - Baoping Zhang
- School of Stomatology, Lanzhou University, Lanzhou 730000, China
- Hospital of Stomatology Lanzhou University, Lanzhou 730000, China
- Correspondence: ; Tel./Fax: +86-931-8915051
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Zhu J, Chu W, Luo J, Yang J, He L, Li J. Dental Materials for Oral Microbiota Dysbiosis: An Update. Front Cell Infect Microbiol 2022; 12:900918. [PMID: 35846759 PMCID: PMC9280126 DOI: 10.3389/fcimb.2022.900918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/07/2022] [Indexed: 11/21/2022] Open
Abstract
The balance or dysbiosis of the microbial community is a major factor in maintaining human health or causing disease. The unique microenvironment of the oral cavity provides optimal conditions for colonization and proliferation of microbiota, regulated through complex biological signaling systems and interactions with the host. Once the oral microbiota is out of balance, microorganisms produce virulence factors and metabolites, which will cause dental caries, periodontal disease, etc. Microbial metabolism and host immune response change the local microenvironment in turn and further promote the excessive proliferation of dominant microbes in dysbiosis. As the product of interdisciplinary development of materials science, stomatology, and biomedical engineering, oral biomaterials are playing an increasingly important role in regulating the balance of the oral microbiome and treating oral diseases. In this perspective, we discuss the mechanisms underlying the pathogenesis of oral microbiota dysbiosis and introduce emerging materials focusing on oral microbiota dysbiosis in recent years, including inorganic materials, organic materials, and some biomolecules. In addition, the limitations of the current study and possible research trends are also summarized. It is hoped that this review can provide reference and enlightenment for subsequent research on effective treatment strategies for diseases related to oral microbiota dysbiosis.
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Affiliation(s)
- Jieyu Zhu
- State Key Laboratory of Oral Diseases, Department of Cariology and Endodontics, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Wenlin Chu
- State Key Laboratory of Oral Diseases, Department of Cariology and Endodontics, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, China
| | - Jun Luo
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, China
| | - Jiaojiao Yang
- State Key Laboratory of Oral Diseases, Department of Cariology and Endodontics, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- *Correspondence: Jiaojiao Yang, ; Libang He,
| | - Libang He
- State Key Laboratory of Oral Diseases, Department of Cariology and Endodontics, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- *Correspondence: Jiaojiao Yang, ; Libang He,
| | - Jiyao Li
- State Key Laboratory of Oral Diseases, Department of Cariology and Endodontics, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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Moussa DG, Ahmad P, Mansour TA, Siqueira WL. Current State and Challenges of the Global Outcomes of Dental Caries Research in the Meta-Omics Era. Front Cell Infect Microbiol 2022; 12:887907. [PMID: 35782115 PMCID: PMC9247192 DOI: 10.3389/fcimb.2022.887907] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/04/2022] [Indexed: 12/20/2022] Open
Abstract
Despite significant healthcare advances in the 21st century, the exact etiology of dental caries remains unsolved. The past two decades have witnessed a tremendous growth in our understanding of dental caries amid the advent of revolutionary omics technologies. Accordingly, a consensus has been reached that dental caries is a community-scale metabolic disorder, and its etiology is beyond a single causative organism. This conclusion was based on a variety of microbiome studies following the flow of information along the central dogma of biology from genomic data to the end products of metabolism. These studies were facilitated by the unprecedented growth of the next- generation sequencing tools and omics techniques, such as metagenomics and metatranscriptomics, to estimate the community composition of oral microbiome and its functional potential. Furthermore, the rapidly evolving proteomics and metabolomics platforms, including nuclear magnetic resonance spectroscopy and/or mass spectrometry coupled with chromatography, have enabled precise quantification of the translational outcomes. Although the majority supports 'conserved functional changes' as indicators of dysbiosis, it remains unclear how caries dynamics impact the microbiota functions and vice versa, over the course of disease onset and progression. What compounds the situation is the host-microbiota crosstalk. Genome-wide association studies have been undertaken to elucidate the interaction of host genetic variation with the microbiome. However, these studies are challenged by the complex interaction of host genetics and environmental factors. All these complementary approaches need to be orchestrated to capture the key players in this multifactorial disease. Herein, we critically review the milestones in caries research focusing on the state-of-art singular and integrative omics studies, supplemented with a bibliographic network analysis to address the oral microbiome, the host factors, and their interactions. Additionally, we highlight gaps in the dental literature and shed light on critical future research questions and study designs that could unravel the complexities of dental caries, the most globally widespread disease.
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Affiliation(s)
- Dina G. Moussa
- College of Dentistry, University of Saskatchewan, Saskatoon, SK, Canada
| | - Paras Ahmad
- College of Dentistry, University of Saskatchewan, Saskatoon, SK, Canada
| | - Tamer A. Mansour
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, United States
- Department of Clinical Pathology, School of Medicine, Mansoura University, Mansoura, Egypt
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Salgado-Peralvo AO, Garcia-Sanchez A, Kewalramani N, Barone A, Martínez-González JM, Velasco-Ortega E, López-López J, Kaiser-Cifuentes R, Guerra F, Matos-Garrido N, Moreno-Muñoz J, Núñez-Márquez E, Ortiz-García I, Jiménez-Guerra Á, Monsalve-Guil L. Consensus Report on Preventive Antibiotic Therapy in Dental Implant Procedures: Summary of Recommendations from the Spanish Society of Implants. Antibiotics (Basel) 2022; 11:antibiotics11050655. [PMID: 35625298 PMCID: PMC9138127 DOI: 10.3390/antibiotics11050655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/11/2022] [Accepted: 05/12/2022] [Indexed: 12/10/2022] Open
Abstract
Current patterns of preventive antibiotic prescribing are encouraging the spread of antimicrobial resistance. Recently, the Spanish Society of Implants (SEI) developed the first clinical practice guidelines published to date, providing clear guidelines on how to prescribe responsible and informed preventive antibiotic therapy (PAT) based on the available scientific evidence on dental implant treatments (DIs). The present document aims to summarise and disseminate the recommendations established by this expert panel. These were based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement. Studies were analysed using the Scottish Intercollegiate Guidelines Network (SIGN) checklist templates and ranked according to their level of evidence. They were then assigned a level of recommendation using the Grading of Recommendations, Assessment, Development and Evaluation system (GRADE). Guidelines were established on the type of PAT, antibiotic and dosage of administration in the placement of DIs without anatomical constraints, in bone augmentation with the placement of DIs in one or two stages, placement of immediate DIs, sinus elevations, implant prosthetic phase, as well as recommendations in patients allergic to penicillin. Therefore, the PAT must be adapted to the type of implant procedure to be performed.
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Affiliation(s)
- Angel-Orión Salgado-Peralvo
- Department of Dental Clinical Specialties, Faculty of Dentistry, Complutense University of Madrid, 28040 Madrid, Spain;
- Science Committee for Antibiotic Research of Spanish Society of Implants (SEI—Sociedad Española de Implantes), 28020 Madrid, Spain; (N.K.); (A.B.); (E.V.-O.); (J.L.-L.); (R.K.-C.); (F.G.); (N.M.-G.); (J.M.-M.); (E.N.-M.); (I.O.-G.); (L.M.-G.)
- Correspondence: (A.-O.S.-P.); (Á.J.-G.)
| | - Alvaro Garcia-Sanchez
- Department of Oral Health and Diagnostic Sciences, School of Dental Medicine, University of Connecticut Health, Farmington, CT 06030, USA;
| | - Naresh Kewalramani
- Science Committee for Antibiotic Research of Spanish Society of Implants (SEI—Sociedad Española de Implantes), 28020 Madrid, Spain; (N.K.); (A.B.); (E.V.-O.); (J.L.-L.); (R.K.-C.); (F.G.); (N.M.-G.); (J.M.-M.); (E.N.-M.); (I.O.-G.); (L.M.-G.)
- Department of Nursery and Stomatology, Faculty of Dentistry, Rey Juan Carlos University, 28922 Madrid, Spain
| | - Antonio Barone
- Science Committee for Antibiotic Research of Spanish Society of Implants (SEI—Sociedad Española de Implantes), 28020 Madrid, Spain; (N.K.); (A.B.); (E.V.-O.); (J.L.-L.); (R.K.-C.); (F.G.); (N.M.-G.); (J.M.-M.); (E.N.-M.); (I.O.-G.); (L.M.-G.)
- Department of Surgical, Medical and Molecular Pathology and Critical Areas, Faculty of Dentistry, University of Pisa, 56126 Pisa, Italy
| | - Jose-María Martínez-González
- Department of Dental Clinical Specialties, Faculty of Dentistry, Complutense University of Madrid, 28040 Madrid, Spain;
- Science Committee for Antibiotic Research of Spanish Society of Implants (SEI—Sociedad Española de Implantes), 28020 Madrid, Spain; (N.K.); (A.B.); (E.V.-O.); (J.L.-L.); (R.K.-C.); (F.G.); (N.M.-G.); (J.M.-M.); (E.N.-M.); (I.O.-G.); (L.M.-G.)
| | - Eugenio Velasco-Ortega
- Science Committee for Antibiotic Research of Spanish Society of Implants (SEI—Sociedad Española de Implantes), 28020 Madrid, Spain; (N.K.); (A.B.); (E.V.-O.); (J.L.-L.); (R.K.-C.); (F.G.); (N.M.-G.); (J.M.-M.); (E.N.-M.); (I.O.-G.); (L.M.-G.)
- Department of Stomatology, Faculty of Dentistry, University of Seville, 41009 Seville, Spain
| | - José López-López
- Science Committee for Antibiotic Research of Spanish Society of Implants (SEI—Sociedad Española de Implantes), 28020 Madrid, Spain; (N.K.); (A.B.); (E.V.-O.); (J.L.-L.); (R.K.-C.); (F.G.); (N.M.-G.); (J.M.-M.); (E.N.-M.); (I.O.-G.); (L.M.-G.)
- Department of Odontostomatology, Faculty of Dentistry, University of Barcelona, 08907 Barcelona, Spain
| | - Rodrigo Kaiser-Cifuentes
- Science Committee for Antibiotic Research of Spanish Society of Implants (SEI—Sociedad Española de Implantes), 28020 Madrid, Spain; (N.K.); (A.B.); (E.V.-O.); (J.L.-L.); (R.K.-C.); (F.G.); (N.M.-G.); (J.M.-M.); (E.N.-M.); (I.O.-G.); (L.M.-G.)
- Faculty of Dentistry, Finis Terrae University, Santiago de Chile 7501015, Chile
| | - Fernando Guerra
- Science Committee for Antibiotic Research of Spanish Society of Implants (SEI—Sociedad Española de Implantes), 28020 Madrid, Spain; (N.K.); (A.B.); (E.V.-O.); (J.L.-L.); (R.K.-C.); (F.G.); (N.M.-G.); (J.M.-M.); (E.N.-M.); (I.O.-G.); (L.M.-G.)
- Faculty of Dental Medicine, University of Coimbra, 3000-075 Coimbra, Portugal
| | - Nuno Matos-Garrido
- Science Committee for Antibiotic Research of Spanish Society of Implants (SEI—Sociedad Española de Implantes), 28020 Madrid, Spain; (N.K.); (A.B.); (E.V.-O.); (J.L.-L.); (R.K.-C.); (F.G.); (N.M.-G.); (J.M.-M.); (E.N.-M.); (I.O.-G.); (L.M.-G.)
- Department of Stomatology, Faculty of Dentistry, University of Seville, 41009 Seville, Spain
| | - Jesús Moreno-Muñoz
- Science Committee for Antibiotic Research of Spanish Society of Implants (SEI—Sociedad Española de Implantes), 28020 Madrid, Spain; (N.K.); (A.B.); (E.V.-O.); (J.L.-L.); (R.K.-C.); (F.G.); (N.M.-G.); (J.M.-M.); (E.N.-M.); (I.O.-G.); (L.M.-G.)
- Department of Stomatology, Faculty of Dentistry, University of Seville, 41009 Seville, Spain
| | - Enrique Núñez-Márquez
- Science Committee for Antibiotic Research of Spanish Society of Implants (SEI—Sociedad Española de Implantes), 28020 Madrid, Spain; (N.K.); (A.B.); (E.V.-O.); (J.L.-L.); (R.K.-C.); (F.G.); (N.M.-G.); (J.M.-M.); (E.N.-M.); (I.O.-G.); (L.M.-G.)
- Department of Stomatology, Faculty of Dentistry, University of Seville, 41009 Seville, Spain
| | - Iván Ortiz-García
- Science Committee for Antibiotic Research of Spanish Society of Implants (SEI—Sociedad Española de Implantes), 28020 Madrid, Spain; (N.K.); (A.B.); (E.V.-O.); (J.L.-L.); (R.K.-C.); (F.G.); (N.M.-G.); (J.M.-M.); (E.N.-M.); (I.O.-G.); (L.M.-G.)
- Department of Stomatology, Faculty of Dentistry, University of Seville, 41009 Seville, Spain
| | - Álvaro Jiménez-Guerra
- Science Committee for Antibiotic Research of Spanish Society of Implants (SEI—Sociedad Española de Implantes), 28020 Madrid, Spain; (N.K.); (A.B.); (E.V.-O.); (J.L.-L.); (R.K.-C.); (F.G.); (N.M.-G.); (J.M.-M.); (E.N.-M.); (I.O.-G.); (L.M.-G.)
- Department of Stomatology, Faculty of Dentistry, University of Seville, 41009 Seville, Spain
- Correspondence: (A.-O.S.-P.); (Á.J.-G.)
| | - Loreto Monsalve-Guil
- Science Committee for Antibiotic Research of Spanish Society of Implants (SEI—Sociedad Española de Implantes), 28020 Madrid, Spain; (N.K.); (A.B.); (E.V.-O.); (J.L.-L.); (R.K.-C.); (F.G.); (N.M.-G.); (J.M.-M.); (E.N.-M.); (I.O.-G.); (L.M.-G.)
- Department of Stomatology, Faculty of Dentistry, University of Seville, 41009 Seville, Spain
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Mechanisms underlying interactions between two abundant oral commensal bacteria. THE ISME JOURNAL 2022; 16:948-957. [PMID: 34732850 PMCID: PMC8940909 DOI: 10.1038/s41396-021-01141-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 09/21/2021] [Accepted: 10/07/2021] [Indexed: 01/12/2023]
Abstract
Complex polymicrobial biofilm communities are abundant in nature particularly in the human oral cavity where their composition and fitness can affect health. While the study of these communities during disease is essential and prevalent, little is known about interactions within the healthy plaque community. Here we describe interactions between two of the most abundant species in this healthy microbiome, Haemophilus parainfluenzae and Streptococcus mitis. We discovered that H. parainfluenzae typically exists adjacent to mitis group streptococci in vivo with which it is also positively correlated based on microbiome data. By comparing in vitro coculture data to ex vivo microscopy we revealed that this co-occurrence is density dependent and further influenced by H2O2 production. We discovered that H. parainfluenzae utilizes a more redundant, multifactorial response to H2O2 than related microorganisms and that this system's integrity enhances streptococcal fitness. Our results indicate that mitis group streptococci are likely the in vivo source of NAD for H. parainfluenzae and also evoke patterns of carbon utilization in vitro for H. parainfluenzae similar to those observed in vivo. Our findings describe mechanistic interactions between two of the most abundant and prevalent members of healthy supragingival plaque that contribute to their in vivo survival.
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Balu P, Venkatesan AS, Mariappan V, Muthu J, Pillai AB, Ravindran S, Chandrasekaran A. Expression of NLRP3 and P2X7 transcripts in gingival tissues of chronic periodontitis patients and its correlation with P. gingivalis load and periodontal parameters. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2021.101444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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31
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A Potential “Vitaminic Strategy” against Caries and Halitosis. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12052457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Streptococcus mutans and Fusobacterium nucleatum are two key bacteria of the oral microbiota. Due to their ability to form biofilms on oral tissues, they are both involved in the onset of the most common oral diseases. F. nucleatum is also the principal producer of hydrogen sulfide (H2S), causative of the awkward bad breath of halitosis. In this study, the oral product Vea® Oris, made by vitamin E and capric/caprylic acid only, was evaluated as a potential treatment for the most common oral diseases. Different concentrations of the product were tested against both S. mutans and F. nucleatum. The effect on planktonic and biofilm growth was investigated for both strains, and for F. nucleatum, the influence on H2S production was evaluated. From our data, the product did not relevantly reduce the planktonic growth of both strains, whereas it validly counteracted biofilm assemblage. Moreover, an interesting trend of H2S reduction was highlighted. Overall, these results suggested, on the one hand, a synergistic antimicrobial–antibiofilm action of two Vea® Oris components and, together, potential modulation activity on H2S production. However, the study should be implemented to confirm these only preliminary findings, certainly extending the panel of tested bacteria and using alternative methods of detection.
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Simon-Soro A, Ren Z, Krom BP, Hoogenkamp MA, Cabello-Yeves PJ, Daniel SG, Bittinger K, Tomas I, Koo H, Mira A. Polymicrobial Aggregates in Human Saliva Build the Oral Biofilm. mBio 2022; 13:e0013122. [PMID: 35189700 PMCID: PMC8903893 DOI: 10.1128/mbio.00131-22] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 01/24/2022] [Indexed: 12/13/2022] Open
Abstract
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.
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Affiliation(s)
- Aurea Simon-Soro
- Biofilm Research Laboratories, Department of Orthodontics, Divisions of Community Oral Health & Pediatric Dentistry, School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Center for Advanced Research in Public Health, FISABIO Foundation, Valencia, Spain
| | - Zhi Ren
- Biofilm Research Laboratories, Department of Orthodontics, Divisions of Community Oral Health & Pediatric Dentistry, School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Bastiaan P. Krom
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Michel A. Hoogenkamp
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | | | - Scott G. Daniel
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Inmaculada Tomas
- Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Universidade de Santiago de Compostela, Health Research Institute Foundation of Santiago (FIDIS), Santiago de Compostela, Spain
| | - Hyun Koo
- Biofilm Research Laboratories, Department of Orthodontics, Divisions of Community Oral Health & Pediatric Dentistry, School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Center for Innovation & Precision Dentistry, School of Dental Medicine and School of Engineering & Applied Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Alex Mira
- Center for Advanced Research in Public Health, FISABIO Foundation, Valencia, Spain
- CIBER Center for Epidemiology and Public Health, Madrid, Spain
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Dame-Teixeira N, de Lima AKA, Do T, Stefani CM. Meta-Analysis Using NGS Data: The Veillonella Species in Dental Caries. FRONTIERS IN ORAL HEALTH 2022; 2:770917. [PMID: 35048071 PMCID: PMC8757819 DOI: 10.3389/froh.2021.770917] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 09/22/2021] [Indexed: 02/01/2023] Open
Abstract
Objectives: In light of recent technological advances in Next-generation sequencing (NGS) and the accumulation of large, publicly available oral microbiome datasets, the need for meta-analysing data on caries microbiome is becoming feasible and essential. A consensus on the identification of enriched organisms in cariogenic dysbiotic biofilms would be reached. For example, members of the Veillonella genus have been detected in caries biofilms, and may have an underestimated contribution to the dysbiotic process. Hence, we aimed to determine the abundance of Veillonella species in dental caries in studies using NGS data. Materials and Methods: Analysis was performed according to the Preferred Reporting Items for Systematic Review and Meta-Analysis (registered at PROSPERO: CRD42020204150). Studies investigating microbial composition in saliva, dental biofilm, or carious dentin were included. Six databases and grey literature were searched. Two independent reviewers selected the papers and assessed the methodological quality. Results: Searches retrieved 1,323 titles, from which 38 studies were included in a qualitative synthesis, comprising a total of 1,374 caries and 745 caries-free individuals. Most studies analysed 16S rRNA amplicons, and only 5 studies used shotgun metagenomics and metatranscriptomics. A geographical bias was observed. The methodological quality was downrated in 81.5% of the studies due to the lack of criteria for defining cases and standard criteria used for measurement of the condition in a reliable way. Six studies on early childhood caries (ECC) were meta-analysed, confirming a significant enrichment of Veillonella spp. in caries-associated biofilms (but not saliva) when compared to caries-free controls [mean difference: 2.22 (0.54–3.90); p = 0.01]. Conclusions:Veillonella spp. is more abundant in individuals suffering with ECC when compared to caries-free controls (very low evidence certainty), and should be considered for further studies to observe their metabolism in dental caries. There is an urgent need for a consensus in methodologies used to allow for more rigorous comparison between NGS studies, particularly including clinical data and details of caries diagnosis, as they are currently scarce. Inconsistent reporting on the NGS data affected the cross-study comparison and the biological connexions of the relative abundances on caries microbiome.
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Affiliation(s)
- Naile Dame-Teixeira
- Department of Dentistry, School of Health Sciences, University of Brasilia, Brasilia, Brazil.,Division of Oral Biology, School of Dentistry, University of Leeds, Leeds, United Kingdom
| | | | - Thuy Do
- Division of Oral Biology, School of Dentistry, University of Leeds, Leeds, United Kingdom
| | - Cristine Miron Stefani
- Department of Dentistry, School of Health Sciences, University of Brasilia, Brasilia, Brazil
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Goswami K, Shope AJ, Tokarev V, Wright JR, Unverdorben LV, Ly T, Chen See J, McLimans CJ, Wong HT, Lock L, Clarkson S, Parvizi J, Lamendella R. Comparative meta-omics for identifying pathogens associated with prosthetic joint infection. Sci Rep 2021; 11:23749. [PMID: 34887434 PMCID: PMC8660779 DOI: 10.1038/s41598-021-02505-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 11/11/2021] [Indexed: 12/26/2022] Open
Abstract
Prosthetic joint infections (PJI) are economically and personally costly, and their incidence has been increasing in the United States. Herein, we compared 16S rRNA amplicon sequencing (16S), shotgun metagenomics (MG) and metatranscriptomics (MT) in identifying pathogens causing PJI. Samples were collected from 30 patients, including 10 patients undergoing revision arthroplasty for infection, 10 patients receiving revision for aseptic failure, and 10 patients undergoing primary total joint arthroplasty. Synovial fluid and peripheral blood samples from the patients were obtained at time of surgery. Analysis revealed distinct microbial communities between primary, aseptic, and infected samples using MG, MT, (PERMANOVA p = 0.001), and 16S sequencing (PERMANOVA p < 0.01). MG and MT had higher concordance with culture (83%) compared to 0% concordance of 16S results. Supervised learning methods revealed MT datasets most clearly differentiated infected, primary, and aseptic sample groups. MT data also revealed more antibiotic resistance genes, with improved concordance results compared to MG. These data suggest that a differential and underlying microbial ecology exists within uninfected and infected joints. This study represents the first application of RNA-based sequencing (MT). Further work on larger cohorts will provide opportunities to employ deep learning approaches to improve accuracy, predictive power, and clinical utility.
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Affiliation(s)
- Karan Goswami
- grid.417844.a0000 0004 4657 7542Rothman Institute, Philadelphia, PA USA
| | - Alexander J. Shope
- grid.417844.a0000 0004 4657 7542Rothman Institute, Philadelphia, PA USA ,Contamination Source Identification LLC, Huntingdon, PA USA
| | - Vasily Tokarev
- Contamination Source Identification LLC, Huntingdon, PA USA
| | | | | | - Truc Ly
- Contamination Source Identification LLC, Huntingdon, PA USA
| | | | | | - Hoi Tong Wong
- Contamination Source Identification LLC, Huntingdon, PA USA
| | - Lauren Lock
- Contamination Source Identification LLC, Huntingdon, PA USA
| | - Samuel Clarkson
- grid.417844.a0000 0004 4657 7542Rothman Institute, Philadelphia, PA USA
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35
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The human microbiome encodes resistance to the antidiabetic drug acarbose. Nature 2021; 600:110-115. [PMID: 34819672 DOI: 10.1038/s41586-021-04091-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 10/01/2021] [Indexed: 12/26/2022]
Abstract
The human microbiome encodes a large repertoire of biochemical enzymes and pathways, most of which remain uncharacterized. Here, using a metagenomics-based search strategy, we discovered that bacterial members of the human gut and oral microbiome encode enzymes that selectively phosphorylate a clinically used antidiabetic drug, acarbose1,2, resulting in its inactivation. Acarbose is an inhibitor of both human and bacterial α-glucosidases3, limiting the ability of the target organism to metabolize complex carbohydrates. Using biochemical assays, X-ray crystallography and metagenomic analyses, we show that microbiome-derived acarbose kinases are specific for acarbose, provide their harbouring organism with a protective advantage against the activity of acarbose, and are widespread in the microbiomes of western and non-western human populations. These results provide an example of widespread microbiome resistance to a non-antibiotic drug, and suggest that acarbose resistance has disseminated in the human microbiome as a defensive strategy against a potential endogenous producer of a closely related molecule.
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36
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Paz HES, Monteiro MF, Stolf CS, Altabtbaei K, Casati MZ, Casarin RCV, Kumar PS. Predicted functional and taxonomic analysis of subgingival biofilm of grade C periodontitis in young patients under maintenance therapy. J Periodontol 2021; 93:1119-1130. [PMID: 34727386 DOI: 10.1002/jper.21-0411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 10/21/2021] [Accepted: 10/21/2021] [Indexed: 11/09/2022]
Abstract
BACKGROUND In Grade C periodontitis in young patients (PerioC-Y), the functional roles of the subgingival community after years of periodontal treatment are still underexplored. This study evaluated the taxonomic and predicted functional content of the subgingival microbiome of PerioC-Y patients under supportive periodontal therapy (SPT). METHODS Clinical and microbiological data from subgingival biofilm were assessed from 10 PerioC-Y patients at two time points: at baseline and after 5.7±1.3 years of SPT. This was compared to 15 patients without a history of periodontitis. The V1-V3 and V4-V5 regions of the 16S rRNA were sequenced using the Illumina Miseq. Microbial composition was evaluated by the core microbiome, and alpha- and beta-diversity. The microbiome functional content was predicted using Picrust2, and the gene differential abundance was analyzed with DESeq2. RESULTS Clinical improvements were seen in PerioC-Y-SPT. Differences in β-diversity between PerioC-Y and Health were observed (Health x PerioC-Y-baseline, p = 0.02; Health x PerioC-Y-SPT, p = 0.05). Moreover, although β-diversity did not statistically change between baseline and SPT in PerioC-Y, the microbial correlation evidenced increased Streptococcus and decreased Treponema network contributions during SPT. Based on predicted functional data, treatment induced a reduction in genes related to flagellar protein and signal transduction in PerioC-Y. However, compared to healthy individuals, some genes remained more highly abundant in PerioC-Y-SPT, such as quorum sensing and efflux pump transporters. CONCLUSION Despite clinical improvements and a shift in taxonomic composition, the PerioC-Y patients' periodontal treatment was not enough to reach a similar microbiome to patients without disease experience. Some functional content in this biofilm remained altered in PerioC-Y regardless of disease control. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Hélvis E S Paz
- Periodontics Division, Department of Prosthodontics and Periodontics, Piracicaba Dental School, University of Campinas, Piracicaba, SP, Brazil
| | - Mabelle F Monteiro
- Periodontics Division, Department of Prosthodontics and Periodontics, Piracicaba Dental School, University of Campinas, Piracicaba, SP, Brazil
| | - Camila S Stolf
- Periodontics Division, Department of Prosthodontics and Periodontics, Piracicaba Dental School, University of Campinas, Piracicaba, SP, Brazil
| | - Khaled Altabtbaei
- Department of Periodontology, School of Dentistry, University of Alberta, Edmonton, Canada
| | - Márcio Z Casati
- Periodontics Division, Department of Prosthodontics and Periodontics, Piracicaba Dental School, University of Campinas, Piracicaba, SP, Brazil
| | - Renato C V Casarin
- Periodontics Division, Department of Prosthodontics and Periodontics, Piracicaba Dental School, University of Campinas, Piracicaba, SP, Brazil
| | - Purnima S Kumar
- Department of Periodontology, College of Dentistry, The Ohio State University, Columbus, OH, USA
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Salgado-Peralvo AO, Peña-Cardelles JF, Kewalramani N, Ortiz-García I, Jiménez-Guerra Á, Uribarri A, Velasco-Ortega E, Moreno-Muñoz J, Núñez-Márquez E, Monsalve-Guil L. Is Penicillin Allergy a Risk Factor for Early Dental Implant Failure? A Systematic Review. Antibiotics (Basel) 2021; 10:antibiotics10101227. [PMID: 34680808 PMCID: PMC8532851 DOI: 10.3390/antibiotics10101227] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 10/03/2021] [Accepted: 10/05/2021] [Indexed: 12/29/2022] Open
Abstract
The prescription of preventive antibiotics in dental implant treatments reduces the incidence of early failures. This study has focused mainly on the influence of amoxicillin, which is contraindicated in penicillin-allergic patients. The present systematic review aimed to determine whether penicillin-allergic patients have a higher risk of implant failure compared to non-allergic patients. An electronic search was performed on Medline and Web of Science using the following MeSH terms: (penicillin allergy OR clindamycin OR erythromycin OR azithromycin OR metronidazole) AND (dental implant OR dental implant failure OR dental implant complications). The criteria employed were those described in the PRISMA® Declaration. Only five articles were included that analyzed the failure rates of implants placed in penicillin-allergic patients who were prescribed clindamycin compared to non-allergic patients who were prescribed amoxicillin. With the limitations of this study, it is not possible to state that penicillin allergy per se constitutes a risk factor for early dental implant failure as most of the studies included self-reported allergic patients. Clindamycin has been associated with a significantly elevated risk of failure and an up to six times increased risk of infection. Immediate implants also have a 5.7 to 10 times higher risk of failure.
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Affiliation(s)
- Angel-Orión Salgado-Peralvo
- Department of Stomatology, University of Seville, 41009 Seville, Spain; (I.O.-G.); (Á.J.-G.); (E.V.-O.); (J.M.-M.); (E.N.-M.); (L.M.-G.)
- Science Committee for Antibiotic Research of Spanish Society of Implants (SEI—Sociedad Española de Implantes), 28020 Madrid, Spain; (J.-F.P.-C.); (N.K.)
- Correspondence:
| | - Juan-Francisco Peña-Cardelles
- Science Committee for Antibiotic Research of Spanish Society of Implants (SEI—Sociedad Española de Implantes), 28020 Madrid, Spain; (J.-F.P.-C.); (N.K.)
- Department of Basic Health Sciences, Rey Juan Carlos University, 28922 Madrid, Spain;
| | - Naresh Kewalramani
- Science Committee for Antibiotic Research of Spanish Society of Implants (SEI—Sociedad Española de Implantes), 28020 Madrid, Spain; (J.-F.P.-C.); (N.K.)
- Department of Nursery and Stomatology, Rey Juan Carlos University, 28922 Madrid, Spain
| | - Iván Ortiz-García
- Department of Stomatology, University of Seville, 41009 Seville, Spain; (I.O.-G.); (Á.J.-G.); (E.V.-O.); (J.M.-M.); (E.N.-M.); (L.M.-G.)
- Science Committee for Antibiotic Research of Spanish Society of Implants (SEI—Sociedad Española de Implantes), 28020 Madrid, Spain; (J.-F.P.-C.); (N.K.)
| | - Álvaro Jiménez-Guerra
- Department of Stomatology, University of Seville, 41009 Seville, Spain; (I.O.-G.); (Á.J.-G.); (E.V.-O.); (J.M.-M.); (E.N.-M.); (L.M.-G.)
- Science Committee for Antibiotic Research of Spanish Society of Implants (SEI—Sociedad Española de Implantes), 28020 Madrid, Spain; (J.-F.P.-C.); (N.K.)
| | - Andrea Uribarri
- Department of Basic Health Sciences, Rey Juan Carlos University, 28922 Madrid, Spain;
| | - Eugenio Velasco-Ortega
- Department of Stomatology, University of Seville, 41009 Seville, Spain; (I.O.-G.); (Á.J.-G.); (E.V.-O.); (J.M.-M.); (E.N.-M.); (L.M.-G.)
- Science Committee for Antibiotic Research of Spanish Society of Implants (SEI—Sociedad Española de Implantes), 28020 Madrid, Spain; (J.-F.P.-C.); (N.K.)
| | - Jesús Moreno-Muñoz
- Department of Stomatology, University of Seville, 41009 Seville, Spain; (I.O.-G.); (Á.J.-G.); (E.V.-O.); (J.M.-M.); (E.N.-M.); (L.M.-G.)
- Science Committee for Antibiotic Research of Spanish Society of Implants (SEI—Sociedad Española de Implantes), 28020 Madrid, Spain; (J.-F.P.-C.); (N.K.)
| | - Enrique Núñez-Márquez
- Department of Stomatology, University of Seville, 41009 Seville, Spain; (I.O.-G.); (Á.J.-G.); (E.V.-O.); (J.M.-M.); (E.N.-M.); (L.M.-G.)
- Science Committee for Antibiotic Research of Spanish Society of Implants (SEI—Sociedad Española de Implantes), 28020 Madrid, Spain; (J.-F.P.-C.); (N.K.)
| | - Loreto Monsalve-Guil
- Department of Stomatology, University of Seville, 41009 Seville, Spain; (I.O.-G.); (Á.J.-G.); (E.V.-O.); (J.M.-M.); (E.N.-M.); (L.M.-G.)
- Science Committee for Antibiotic Research of Spanish Society of Implants (SEI—Sociedad Española de Implantes), 28020 Madrid, Spain; (J.-F.P.-C.); (N.K.)
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Corralo DJ, Ev LD, Damé-Teixeira N, Maltz M, Arthur RA, Do T, Fatturi Parolo CC. Functional Active Microbiome in Supragingival Biofilms in Health and Caries. Caries Res 2021; 55:603-616. [PMID: 34380135 DOI: 10.1159/000518963] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 08/09/2021] [Indexed: 11/19/2022] Open
Affiliation(s)
- Daniela Jorge Corralo
- PhD by Faculty of Dentistry, Federal University of Rio Grande do Sul (UFRGS), Passo Fundo University (UPF), Passo Fundo, Brazil
| | - Laís Daniela Ev
- Department of Social and Preventive Dentistry, Faculty of Dentistry, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Nailê Damé-Teixeira
- Department of Dentistry, School of Health Sciences, University of Brasília, Federal District, Brasília, Brazil
- Division of Oral Biology, School of Dentistry, University of Leeds, Leeds, United Kingdom
| | - Marisa Maltz
- Department of Social and Preventive Dentistry, Faculty of Dentistry, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Rodrigo Alex Arthur
- Department of Social and Preventive Dentistry, Faculty of Dentistry, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Thuy Do
- Division of Oral Biology, School of Dentistry, University of Leeds, Leeds, United Kingdom
| | - Clarissa Cavalcanti Fatturi Parolo
- Department of Social and Preventive Dentistry, Faculty of Dentistry, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
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Pattem J, Davrandi M, Aguayo S, Slak B, Maev R, Allan E, Spratt D, Bozec L. Dependency of hydration and growth conditions on the mechanical properties of oral biofilms. Sci Rep 2021; 11:16234. [PMID: 34376751 PMCID: PMC8355335 DOI: 10.1038/s41598-021-95701-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 07/21/2021] [Indexed: 11/21/2022] Open
Abstract
Within the oral cavity, dental biofilms experience dynamic environments, in part due to changes in dietary content, frequency of intake and health conditions. This can impact bacterial diversity and morpho-mechanical properties. While phenotypic properties of oral biofilms are closely related to their composition, these can readily change according to dynamic variations in the growth environment and nutrient availability. Understanding the interlink between phenotypic properties, variable growth conditions, and community characterization is an essential requirement to develop structure–property relationships in oral-biofilms. In this study, the impact of two distinct growth media types with increasing richness on the properties of oral biofilms was assessed through a new combination of in-vitro time-lapse biophysical methods with microbiological assays. Oral biofilms grown in the enriched media composition presented a decrease in their pH, an increase in soluble EPS production, and a severe reduction in bacterial diversity. Additionally, enriched media conditions presented an increase in biofilm volumetric changes (upon hydration) as well as a reduction in elastic modulus upon indentation. With hydration time considered a major factor contributing to changes in biofilm mechanical properties, we have shown that it is less associated than media richness. Future investigations can now use this time-lapse approach, with a clearer focus on the extracellular matrix of oral biofilms dictating their morpho-mechanical properties.
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Affiliation(s)
- J Pattem
- Division of Biomaterials and Tissue Engineering, UCL Eastman Dental Institute, University College London, London, UK. .,National Centre for Molecular Hydrodynamics, and Soft Matter Biomaterials and Bio-Interfaces, University of Nottingham, The Limes Building, Sutton Bonington Campus, Sutton Bonington, Leicestershire, LE12 5RD, UK.
| | - M Davrandi
- Division of Microbial Diseases, UCL Eastman Dental Institute, University College London, London, UK
| | - S Aguayo
- School of Dentistry, Faculty of Medicine, Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - B Slak
- Department of Electrical and Computer Engineering, University of Windsor, Windsor, Canada
| | - R Maev
- Department of Electrical and Computer Engineering, University of Windsor, Windsor, Canada
| | - E Allan
- Division of Microbial Diseases, UCL Eastman Dental Institute, University College London, London, UK
| | - D Spratt
- Division of Microbial Diseases, UCL Eastman Dental Institute, University College London, London, UK
| | - L Bozec
- Division of Biomaterials and Tissue Engineering, UCL Eastman Dental Institute, University College London, London, UK.,Faculty of Dentistry, University of Toronto, Toronto, Canada
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Zhang Y, Thompson KN, Branck T, Yan Yan, Nguyen LH, Franzosa EA, Huttenhower C. Metatranscriptomics for the Human Microbiome and Microbial Community Functional Profiling. Annu Rev Biomed Data Sci 2021; 4:279-311. [PMID: 34465175 DOI: 10.1146/annurev-biodatasci-031121-103035] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Shotgun metatranscriptomics (MTX) is an increasingly practical way to survey microbial community gene function and regulation at scale. This review begins by summarizing the motivations for community transcriptomics and the history of the field. We then explore the principles, best practices, and challenges of contemporary MTX workflows: beginning with laboratory methods for isolation and sequencing of community RNA, followed by informatics methods for quantifying RNA features, and finally statistical methods for detecting differential expression in a community context. In thesecond half of the review, we survey important biological findings from the MTX literature, drawing examples from the human microbiome, other (nonhuman) host-associated microbiomes, and the environment. Across these examples, MTX methods prove invaluable for probing microbe-microbe and host-microbe interactions, the dynamics of energy harvest and chemical cycling, and responses to environmental stresses. We conclude with a review of open challenges in the MTX field, including making assays and analyses more robust, accessible, and adaptable to new technologies; deciphering roles for millions of uncharacterized microbial transcripts; and solving applied problems such as biomarker discovery and development of microbial therapeutics.
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Affiliation(s)
- Yancong Zhang
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Kelsey N Thompson
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Tobyn Branck
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Systems, Synthetic, and Quantitative Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Yan Yan
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Long H Nguyen
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA.,Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02108, USA
| | - Eric A Franzosa
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Curtis Huttenhower
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA
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Evaluation of Clinical, Biochemical and Microbiological Markers Related to Dental Caries. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18116049. [PMID: 34199794 PMCID: PMC8200118 DOI: 10.3390/ijerph18116049] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 05/31/2021] [Accepted: 06/02/2021] [Indexed: 11/17/2022]
Abstract
Our aim was to evaluate clinical, biochemical and microbiological markers related to dental caries in adults. A sample that consisted of 75 volunteers was utilized. The presence of caries and the presence of plaque and gingival indices were determined. Unstimulated salivary flow, pH, lactate, Streptococcus mutans and Streptococcus dentisani were measured in the participants’ plaque and saliva samples before and after rinsing with a sugar solution. Lactate in plaque was found to be significantly related to age, gender, tooth-brushing frequency, the presence of cavitated caries lesions and plaque and gingival indices (p < 0.05). The levels of S. dentisani in plaque increased significantly with tooth-brushing frequency (p = 0.03). Normalized plaque S. dentisani values and the percentage of S. dentisani were slightly higher in patients with basal lactic acid levels ≤ 50 mg/L. After rinsing with a sugary solution, the percentage of S. mutans levels in plaque were higher in patients with lactic acid levels > 350 mg/L (p = 0.03). Tooth-brushing frequency was the factor which was most associated with oral health. Women reflected better clinical and biochemical parameters than men. Low pH and high lactic acid levels tended to be associated with high caries rates. No association was found between bacteria levels and caries indices.
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Hassan MG, Zaher AR, Athanasiou AE. How orthodontic research can be enriched and advanced by the novel and promising evolutions in biomedicine. J Orthod 2021; 48:288-294. [PMID: 33860691 DOI: 10.1177/14653125211006116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Recent advances in developmental, molecular and cellular biology as well as biomedical technologies show a promising future for crossing the gap between biomedical basic sciences and clinical orthodontics. Orthodontic research shall utilise the advances and technologies in biomedical fields including genomics, molecular biology, bioinformatics and developmental biology. This review provides an update on the novel and promising evolutions in biomedicine and highlights their current and likely future implementation to orthodontic practice. Biotechnological opportunities in orthodontics and dentofacial orthopaedics are presented with regards to CRISPR technology, multi-omics sequencing, gene therapy, stem cells and regenerative medicine. Future orthodontic advances in terms of translational research are also discussed. Given the breadth of applications and the great number of questions that the presently available novel biomedical tools and techniques raise, their use may provide orthodontic research in the future with a great potential in understanding the aetiology of dentofacial deformities and malocclusions as well as in improving the practice of this clinical specialty.
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Affiliation(s)
- Mohamed G Hassan
- Department of Orthodontics, Faculty of Oral and Dental Medicine, South Valley University, Qena, Egypt
| | - Abbas R Zaher
- Department of Orthodontics, Faculty of Dentistry, Alexandria University, Alexandria, Egypt
| | - Athanasios E Athanasiou
- Department of Dentistry, School of Medicine, European University Cyprus, Nicosia, Cyprus.,Hamdan Bin Mohammed College of Dental Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
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43
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Rodrigues MX, Fiani N, Bicalho RC, Peralta S. Preliminary functional analysis of the subgingival microbiota of cats with periodontitis and feline chronic gingivostomatitis. Sci Rep 2021; 11:6896. [PMID: 33767308 PMCID: PMC7994850 DOI: 10.1038/s41598-021-86466-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 03/16/2021] [Indexed: 01/04/2023] Open
Abstract
The subgingival microbial communities of domestic cats remain incompletely characterized and it is unknown whether their functional profiles are associated with disease. In this study, we used a shotgun metagenomic approach to explore the functional potential of subgingival microbial communities in client-owned cats, comparing findings between periodontally healthy cats and cats with naturally occurring chronic periodontitis, aggressive periodontitis, and feline chronic gingivostomatitis. Subgingival samples were subjected to shotgun sequencing and the metagenomic datasets were analyzed using the MG-RAST metagenomic analysis server and STAMP v2.1.3 (Statistical Analysis of Metagenomic Profiles) software. The microbial composition was also described to better understand the predicted features of the communities. The Respiration category in the level 1 Subsystems database varied significantly among groups. In this category, the abundance of V-Type ATP-synthase and Biogenesis of cytochrome c oxidases were significantly enriched in the diseased and in the healthy groups, respectively. Both features have been previously described in periodontal studies in people and are in consonance with the microbial composition of feline subgingival sites. In addition, the narH (nitrate reductase) gene frequency, identified using the KEGG Orthology database, was significantly increased in the healthy group. The results of this study provide preliminary functional insights of the microbial communities associated with periodontitis in domestic cats and suggest that the ATP-synthase and nitrate-nitrite-NO pathways may represent appropriate targets for the treatment of this common disease.
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Affiliation(s)
- Marjory Xavier Rodrigues
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Nadine Fiani
- Department of Clinical Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Rodrigo Carvalho Bicalho
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Santiago Peralta
- Department of Clinical Sciences, Cornell University, Ithaca, NY, 14853, USA.
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44
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Salgado-Peralvo AO, Kewalramani N, Peña-Cardelles JF, Mateos-Moreno MV, Monsalve-Guil L, Jiménez-Guerra Á, Ortiz-García I, Velasco-Ortega E. Preventive Antibiotic Prescribing Habits among Professionals Dedicated to Oral Implantology: An Observational Study. Antibiotics (Basel) 2021; 10:antibiotics10030301. [PMID: 33799411 PMCID: PMC7999193 DOI: 10.3390/antibiotics10030301] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/05/2021] [Accepted: 03/12/2021] [Indexed: 12/11/2022] Open
Abstract
The prescription of preventive antibiotics (PA) in oral implantology is a controversial issue. The study aimed to determine the prescribing habits of PA in professionals dedicated to oral implantology in various treatments in healthy and at-risk patients. This is a cross-sectional observational study based on the STROBE (Strengthening the Reporting of Observational Studies in Epidemiology) guidelines. An electronic survey consisting of 4 blocks of questions was sent to members of the Spanish Society of Implants. The data were analyzed using descriptive analysis. A total of 303 participants (20.8%) responded to the questionnaire. One percent never prescribed PA, 55.4% prescribed them always, and 43.6% prescribed them sometimes. Ninety-six percent administered them preoperatively, while 92.4% administered them postoperatively. The most commonly used antibiotic is amoxicillin followed by amoxicillin with clavulanic acid (875/125 mg). Clindamycin is the most commonly administered antibiotic in patients with allergies. Professionals dedicated to oral implantology frequently prescribe PA in both healthy and at-risk patients, especially perioperatively. Immediate implant placement, sinus lifts, bone regeneration, and multiple implant placement are the treatments in which PA are most commonly prescribed, as well as in patients with heart valve prostheses or a history of bacterial endocarditis and immunodeficiency.
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Affiliation(s)
- Angel Orión Salgado-Peralvo
- Department of Stomatology, University of Seville, 41009 Seville, Spain; (L.M.-G.); (Á.J.-G.); (I.O.-G.); (E.V.-O.)
- Science Committee for Antibiotic Research of Spanish Society of Implants (SEI–Sociedad Española de Implantes), 28020 Madrid, Spain; (J.F.P.-C.); (M.V.M.-M.)
- Correspondence:
| | - Naresh Kewalramani
- Department of Nursery and Stomatology, Rey Juan Carlos University, 28922 Madrid, Spain;
| | - Juan Francisco Peña-Cardelles
- Science Committee for Antibiotic Research of Spanish Society of Implants (SEI–Sociedad Española de Implantes), 28020 Madrid, Spain; (J.F.P.-C.); (M.V.M.-M.)
- Department of Basic Health Sciences, Rey Juan Carlos University, 28922 Madrid, Spain
| | - María Victoria Mateos-Moreno
- Science Committee for Antibiotic Research of Spanish Society of Implants (SEI–Sociedad Española de Implantes), 28020 Madrid, Spain; (J.F.P.-C.); (M.V.M.-M.)
- Department of Clinical Specialties, Faculty of Dentistry, Complutense University of Madrid, 28040 Madrid, Spain
| | - Loreto Monsalve-Guil
- Department of Stomatology, University of Seville, 41009 Seville, Spain; (L.M.-G.); (Á.J.-G.); (I.O.-G.); (E.V.-O.)
- Science Committee for Antibiotic Research of Spanish Society of Implants (SEI–Sociedad Española de Implantes), 28020 Madrid, Spain; (J.F.P.-C.); (M.V.M.-M.)
| | - Álvaro Jiménez-Guerra
- Department of Stomatology, University of Seville, 41009 Seville, Spain; (L.M.-G.); (Á.J.-G.); (I.O.-G.); (E.V.-O.)
- Science Committee for Antibiotic Research of Spanish Society of Implants (SEI–Sociedad Española de Implantes), 28020 Madrid, Spain; (J.F.P.-C.); (M.V.M.-M.)
| | - Iván Ortiz-García
- Department of Stomatology, University of Seville, 41009 Seville, Spain; (L.M.-G.); (Á.J.-G.); (I.O.-G.); (E.V.-O.)
- Science Committee for Antibiotic Research of Spanish Society of Implants (SEI–Sociedad Española de Implantes), 28020 Madrid, Spain; (J.F.P.-C.); (M.V.M.-M.)
| | - Eugenio Velasco-Ortega
- Department of Stomatology, University of Seville, 41009 Seville, Spain; (L.M.-G.); (Á.J.-G.); (I.O.-G.); (E.V.-O.)
- Science Committee for Antibiotic Research of Spanish Society of Implants (SEI–Sociedad Española de Implantes), 28020 Madrid, Spain; (J.F.P.-C.); (M.V.M.-M.)
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Cugini C, Ramasubbu N, Tsiagbe VK, Fine DH. Dysbiosis From a Microbial and Host Perspective Relative to Oral Health and Disease. Front Microbiol 2021; 12:617485. [PMID: 33763040 PMCID: PMC7982844 DOI: 10.3389/fmicb.2021.617485] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 02/09/2021] [Indexed: 12/14/2022] Open
Abstract
The significance of microbiology and immunology with regard to caries and periodontal disease gained substantial clinical or research consideration in the mid 1960's. This enhanced emphasis related to several simple but elegant experiments illustrating the relevance of bacteria to oral infections. Since that point, the understanding of oral diseases has become increasingly sophisticated and many of the original hypotheses related to disease causality have either been abandoned or amplified. The COVID pandemic has reminded us of the importance of history relative to infectious diseases and in the words of Churchill "those who fail to learn from history are condemned to repeat it." This review is designed to present an overview of broad general directions of research over the last 60 years in oral microbiology and immunology, reviewing significant contributions, indicating emerging foci of interest, and proposing future directions based on technical advances and new understandings. Our goal is to review this rich history (standard microbiology and immunology) and point to potential directions in the future (omics) that can lead to a better understanding of disease. Over the years, research scientists have moved from a position of downplaying the role of bacteria in oral disease to one implicating bacteria as true pathogens that cause disease. More recently it has been proposed that bacteria form the ecological first line of defense against "foreign" invaders and also serve to train the immune system as an acquired host defensive stimulus. While early immunological research was focused on immunological exposure as a modulator of disease, the "hygiene hypothesis," and now the "old friends hypothesis" suggest that the immune response could be trained by bacteria for long-term health. Advanced "omics" technologies are currently being used to address changes that occur in the host and the microbiome in oral disease. The "omics" methodologies have shaped the detection of quantifiable biomarkers to define human physiology and pathologies. In summary, this review will emphasize the role that commensals and pathobionts play in their interaction with the immune status of the host, with a prediction that current "omic" technologies will allow researchers to better understand disease in the future.
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Affiliation(s)
- Carla Cugini
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, United States
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Radaic A, Kapila YL. The oralome and its dysbiosis: New insights into oral microbiome-host interactions. Comput Struct Biotechnol J 2021; 19:1335-1360. [PMID: 33777334 PMCID: PMC7960681 DOI: 10.1016/j.csbj.2021.02.010] [Citation(s) in RCA: 173] [Impact Index Per Article: 57.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 02/13/2021] [Accepted: 02/16/2021] [Indexed: 02/06/2023] Open
Abstract
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.
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Affiliation(s)
- Allan Radaic
- Kapila Laboratory, Orofacial Sciences Department, School of Dentistry, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Yvonne L. Kapila
- Kapila Laboratory, Orofacial Sciences Department, School of Dentistry, University of California, San Francisco (UCSF), San Francisco, CA, USA
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Miran W, Naradasu D, Okamoto A. Pathogens electrogenicity as a tool for in-situ metabolic activity monitoring and drug assessment in biofilms. iScience 2021; 24:102068. [PMID: 33554070 PMCID: PMC7859304 DOI: 10.1016/j.isci.2021.102068] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Concerns regarding increased antibiotic resistance arising from the emergent properties of biofilms have spurred interest in the discovery of novel antibiotic agents and techniques to directly estimate metabolic activity in biofilms. Although a number of methods have been developed to quantify biofilm formation, real-time quantitative assessment of metabolic activity in label-free biofilms remains a challenge. Production of electrical current via extracellular electron transport (EET) has recently been found in pathogens and appears to correlate with their metabolic activity. Accordingly, monitoring the production of electrical currents as an indicator of cellular metabolic activity in biofilms represents a new direction for research aiming to assess and screen the effects of antimicrobials on biofilm activity. In this article, we reviewed EET-capable pathogens and the methods to monitor biofilm activity to discuss advantages of using the capability of pathogens to produce electrical currents and effective combination of these methods. Moreover, we discussed EET mechanisms by pathogenic and environmental bacteria and open questions for the physiological roles of EET in pathogen's biofilm. The present limitations and possible future directions of in situ biofilm metabolic activity assessment for large-scale screening of antimicrobials are also discussed.
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Affiliation(s)
- Waheed Miran
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
| | - Divya Naradasu
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
| | - Akihiro Okamoto
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
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Quantifying Live Microbial Load in Human Saliva Samples over Time Reveals Stable Composition and Dynamic Load. mSystems 2021; 6:6/1/e01182-20. [PMID: 33594005 PMCID: PMC8561659 DOI: 10.1128/msystems.01182-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Evaluating microbial community composition through next-generation sequencing has become increasingly accessible. However, metagenomic sequencing data sets provide researchers with only a snapshot of a dynamic ecosystem and do not provide information about the total microbial number, or load, of a sample. Additionally, DNA can be detected long after a microorganism is dead, making it unsafe to assume that all microbial sequences detected in a community came from living organisms. By combining relic DNA removal by propidium monoazide (PMA) with microbial quantification with flow cytometry, we present a novel workflow to quantify live microbial load in parallel with metagenomic sequencing. We applied this method to unstimulated saliva samples, which can easily be collected longitudinally and standardized by passive collection time. We found that the number of live microorganisms detected in saliva was inversely correlated with salivary flow rate and fluctuated by an order of magnitude throughout the day in healthy individuals. In an acute perturbation experiment, alcohol-free mouthwash resulted in a massive decrease in live bacteria, which would have been missed if we did not consider dead cell signal. While removing relic DNA from saliva samples did not greatly impact the microbial composition, it did increase our resolution among samples collected over time. These results provide novel insight into the dynamic nature of host-associated microbiomes and underline the importance of applying scale-invariant tools in the analysis of next-generation sequencing data sets. IMPORTANCE Human microbiomes are dynamic ecosystems often composed of hundreds of unique microbial taxa. To detect fluctuations over time in the human oral microbiome, we developed a novel workflow to quantify live microbial cells with flow cytometry in parallel with next-generation sequencing, and applied this method to over 150 unstimulated, timed saliva samples. Microbial load was inversely correlated with salivary flow rate and fluctuated by an order of magnitude within a single participant throughout the day. Removing relic DNA improved our ability to distinguish samples over time and revealed that the percentage of sequenced bacteria in a given saliva sample that are alive can range from nearly 0% up to 100% throughout a typical day. These findings highlight the dynamic ecosystem of the human oral microbiome and the benefit of removing relic DNA signals in longitudinal microbiome study designs.
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Monleon‐Getino T, Frias‐Lopez J. A priori estimation of sequencing effort in complex microbial metatranscriptomes. Ecol Evol 2020; 10:13382-13394. [PMID: 33304545 PMCID: PMC7713979 DOI: 10.1002/ece3.6941] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/24/2020] [Accepted: 09/22/2020] [Indexed: 11/09/2022] Open
Abstract
Metatranscriptome analysis or the analysis of the expression profiles of whole microbial communities has the additional challenge of dealing with a complex system with dozens of different organisms expressing genes simultaneously. An underlying issue for virtually all metatranscriptomic sequencing experiments is how to allocate the limited sequencing budget while guaranteeing that the libraries have sufficient depth to cover the breadth of expression of the community. Estimating the required sequencing depth to effectively sample the target metatranscriptome using RNA-seq is an essential first step to obtain robust results in subsequent analysis and to avoid overexpansion, once the information contained in the library reaches saturation. Here, we present a method to calculate the sequencing effort using a simulated series of metatranscriptomic/metagenomic matrices. This method is based on an extrapolation rarefaction curve using a Weibull growth model to estimate the maximum number of observed genes as a function of sequencing depth. This approach allowed us to compute the effort at different confidence intervals and to obtain an approximate a priori effort based on an initial fraction of sequences. The analytical pipeline presented here may be successfully used for the in-depth and time-effective characterization of complex microbial communities, representing a useful tool for the microbiome research community.
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Affiliation(s)
- Toni Monleon‐Getino
- Section of Statistics (Department of Genetics, Microbiology, and Statistics)University of BarcelonaBarcelonaSpain
- BIOSTGRBIO (Research Group in Biostatistics and Bioinformatics)BarcelonaSpain
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Walther C, Zumbülte S, Faerber CM, Wierichs RJ, Meyer-Lueckel H, Conrads G, Henne K, Esteves-Oliveira M. Analysis of relative bacterial activity and lactate dehydrogenase gene expression of caries-associated bacteria in a site-specific natural biofilm: an ex vivo study. Clin Oral Investig 2020; 25:3669-3679. [PMID: 33226500 PMCID: PMC8137627 DOI: 10.1007/s00784-020-03691-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 11/10/2020] [Indexed: 11/30/2022]
Abstract
Objectives Detecting bacterial activity is considered a promising approach to monitor shifts from symbiosis to dysbiosis in oral microbiome. The present study aimed at investigating both the relative bacterial activity and the lactate dehydrogenase (ldh) gene expression of caries-associated bacteria in a site-specific natural biofilm. Material and methods Sixty subjects (age, mean ± SE: 30.1 ± 1.4) were allocated to two groups: caries-free subjects (CF) or caries-active subjects (CA). CF presented one sound surface (CFS, n = 30). CA presented two donor sites: a cavitated caries lesion (CAC, n = 30) and a sound reference surface (CAS, n = 30). Real-time quantitative PCR (q-PCR) on species or genus level and total bacteria was performed targeting the 16S gene, the 16S rRNA, the ldh gene, and the ldh mRNA (increasing 16S ribosomal RNA copy numbers can function as an indicator of increased energy metabolism). As the 16S rRNA abundance represents the number of ribosomes, while the 16S gene abundance represents the number of genomes, the quotient of the relative abundances functions as a measure for the relative bacterial activity (%). Results Both lactobacilli and S. mutans showed the highest relative bacterial activity in CAC ((mean ± SE) 218 ± 60% and 61 ± 16%, respectively) and the lowest values for both sound reference surfaces (69 ± 48%; 8 ± 3%). Significant differences were found between CAC and CAS as well as between CAC and CFS for both lactobacilli and S. mutans (p < 0.05). The ldh gene expression of lactobacilli and S. mutans only showed moderate values in CAC (1.90E+03 ± 2.11E+03; 2.08E+04 ± 4.44E+04 transcripts/μl) and CFS (2.04E+03 ± 2.74E+03; 8.16E+03 ± 6.64E+03 transcripts/μl); consequently no significant differences were detected. Conclusion and clinical relevance Caries-associated bacteria (lactobacilli and S. mutans) showed the highest relative bacterial activity in plaque of cavitated lesions, the lowest in sound surfaces, allowing the detection of a significant activity shift in health and disease for caries-active patients. However, no significant differences in ldh gene expression could be determined.
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Affiliation(s)
- Carolin Walther
- Department of Prosthetic Dentistry, Center for Dental and Oral Medicine, University Medical Center, Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany.
| | - Sandra Zumbülte
- Division of Oral Microbiology and Immunology, Department of Operative Dentistry, Periodontology, and Preventive Dentistry, RWTH Aachen University, Aachen, Germany
| | - Christoph M Faerber
- Department of Operative Dentistry, Periodontology, and Preventive Dentistry, RWTH Aachen University, Aachen, Germany
| | - Richard Johannes Wierichs
- Department of Restorative, Preventive and Pediatric Dentistry, zmk bern, University of Bern, Bern, Switzerland
| | - Hendrik Meyer-Lueckel
- Department of Restorative, Preventive and Pediatric Dentistry, zmk bern, University of Bern, Bern, Switzerland
| | - Georg Conrads
- Division of Oral Microbiology and Immunology, Department of Operative Dentistry, Periodontology, and Preventive Dentistry, RWTH Aachen University, Aachen, Germany
| | - Karsten Henne
- Division of Oral Microbiology and Immunology, Department of Operative Dentistry, Periodontology, and Preventive Dentistry, RWTH Aachen University, Aachen, Germany
| | - Marcella Esteves-Oliveira
- Department of Operative Dentistry, Periodontology, and Preventive Dentistry, RWTH Aachen University, Aachen, Germany.,Department of Cariology, Endodontology and Periodontology, University of Leipzig, Leipzig, Germany
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