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Microbiome Jul 2019Dental calculus, calcified oral plaque biofilm, contains microbial and host biomolecules that can be used to study historic microbiome communities and host responses.... (Comparative Study)
Comparative Study
BACKGROUND
Dental calculus, calcified oral plaque biofilm, contains microbial and host biomolecules that can be used to study historic microbiome communities and host responses. Dental calculus does not typically accumulate as much today as historically, and clinical oral microbiome research studies focus primarily on living dental plaque biofilm. However, plaque and calculus reflect different conditions of the oral biofilm, and the differences in microbial characteristics between the sample types have not yet been systematically explored. Here, we compare the microbial profiles of modern dental plaque, modern dental calculus, and historic dental calculus to establish expected differences between these substrates.
RESULTS
Metagenomic data was generated from modern and historic calculus samples, and dental plaque metagenomic data was downloaded from the Human Microbiome Project. Microbial composition and functional profile were assessed. Metaproteomic data was obtained from a subset of historic calculus samples. Comparisons between microbial, protein, and metabolomic profiles revealed distinct taxonomic and metabolic functional profiles between plaque, modern calculus, and historic calculus, but not between calculus collected from healthy teeth and periodontal disease-affected teeth. Species co-exclusion was related to biofilm environment. Proteomic profiling revealed that healthy tooth samples contain low levels of bacterial virulence proteins and a robust innate immune response. Correlations between proteomic and metabolomic profiles suggest co-preservation of bacterial lipid membranes and membrane-associated proteins.
CONCLUSIONS
Overall, we find that there are systematic microbial differences between plaque and calculus related to biofilm physiology, and recognizing these differences is important for accurate data interpretation in studies comparing dental plaque and calculus.
Topics: Bacteria; Bacterial Physiological Phenomena; Bacterial Proteins; Biofilms; Bone and Bones; DNA, Ancient; DNA, Bacterial; Dental Calculus; Dental Plaque; Female; History, Ancient; Humans; Male; Metagenomics; Microbiota; Periodontal Diseases; Proteomics; Tooth
PubMed: 31279340
DOI: 10.1186/s40168-019-0717-3 -
Nature Apr 2017Recent genomic data have revealed multiple interactions between Neanderthals and modern humans, but there is currently little genetic evidence regarding Neanderthal...
Recent genomic data have revealed multiple interactions between Neanderthals and modern humans, but there is currently little genetic evidence regarding Neanderthal behaviour, diet, or disease. Here we describe the shotgun-sequencing of ancient DNA from five specimens of Neanderthal calcified dental plaque (calculus) and the characterization of regional differences in Neanderthal ecology. At Spy cave, Belgium, Neanderthal diet was heavily meat based and included woolly rhinoceros and wild sheep (mouflon), characteristic of a steppe environment. In contrast, no meat was detected in the diet of Neanderthals from El Sidrón cave, Spain, and dietary components of mushrooms, pine nuts, and moss reflected forest gathering. Differences in diet were also linked to an overall shift in the oral bacterial community (microbiota) and suggested that meat consumption contributed to substantial variation within Neanderthal microbiota. Evidence for self-medication was detected in an El Sidrón Neanderthal with a dental abscess and a chronic gastrointestinal pathogen (Enterocytozoon bieneusi). Metagenomic data from this individual also contained a nearly complete genome of the archaeal commensal Methanobrevibacter oralis (10.2× depth of coverage)-the oldest draft microbial genome generated to date, at around 48,000 years old. DNA preserved within dental calculus represents a notable source of information about the behaviour and health of ancient hominin specimens, as well as a unique system that is useful for the study of long-term microbial evolution.
Topics: Animals; Belgium; Carnivory; Caves; DNA, Ancient; Dental Calculus; Diet; Enterocytozoon; Food Preferences; Genome, Bacterial; Health; History, Ancient; Humans; Intestines; Meat; Methanobrevibacter; Mouth; Neanderthals; Pan troglodytes; Penicillium; Perissodactyla; Sheep; Spain; Stomach; Symbiosis; Time Factors; Vegetarians
PubMed: 28273061
DOI: 10.1038/nature21674 -
Chemical Reviews Aug 2022Paleoproteomics, the study of ancient proteins, is a rapidly growing field at the intersection of molecular biology, paleontology, archaeology, paleoecology, and... (Review)
Review
Paleoproteomics, the study of ancient proteins, is a rapidly growing field at the intersection of molecular biology, paleontology, archaeology, paleoecology, and history. Paleoproteomics research leverages the longevity and diversity of proteins to explore fundamental questions about the past. While its origins predate the characterization of DNA, it was only with the advent of soft ionization mass spectrometry that the study of ancient proteins became truly feasible. Technological gains over the past 20 years have allowed increasing opportunities to better understand preservation, degradation, and recovery of the rich bioarchive of ancient proteins found in the archaeological and paleontological records. Growing from a handful of studies in the 1990s on individual highly abundant ancient proteins, paleoproteomics today is an expanding field with diverse applications ranging from the taxonomic identification of highly fragmented bones and shells and the phylogenetic resolution of extinct species to the exploration of past cuisines from dental calculus and pottery food crusts and the characterization of past diseases. More broadly, these studies have opened new doors in understanding past human-animal interactions, the reconstruction of past environments and environmental changes, the expansion of the hominin fossil record through large scale screening of nondiagnostic bone fragments, and the phylogenetic resolution of the vertebrate fossil record. Even with these advances, much of the ancient proteomic record still remains unexplored. Here we provide an overview of the history of the field, a summary of the major methods and applications currently in use, and a critical evaluation of current challenges. We conclude by looking to the future, for which innovative solutions and emerging technology will play an important role in enabling us to access the still unexplored "dark" proteome, allowing for a fuller understanding of the role ancient proteins can play in the interpretation of the past.
Topics: Animals; Archaeology; Fossils; Humans; Paleontology; Phylogeny; Proteome; Proteomics
PubMed: 35839101
DOI: 10.1021/acs.chemrev.1c00703 -
Journal of Periodontology Mar 2009Implant-supported restorations have become the most popular therapeutic option for professionals and patients for the treatment of total and partial edentulism. When... (Meta-Analysis)
Meta-Analysis
BACKGROUND
Implant-supported restorations have become the most popular therapeutic option for professionals and patients for the treatment of total and partial edentulism. When implants are placed in an ideal position, with adequate prosthetic loading and proper maintenance, they can have success rates >90% over 15 years of function. Implants may be considered a better therapeutic alternative than performing more extensive conservative procedures in an attempt to save or maintain a compromised tooth. Inadequate indication for tooth extraction has resulted in the sacrifice of many sound savable teeth. This article presents a chart that can assist clinicians in making the right decision when they are deciding which route to take.
METHODS
Articles published in peer-reviewed English journals were selected using several scientific databases and subsequently reviewed. Book sources were also searched. Individual tooth- and patient-related features were thoroughly analyzed, particularly when determining if a tooth should be indicated for extraction.
RESULTS
A color-based decision-making chart with six different levels, including several factors, was developed based upon available scientific literature. The rationale for including these factors is provided, and its interpretation is justified with literature support.
CONCLUSION
The decision-making chart provided may serve as a reference guide for dentists when making the decision to save or extract a compromised tooth.
Topics: Alveolar Bone Loss; Attitude to Health; Bone Density Conservation Agents; Databases as Topic; Decision Making; Decision Support Techniques; Decision Trees; Dental Calculus; Dental Caries; Dental Restoration, Permanent; Esthetics, Dental; Furcation Defects; Health Status; Humans; Oral Surgical Procedures; Patient Compliance; Periodontal Abscess; Periodontal Diseases; Periodontal Pocket; Post and Core Technique; Retreatment; Review Literature as Topic; Root Canal Therapy; Smoking; Tooth Diseases; Tooth Extraction; Tooth Mobility; Tooth Root; Treatment Outcome
PubMed: 19254132
DOI: 10.1902/jop.2009.080454 -
Cell Discovery Dec 2021The oral microbiota contains billions of microbial cells, which could contribute to diseases in many body sites. Challenged by eating, drinking, and dental hygiene on a...
The oral microbiota contains billions of microbial cells, which could contribute to diseases in many body sites. Challenged by eating, drinking, and dental hygiene on a daily basis, the oral microbiota is regarded as highly dynamic. Here, we report significant human genomic associations with the oral metagenome from more than 1915 individuals, for both the tongue dorsum (n = 2017) and saliva (n = 1915). We identified five genetic loci associated with oral microbiota at study-wide significance (p < 3.16 × 10). Four of the five associations were well replicated in an independent cohort of 1439 individuals: rs1196764 at APPL2 with Prevotella jejuni, Oribacterium uSGB 3339 and Solobacterium uSGB 315; rs3775944 at the serum uric acid transporter SLC2A9 with Oribacterium uSGB 1215, Oribacterium uSGB 489 and Lachnoanaerobaculum umeaense; rs4911713 near OR11H1 with species F0422 uSGB 392; and rs36186689 at LOC105371703 with Eggerthia. Further analyses confirmed 84% (386/455 for tongue dorsum) and 85% (391/466 for saliva) of host genome-microbiome associations including six genome-wide significant associations mutually validated between the two niches. As many of the oral microbiome-associated genetic variants lie near miRNA genes, we tentatively validated the potential of host miRNAs to modulate the growth of specific oral bacteria. Human genetics accounted for at least 10% of oral microbiome compositions between individuals. Machine learning models showed that polygenetic risk scores dominated over oral microbiome in predicting risk of dental diseases such as dental calculus and gingival bleeding. These findings indicate that human genetic differences are one explanation for a stable or recurrent oral microbiome in each individual.
PubMed: 34873157
DOI: 10.1038/s41421-021-00356-0 -
Journal of Clinical Periodontology Dec 2017To assess long-term attachment and periodontitis-related tooth loss (PTL) in untreated periodontal disease over 40 years.
OBJECTIVES
To assess long-term attachment and periodontitis-related tooth loss (PTL) in untreated periodontal disease over 40 years.
MATERIAL AND METHODS
Data originated from the natural history of periodontitis study in Sri Lankan tea labourers first examined in 1970. In 2010, 75 subjects (15.6%) of the original cohort were re-examined.
RESULTS
PTL over 40 years varied between 0 and 28 teeth (mean 13.1). Four subjects presented with no PTL, while 12 were edentulous. Logistic regression revealed attachment loss as a statistically significant covariate for PTL (p < .004). Markov chain analysis showed that smoking and calculus were associated with disease initiation and that calculus, plaque, and gingivitis were associated with loss of attachment and progression to advanced disease. Mean attachment loss <1.81 mm at the age of 30 yielded highest sensitivity and specificity (0.71) to allocate subjects into a cohort with a dentition of at least 20 teeth at 60 years of age.
CONCLUSIONS
These results highlight the importance of treating early periodontitis along with smoking cessation, in those under 30 years of age. They further show that calculus removal, plaque control, and the control of gingivitis are essential in preventing disease progression, further loss of attachment and ultimately tooth loss.
Topics: Adolescent; Adult; Areca; Chronic Periodontitis; Dental Calculus; Dental Plaque; Disease Progression; Gingivitis; Habits; Hong Kong; Humans; Jaw, Edentulous, Partially; Logistic Models; Longitudinal Studies; Male; Markov Chains; Mouth, Edentulous; Periodontal Attachment Loss; Periodontal Diseases; Periodontal Index; Periodontitis; Risk Factors; Sensitivity and Specificity; Smoking; Smoking Cessation; Time Factors; Tooth Loss; Young Adult
PubMed: 28733997
DOI: 10.1111/jcpe.12782 -
Frontiers in Cellular and Infection... 2022Dental calculus has long been considered as a vital contributing factor of periodontal diseases. Our review focuses on the role of dental calculus as a repository and... (Review)
Review
Dental calculus has long been considered as a vital contributing factor of periodontal diseases. Our review focuses on the role of dental calculus as a repository and discusses the bioinformation recently reported to be concealed in dental calculus from three perspectives: time-varying oral condition, systemic diseases, and anthropology at various times. Molecular information representing an individual's contemporary oral health status could be detected in dental calculus. Additionally, pathogenic factors of systemic diseases were found in dental calculus, including bacteria, viruses and toxic heavy metals. Thus, dental calculus has been proposed to play a role as biological data storage for detection of molecular markers of latent health concerns. Through the study of environmental debris in dental calculus, an overview of an individual's historical dietary habits and information about the environment, individual behaviors and social culture changes can be unveiled. This review summarizes a new role of dental calculus as a repository of bioinformation, with potential use in the prediction of oral diseases, systemic diseases, and even anthropology.
Topics: Humans; Dental Calculus; Periodontal Diseases; Bacteria; Microbiota
PubMed: 36579339
DOI: 10.3389/fcimb.2022.1035324 -
British Dental Journal Dec 2022Dental calculus is recognised as a secondary aetiological factor in periodontal disease, and being a prominent plaque retentive factor, it is routinely removed by the... (Review)
Review
Dental calculus is recognised as a secondary aetiological factor in periodontal disease, and being a prominent plaque retentive factor, it is routinely removed by the dental team to maintain oral health. Conversely, dental calculus can potentially be useful in forensic studies by supplying data that may be helpful in the identification of human remains and assist in determining the cause of death. During the last few decades, dental calculus has been increasingly recognised as an informative tool to understand ancient diet and health. As an archaeological deposit, it may contain non-dietary debris which permits the exploration of human behaviour and activities. While optical and scanning electron microscopy were the original analytical methods utilised to study microparticles entrapped within the calcified matrix, more recently, molecular approaches, including ancient DNA (aDNA) and protein analyses, have been applied. Oral bacteria, a major component of calculus, is the primary target of these aDNA studies. Such analyses can detect changes in the oral microbiota, including those that have reflected the shift from agriculture to industrialisation, as well as identifying markers for various systemic diseases.
Topics: Humans; Dental Calculus; Oral Health; Archaeology; Dental Plaque; Microbiota
PubMed: 36494546
DOI: 10.1038/s41415-022-5266-7 -
Journal of Human Evolution Feb 2015Very recently, we discovered a vast new microbial self: the human microbiome. Our native microbiota interface with our biology and culture to influence our health,...
Very recently, we discovered a vast new microbial self: the human microbiome. Our native microbiota interface with our biology and culture to influence our health, behavior, and quality of life, and yet we know very little about their origin, evolution, or ecology. With the advent of industrialization, globalization, and modern sanitation, it is intuitive that we have changed our relationship with microbes, but we have little information about the ancestral state of our microbiome, and we therefore lack a foundation for characterizing this change. High-throughput sequencing has opened up new opportunities in the field of paleomicrobiology, allowing us to investigate the evolution of the complex microbial ecologies that inhabit our bodies. By focusing on recent coprolite and dental calculus research, we explore how emerging research on ancient human microbiomes is changing the way we think about ancient disease and how archaeological studies can contribute to a medical understanding of health and nutrition today.
Topics: Dental Calculus; Diet; Feces; Health; High-Throughput Nucleotide Sequencing; History, Ancient; Humans; Metagenomics; Microbiota; Paleontology
PubMed: 25559298
DOI: 10.1016/j.jhevol.2014.10.016