scholarly journals Dental Calculus as a Tool to Study the Evolution of the Mammalian Oral Microbiome

2020 ◽  
Vol 37 (10) ◽  
pp. 3003-3022 ◽  
Author(s):  
Jaelle C Brealey ◽  
Henrique G Leitão ◽  
Tom van der Valk ◽  
Wenbo Xu ◽  
Katia Bougiouri ◽  
...  
Keyword(s):  
Mammalian Species ◽  
Antibiotic Resistance Genes ◽  
Oral Microbiome ◽  
Oral Disease ◽  
Dental Calculus ◽  
Diverse Range ◽  
Shotgun Metagenomics ◽  
Host Diet ◽  
Genetic Profiles ◽  
The Impact

Abstract Dental calculus, the calcified form of the mammalian oral microbial plaque biofilm, is a rich source of oral microbiome, host, and dietary biomolecules and is well preserved in museum and archaeological specimens. Despite its wide presence in mammals, to date, dental calculus has primarily been used to study primate microbiome evolution. We establish dental calculus as a valuable tool for the study of nonhuman host microbiome evolution, by using shotgun metagenomics to characterize the taxonomic and functional composition of the oral microbiome in species as diverse as gorillas, bears, and reindeer. We detect oral pathogens in individuals with evidence of oral disease, assemble near-complete bacterial genomes from historical specimens, characterize antibiotic resistance genes, reconstruct components of the host diet, and recover host genetic profiles. Our work demonstrates that metagenomic analyses of dental calculus can be performed on a diverse range of mammalian species, which will allow the study of oral microbiome and pathogen evolution from a comparative perspective. As dental calculus is readily preserved through time, it can also facilitate the quantification of the impact of anthropogenic changes on wildlife and the environment.

scholarly journals A roadmap to mammalian oral microbiome evolution with dental calculus

2019 ◽  
Author(s):  
Jaelle C. Brealey ◽  
Henrique G. Leitão ◽  
Tom van der Valk ◽  
Wenbo Xu ◽  
Katia Bougiouri ◽  
...  
Keyword(s):  
Antibiotic Production ◽  
Antibiotic Resistance Genes ◽  
Oral Microbiome ◽  
Oral Disease ◽  
Dental Calculus ◽  
Wild Mammals ◽  
Host Diet ◽  
Host Genetic ◽  
Genetic Profiles ◽  
The Impact

AbstractAnimals and their associated microbiomes share a long evolutionary history, influenced by a complex interplay between extrinsic environmental and intrinsic host factors. However, we know little about microbiome responses to long-lasting environmental and host-centred processes, which require studying microbiome changes through time. Here, we apply a temporal metagenomics approach to dental calculus, the calcified oral microbial biofilm. We establish dental calculus as a valuable tool for the study of host microbiome evolution by characterising the taxonomic and functional composition of the oral microbiome in a variety of wild mammals. We detect oral pathogens in individuals with evidence of oral disease, assemble near-complete bacterial genomes from historical specimens, characterise antibiotic resistance genes even before the advent of industrial antibiotic production, reconstruct components of the host diet and recover host genetic profiles. Our work demonstrates how dental calculus can be used in the future to study the evolution of oral microbiomes and pathogens, and the impact of anthropogenic changes on wildlife and the environment.

scholarly journals Wild animal oral microbiomes reflect the history of human antibiotics use

2020 ◽  
Author(s):  
Jaelle C. Brealey ◽  
Henrique G. Leitão ◽  
Thijs Hofstede ◽  
Daniela C. Kalthoff ◽  
Katerina Guschanski
Keyword(s):  
Wild Animal ◽  
Oral Microbiome ◽  
Health Policies ◽  
Museum Specimens ◽  
Wild Animals ◽  
Dental Calculus ◽  
Shotgun Metagenomics ◽  
Public Health Policies ◽  
Antibiotics Use ◽  
History Of

AbstractFollowing the advent of industrial-scale antibiotics production in the 1940s, antimicrobial resistance (AMR) has been on the rise and now poses a major global health threat. Because AMR can be exchanged between humans, livestock and wildlife, evaluating the potential of wild animals to act as AMR reservoirs is essential. We used shotgun metagenomics sequencing of dental calculus, the calcified form of the oral microbial biofilm, to determine the abundance and repertoire of AMR genes in the oral microbiome of Swedish brown bears from museum specimens collected over the last 200 years. Our temporal metagenomics approach allowed us to establish a baseline of natural AMR in the pre-antibiotics era and to quantify a significant increase in total AMR load and diversity of AMR genes that is correlated with human antibiotics use. We also demonstrated that Swedish public health policies were effective in limiting AMR spillover into wildlife.

scholarly journals Metagenomic analysis of dental calculus in ancient Egyptian baboons

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Claudio Ottoni ◽  
Meriam Guellil ◽  
Andrew T. Ozga ◽  
Anne C. Stone ◽  
Oliver Kersten ◽  
...  
Keyword(s):  
Oral Microbiome ◽  
Dietary Behaviour ◽  
Wild Chimpanzee ◽  
Dental Calculus ◽  
Shotgun Metagenomics ◽  
The Past ◽  
Ancient Egyptian ◽  
Starting Point ◽  
Wide Range ◽  
Human Management

AbstractDental calculus, or mineralized plaque, represents a record of ancient biomolecules and food residues. Recently, ancient metagenomics made it possible to unlock the wealth of microbial and dietary information of dental calculus to reconstruct oral microbiomes and lifestyle of humans from the past. Although most studies have so far focused on ancient humans, dental calculus is known to form in a wide range of animals, potentially informing on how human-animal interactions changed the animals’ oral ecology. Here, we characterise the oral microbiome of six ancient Egyptian baboons held in captivity during the late Pharaonic era (9th–6th centuries BC) and of two historical baboons from a zoo via shotgun metagenomics. We demonstrate that these captive baboons possessed a distinctive oral microbiome when compared to ancient and modern humans, Neanderthals and a wild chimpanzee. These results may reflect the omnivorous dietary behaviour of baboons, even though health, food provisioning and other factors associated with human management, may have changed the baboons’ oral microbiome. We anticipate our study to be a starting point for more extensive studies on ancient animal oral microbiomes to examine the extent to which domestication and human management in the past affected the diet, health and lifestyle of target animals.

scholarly journals Tracking the transition to agriculture in Southern Europe through ancient DNA analysis of dental calculus

2021 ◽  
Vol 118 (32) ◽  
pp. e2102116118
Author(s):  
Claudio Ottoni ◽  
Dušan Borić ◽  
Olivia Cheronet ◽  
Vitale Sparacello ◽  
Irene Dori ◽  
...  
Keyword(s):  
Dna Analysis ◽  
Oral Microbiome ◽  
Oral Microbiota ◽  
Southern Europe ◽  
Dental Calculus ◽  
Oral Flora ◽  
Shotgun Metagenomics ◽  
Near Eastern ◽  
Microbiome Composition ◽  
The Balkans

Archaeological dental calculus, or mineralized plaque, is a key tool to track the evolution of oral microbiota across time in response to processes that impacted our culture and biology, such as the rise of farming during the Neolithic. However, the extent to which the human oral flora changed from prehistory until present has remained elusive due to the scarcity of data on the microbiomes of prehistoric humans. Here, we present our reconstruction of oral microbiomes via shotgun metagenomics of dental calculus in 44 ancient foragers and farmers from two regions playing a pivotal role in the spread of farming across Europe—the Balkans and the Italian Peninsula. We show that the introduction of farming in Southern Europe did not alter significantly the oral microbiomes of local forager groups, and it was in particular associated with a higher abundance of the species Olsenella sp. oral taxon 807. The human oral environment in prehistory was dominated by a microbial species, Anaerolineaceae bacterium oral taxon 439, that diversified geographically. A Near Eastern lineage of this bacterial commensal dispersed with Neolithic farmers and replaced the variant present in the local foragers. Our findings also illustrate that major taxonomic shifts in human oral microbiome composition occurred after the Neolithic and that the functional profile of modern humans evolved in recent times to develop peculiar mechanisms of antibiotic resistance that were previously absent.

scholarly journals Distinct impact of antibiotics on the gut microbiome and resistome: a longitudinal multicenter cohort study

BMC Biology ◽  
2019 ◽  
Vol 17 (1) ◽  
Author(s):  
Matthias Willmann ◽  
Maria J. G. T. Vehreschild ◽  
Lena M. Biehl ◽  
Wichard Vogel ◽  
Daniela Dörfel ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Human Microbiome ◽  
Antibiotic Resistance Genes ◽  
Antimicrobial Treatment ◽  
Treatment Programs ◽  
Defined Daily Dose ◽  
Multicenter Cohort Study ◽  
Shotgun Metagenomics ◽  
Antibiotic Drugs ◽  
The Impact

Abstract Background The selection pressure exercised by antibiotic drugs is an important consideration for the wise stewardship of antimicrobial treatment programs. Treatment decisions are currently based on crude assumptions, and there is an urgent need to develop a more quantitative knowledge base that can enable predictions of the impact of individual antibiotics on the human gut microbiome and resistome. Results Using shotgun metagenomics, we quantified changes in the gut microbiome in two cohorts of hematological patients receiving prophylactic antibiotics; one cohort was treated with ciprofloxacin in a hospital in Tübingen and the other with cotrimoxazole in a hospital in Cologne. Analyzing this rich longitudinal dataset, we found that gut microbiome diversity was reduced in both treatment cohorts to a similar extent, while effects on the gut resistome differed. We observed a sharp increase in the relative abundance of sulfonamide antibiotic resistance genes (ARGs) by 148.1% per cumulative defined daily dose of cotrimoxazole in the Cologne cohort, but not in the Tübingen cohort treated with ciprofloxacin. Through multivariate modeling, we found that factors such as individual baseline microbiome, resistome, and plasmid diversity; liver/kidney function; and concurrent medication, especially virostatic agents, influence resistome alterations. Strikingly, we observed different effects on the plasmidome in the two treatment groups. There was a substantial increase in the abundance of ARG-carrying plasmids in the cohort treated with cotrimoxazole, but not in the cohort treated with ciprofloxacin, indicating that cotrimoxazole might contribute more efficiently to the spread of resistance. Conclusions Our study represents a step forward in developing the capability to predict the effect of individual antimicrobials on the human microbiome and resistome. Our results indicate that to achieve this, integration of the individual baseline microbiome, resistome, and mobilome status as well as additional individual patient factors will be required. Such personalized predictions may in the future increase patient safety and reduce the spread of resistance. Trial registration ClinicalTrials.gov, NCT02058888. Registered February 10 2014

The Oxford Handbook of Adult Cognitive Disorders

2019 ◽  
Keyword(s):  
Cognitive Impairment ◽  
Cognitive Function ◽  
Neurodevelopmental Disorders ◽  
Brain Aging ◽  
Cognitive Disorders ◽  
Diverse Range ◽  
Medical Specialties ◽  
Psychiatric Illnesses ◽  
Medical Disorders ◽  
The Impact

The prevalence of cognitive impairment caused by neurodegenerative diseases and other neurologic disorders associated with aging is expected to rise dramatically between now and year 2050, when the population of Americans aged 65 or older will nearly double. Cognitive impairment also commonly occurs in other neurologic conditions, as well as in non-neurologic medical disorders (and their treatments), idiopathic psychiatric illnesses, and adult neurodevelopmental disorders. Cognitive impairment can thus infiltrate all aspects of healthcare, making it necessary for clinicians and clinical researchers to have an integrated knowledge of the spectrum of adult cognitive disorders. The Oxford Handbook of Adult Cognitive Disorders is meant to serve as an up-to-date, scholarly, and comprehensive volume covering most diseases, conditions, and injuries resulting in impairments in cognitive function in adults. Topics covered include normal cognitive and brain aging, the impact of medical disorders (e.g., cardiovascular, liver, pulmonary) and psychiatric illnesses (e.g., depression and bipolar disorder) on cognitive function, adult neurodevelopmental disorders (e.g., Down Syndrome, Attention Deficit/Hyperactivity Disorder), as well as the various neurological conditions (e.g., Alzheimer’s disease, chronic traumatic encephalopathy, concussion). A section of the Handbook is also dedicated to unique perspectives and special considerations for the clinicians and clinical researchers, covering topics such as cognitive reserve, genetics, diversity, and neuroethics. The target audience of this Handbook includes: (1) clinicians, particularly psychologists, neuropsychologists, neurologists (including behavioral and cognitive neurologists), geriatricians, and psychiatrists (including neuropsychiatrists), who provide clinical care and management for adults with a diverse range of cognitive disorders; (2) clinical researchers who investigate cognitive outcomes and functioning in adult populations; and (3) graduate level students and post-doctoral trainees studying psychology, clinical neuroscience, and various medical specialties.

scholarly journals The impact of fixed orthodontic appliances on oral microbiome dynamics in Japanese patients

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Isamu Kado ◽  
Junzo Hisatsune ◽  
Keiko Tsuruda ◽  
Kotaro Tanimoto ◽  
Motoyuki Sugai
Keyword(s):  
Relative Abundance ◽  
Japanese Patients ◽  
Oral Microbiome ◽  
Orthodontic Appliances ◽  
Periodontal Pathogens ◽  
Supragingival Plaque ◽  
Fixed Orthodontic Appliances ◽  
Microbial Dna ◽  
The Impact ◽  
Level Analysis

AbstractFixed orthodontic appliances are common and effective tools to treat malocclusion. Adverse effects of these appliances, such as dental caries and periodontitis, may be associated with alteration of the microbiome. This study investigated the impact of these appliances on the dynamics of the oral microbiome. Seventy-one patients were selected. Supragingival plaque samples were collected before placement (T0) and six months after placement (T1). Saliva samples were collected at T0 and T1, and then when appliance removal (T2). Microbial DNA was analyzed by 16S rRNA meta-sequencing. The diversity analysis indicated dynamic changes in the structure of the oral microbiome. Taxonomic analysis at phylum level showed a significant increase in Bacteroidetes and Saccharibacteria (formally TM7) and decrease in Proteobacteria and Actinobacteria over time, in both plaque and saliva. Genus level analysis of relative abundance indicated a significant increase in anaerobic and facultative anaerobes in both plaque and saliva. Fixed orthodontic appliances induced measurable changes in the oral microbiome. This was characterized by an increase in relative abundance of obligate anaerobes, including periodontal pathogens. It can be concluded that this dysbiosis induced by fixed orthodontic appliances is likely to represent a transitional stage in the shift in microbiome from healthy to periodontitis.

scholarly journals Transitions in oral and gut microbiome of HPV+ oropharyngeal squamous cell carcinoma following definitive chemoradiotherapy (ROMA LA-OPSCC study)

2021 ◽  
Author(s):  
Marc Oliva ◽  
Pierre H. H. Schneeberger ◽  
Victor Rey ◽  
Matthew Cho ◽  
Rachel Taylor ◽  
...  
Keyword(s):  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Taxonomic Composition ◽  
Oropharyngeal Squamous Cell Carcinoma ◽  
Oral Microbiome ◽  
Metagenomic Sequencing ◽  
Α Diversity ◽  
16S Rna ◽  
The Impact

Abstract Background Oral and gut microbiomes have emerged as potential biomarkers in cancer. We characterised the oral and gut microbiomes in a prospective observational cohort of HPV+ oropharyngeal squamous cell carcinoma (OPSCC) patients and evaluated the impact of chemoradiotherapy (CRT). Methods Saliva, oropharyngeal swabs over the tumour site and stool were collected at baseline and post-CRT. 16S RNA and shotgun metagenomic sequencing were used to generate taxonomic profiles, including relative abundance (RA), bacterial density, α-diversity and β-diversity. Results A total of 132 samples from 22 patients were analysed. Baseline saliva and swabs had similar taxonomic composition (R2 = 0.006; p = 0.827). Oropharyngeal swabs and stool taxonomic composition varied significantly by stage, with increased oral RA of Fusobacterium nucleatum observed in stage III disease (p < 0.05). CRT significantly reduced the species richness and increased the RA of gut-associated taxa in oropharyngeal swabs (p < 0.05), while it had no effect in stool samples. These findings remained significant when adjusted by stage, smoking status and antibiotic use. Conclusions Baseline oral and gut microbiomes differ by stage in this HPV+ cohort. CRT caused a shift towards a gut-like microbiome composition in oropharyngeal swabs. Stage-specific features and the transitions in oral microbiome might have prognostic and therapeutic implications.

scholarly journals Relationship between dental and periodontal health status and the salivary microbiome: bacterial diversity, co-occurrence networks and predictive models

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
M. Relvas ◽  
A. Regueira-Iglesias ◽  
C. Balsa-Castro ◽  
F. Salazar ◽  
J. J. Pacheco ◽  
...  
Keyword(s):  
Oral Health ◽  
Periodontal Disease ◽  
Bacterial Diversity ◽  
Predictive Models ◽  
Oral Disease ◽  
Rrna Gene ◽  
Convenience Sample ◽  
Core Microbiome ◽  
Rdna Sequencing ◽  
The Impact

AbstractThe present study used 16S rRNA gene amplicon sequencing to assess the impact on salivary microbiome of different grades of dental and periodontal disease and the combination of both (hereinafter referred to as oral disease), in terms of bacterial diversity, co-occurrence network patterns and predictive models. Our scale of overall oral health was used to produce a convenience sample of 81 patients from 270 who were initially recruited. Saliva samples were collected from each participant. Sequencing was performed in Illumina MiSeq with 2 × 300 bp reads, while the raw reads were processed according to the Mothur pipeline. The statistical analysis of the 16S rDNA sequencing data at the species level was conducted using the phyloseq, DESeq2, Microbiome, SpiecEasi, igraph, MixOmics packages. The simultaneous presence of dental and periodontal pathology has a potentiating effect on the richness and diversity of the salivary microbiota. The structure of the bacterial community in oral health differs from that present in dental, periodontal or oral disease, especially in high grades. Supragingival dental parameters influence the microbiota’s abundance more than subgingival periodontal parameters, with the former making a greater contribution to the impact that oral health has on the salivary microbiome. The possible keystone OTUs are different in the oral health and disease, and even these vary between dental and periodontal disease: half of them belongs to the core microbiome and are independent of the abundance parameters. The salivary microbiome, involving a considerable number of OTUs, shows an excellent discriminatory potential for distinguishing different grades of dental, periodontal or oral disease; considering the number of predictive OTUs, the best model is that which predicts the combined dental and periodontal status.

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