The Oral Microbiota in Health and Disease: An Overview of Molecular Findings

2016 ◽  
pp. 127-138 ◽  
Author(s):  
José F. Siqueira ◽  
Isabela N. Rôças
Keyword(s):  
Oral Microbiota ◽  
Health And Disease

scholarly journals Cariogenic Biofilm: Pathology-Related Phenotypes and Targeted Therapy

2021 ◽  
Vol 9 (6) ◽  
pp. 1311
Author(s):  
Xiuqin Chen ◽  
Eric Banan-Mwine Daliri ◽  
Akanksha Tyagi ◽  
Deog-Hwan Oh
Keyword(s):  
Treatment Strategies ◽  
High Specificity ◽  
Low Ph ◽  
Oral Microbiota ◽  
Extracellular Polymers ◽  
Dental Biofilm ◽  
Health And Disease ◽  
Promising Treatment ◽  
Cariogenic Biofilm

The initiation and development of cariogenic (that is, caries-related) biofilms are the result of the disruption of homeostasis in the oral microenvironment. There is a daily accumulation of dental biofilm on the surface of teeth and its matrix of extracellular polymers supports the host in its defense against invading microbes, thus helping to achieve oral microbial homeostasis. However, the homeostasis can be broken down under certain circumstances such as during long-term exposure to a low pH environment which results in the dominance of acidogenic and acid-tolerating species in the dental biofilm and, thus, triggers the shift of harmless biofilm to an acidic one. This work aims to explore microbial diversity and the quorum sensing of dental biofilm and their important contributions to oral health and disease. The complex and multispecies ecosystems of the cariogenic biofilm pose significant challenges for the modulation of the oral microenvironment. Promising treatment strategies are those that target cariogenic niches with high specificity without disrupting the balance of the surrounding oral microbiota. Here, we summarized the recent advances in modulating cariogenic biofilm and/or controlling its pathogenic traits.

scholarly journals OTUs clustering should be avoided for defining oral microbiome

2021 ◽  
Author(s):  
Alba Regueira-Iglesias ◽  
Lara Vazquez-Gonzalez ◽  
Carlos Balsa-Castro ◽  
Triana Blanco-Pintos ◽  
Victor Manuel Arce ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Operational Taxonomic Unit ◽  
Oral Bacteria ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Oral Microbiota ◽  
High Coverage ◽  
Archaeal Species ◽  
Health And Disease ◽  
Similarity Relationships

This in silico investigation aimed to: 1) evaluate a set of primer pairs with high coverage, including those most commonly used in the literature, to find the different oral species with 16S rRNA gene amplicon similarity/identity (ASI) values ≥97%; and 2) identify oral species that may be erroneously clustered in the same operational taxonomic unit (OTU) and ascertain whether they belong to distinct genera or other higher taxonomic ranks. Thirty-nine primer pairs were employed to obtain amplicon sequence variants (ASVs) from the complete genomes of 186 bacterial and 135 archaeal species. For each primer, ASVs without mismatches were aligned using BLASTN and their similarity values were obtained. Finally, we selected ASVs from different species with an ASI value ≥97% that were covered 100% by the query sequences. For each primer, the percentage of species-level coverage with no ASI≥97% (SC-NASI≥97%) was calculated. Based on the SC-NASI≥97% values, the best primer pairs were OP_F053-KP_R020 for bacteria (65.05%), KP_F018-KP_R002 for archaea (51.11%), and OP_F114-KP_R031 for bacteria and archaea together (52.02%). Eighty percent of the oral-bacteria and oral-archaea species shared an ASI≥97% with at least one other taxa, including Campylobacter, Rothia, Streptococcus, and Tannerella, which played conflicting roles in the oral microbiota. Moreover, around a quarter and a third of these two-by-two similarity relationships were between species from different bacteria and archaea genera, respectively. Furthermore, even taxa from distinct families, orders, and classes could be grouped in the same cluster. Consequently, irrespective of the primer pair used, OTUs constructed with a 97% similarity provide an inaccurate description of oral-bacterial and oral-archaeal species, greatly affecting microbial diversity parameters. As a result, clustering by OTUs impacts the credibility of the associations between some oral species and certain health and disease conditions. This limits significantly the comparability of the microbial diversity findings reported in oral microbiome literature.

scholarly journals Biological and cultural drivers of oral microbiota in Medieval and Post-Medieval London, UK

2018 ◽  
Author(s):  
A. G. Farrer ◽  
J. Bekvalac ◽  
R. Redfern ◽  
N. Gully ◽  
K. Dobney ◽  
...  
Keyword(s):  
Low Socioeconomic Status ◽  
Evolutionary History ◽  
Tooth Surface ◽  
Oral Microbiota ◽  
Low Socioeconomic ◽  
The Past ◽  
Health And Disease ◽  
Tooth Type ◽  
Relationship Of ◽  
Microbiota Diversity

AbstractThe trillions of microorganisms that live in association with the human body (microbiota) are critical for human health and disease, but there is a limited understanding of how cultural and environmental factors shaped our microbiota diversity through time. However, biomolecular remnants of the human oral microbiota - recovered from the calcified dental plaque (calculus) of our long-dead ancestors - are providing a new means of exploring this key relationship of our evolutionary history. Here, we correlate extensive experimental, archaeological, and biological metadata with 128 ancient dental calculus specimens from Medieval and Post-Medieval London, UK (1066 – 1853 CE). We identify a significant association between microbiota and oral geography (i.e. tooth type and tooth surface), which has confounded ancient microbiota studies to date. By controlling for oral geography, however, we identify the first associations between ancient microbiota and cultural and environmental signatures. We find significant links between ancient British microbiota structure and health, including skeletal markers of stress that may reflect low socioeconomic status. Furthermore, this study provides baseline data to explore factors that drive microbiota differentiation within and between ancient populations and highlights the potential of ancient microbiota to infer detailed health and sociocultural information about the past.

scholarly journals Antibiotic treatment at delivery shapes the initial oral microbiome in neonates

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Luisa F. Gomez-Arango ◽  
Helen L. Barrett ◽  
H. David. McIntyre ◽  
Leonie K. Callaway ◽  
Mark Morrison ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Antibiotic Treatment ◽  
Antibiotic Resistance Gene ◽  
Antibiotic Resistance Genes ◽  
Oral Microbiome ◽  
Oral Microbiota ◽  
Obese Mother ◽  
Health And Disease ◽  
Intrapartum Antibiotic ◽  
Oral Microorganisms

Abstract Oral microorganisms are important determinants of health and disease. The source of the initial neonatal microbiome and the factors dictating initial human oral microbiota development are unknown. This study aimed to investigate this in placental, oral and gut microbiome profiles from 36 overweight or obese mother-baby dyads as determined by 16S rRNA sequencing. Expression of five antibiotic resistance genes of the β-lactamase class was analysed in the infant oral microbiota samples by QPCR. The neonatal oral microbiota was 65.35% of maternal oral, 3.09% of placental, 31.56% of unknown and 0% of maternal gut origin. Two distinct neonatal oral microbiota profiles were observed: one strongly resembling the maternal oral microbiota and one with less similarity. Maternal exposure to intrapartum antibiotics explained the segregation of the profiles. Families belonging to Proteobacteria were abundant after antibiotics exposure while the families Streptococcaceae, Gemellaceae and Lactobacillales dominated in unexposed neonates. 26% of exposed neonates expressed the Vim-1 antibiotic resistance gene. These findings indicate that maternal intrapartum antibiotic treatment is a key regulator of the initial neonatal oral microbiome.

scholarly journals The Human Oral Microbiome

2010 ◽  
Vol 192 (19) ◽  
pp. 5002-5017 ◽  
Author(s):  
Floyd E. Dewhirst ◽  
Tuste Chen ◽  
Jacques Izard ◽  
Bruce J. Paster ◽  
Anne C. R. Tanner ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Species Level ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Oral Microbiota ◽  
16S Rrna Gene Sequences ◽  
Culture Independent ◽  
Health And Disease

ABSTRACT The human oral cavity contains a number of different habitats, including the teeth, gingival sulcus, tongue, cheeks, hard and soft palates, and tonsils, which are colonized by bacteria. The oral microbiome is comprised of over 600 prevalent taxa at the species level, with distinct subsets predominating at different habitats. The oral microbiome has been extensively characterized by cultivation and culture-independent molecular methods such as 16S rRNA cloning. Unfortunately, the vast majority of unnamed oral taxa are referenced by clone numbers or 16S rRNA GenBank accession numbers, often without taxonomic anchors. The first aim of this research was to collect 16S rRNA gene sequences into a curated phylogeny-based database, the Human Oral Microbiome Database (HOMD), and make it web accessible (www.homd.org ). The HOMD includes 619 taxa in 13 phyla, as follows: Actinobacteria, Bacteroidetes, Chlamydiae, Chloroflexi, Euryarchaeota, Firmicutes, Fusobacteria, Proteobacteria, Spirochaetes, SR1, Synergistetes, Tenericutes, and TM7. The second aim was to analyze 36,043 16S rRNA gene clones isolated from studies of the oral microbiota to determine the relative abundance of taxa and identify novel candidate taxa. The analysis identified 1,179 taxa, of which 24% were named, 8% were cultivated but unnamed, and 68% were uncultivated phylotypes. Upon validation, 434 novel, nonsingleton taxa will be added to the HOMD. The number of taxa needed to account for 90%, 95%, or 99% of the clones examined is 259, 413, and 875, respectively. The HOMD is the first curated description of a human-associated microbiome and provides tools for use in understanding the role of the microbiome in health and disease.

scholarly journals Oral microbiota of periodontal health and disease and their changes after nonsurgical periodontal therapy

2018 ◽  
Vol 12 (5) ◽  
pp. 1210-1224 ◽  
Author(s):  
Casey Chen ◽  
Chris Hemme ◽  
Joan Beleno ◽  
Zhou Jason Shi ◽  
Daliang Ning ◽  
...  
Keyword(s):  
Periodontal Therapy ◽  
Oral Microbiota ◽  
Periodontal Health ◽  
Nonsurgical Periodontal Therapy ◽  
Health And Disease

scholarly journals Fusobacterium nucleatum metabolically integrates commensals and pathogens in oral biofilms

2021 ◽  
Author(s):  
Akito Sakanaka ◽  
Masae Kuboniwa ◽  
Shuichi Shimma ◽  
Samar A. Alghamdi ◽  
Shota Mayumi ◽  
...  
Keyword(s):  
Fusobacterium Nucleatum ◽  
Periodontal Pathogen ◽  
Oral Microbiota ◽  
Periodontal Health ◽  
Amino Acid Availability ◽  
Metabolic Capability ◽  
Oral Biofilms ◽  
Health And Disease ◽  
Biofilm Development ◽  
Polymicrobial Communities

Fusobacterium nucleatum is a common constituent of the oral microbiota in both periodontal health and disease. Previously, we discovered ornithine cross-feeding between F. nucleatum and Streptococcus gordonii, where S. gordonii secretes ornithine via an arginine-ornithine antiporter (ArcD), which in turn supports the growth and biofilm development of F. nucleatum; however, broader metabolic aspects of F. nucleatum within polymicrobial communities and their impact on periodontal pathogenesis have not been addressed. Here, we show that when co-cultured with S. gordonii, F. nucleatum increased amino acid availability to enhance the production of butyrate and putrescine, a polyamine produced by ornithine decarboxylation. Co-culture with Veillonella parvula, another common inhabitant of the oral microbiota, also increased lysine availability, promoting cadaverine production by F. nucleatum. We confirmed that ArcD-dependent ornithine excretion by S. gordonii results in synergistic putrescine production, and mass spectrometry imaging revealed this metabolic capability creates a putrescine-rich microenvironment inside F. nucleatum biofilms. We further demonstrated that polyamines caused significant changes in the biofilm phenotype of a periodontal pathogen, Porphyromonas gingivalis, with putrescine being a potent stimulator of biofilm development and dispersal, and confirmed that F. nucleatum-mediated conversion of ornithine to putrescine enhances biofilm formation by P. gingivalis. Lastly, analysis of plaque samples revealed cooccurrence of P. gingivalis with genetic modules for putrescine production by S. gordonii and F. nucleatum. Overall, our results highlight the ability of F. nucleatum to induce synergistic polyamine production within multi-species consortia, and provide insight into how the trophic web in oral biofilm ecosystems can eventually shape disease-associated communities.

scholarly journals Inflammatory Networks Linking Oral Microbiome with Systemic Health and Disease

2020 ◽  
Vol 99 (10) ◽  
pp. 1131-1139 ◽  
Author(s):  
S.E. Kleinstein ◽  
K.E. Nelson ◽  
M. Freire
Keyword(s):  
Immune System ◽  
The Body ◽  
Oral Microbiome ◽  
Oral Microbiota ◽  
Disease States ◽  
Healthy State ◽  
Health And Disease ◽  
Active Research ◽  
Diseased State ◽  
Systemic Health

The dance between microbes and the immune system takes place in all biological systems, including the human body, but this interaction is especially complex in the primary gateway to the body: the oral cavity. Recent advances in technology have enabled deep sequencing and analysis of members and signals of these communities. In a healthy state, the oral microbiome is composed of commensals, and their genes and phenotypes may be selected by the immune system to survive in symbiosis. These highly regulated signals are modulated by a network of microbial and host metabolites. However, in a diseased state, host-microbial networks lead to dysbiosis and considerable burden to the host prior to systemic impact that extends beyond the oral compartment. Interestingly, we presented data demonstrating similarities between human and mice immune dysbiosis and discussed how this affects the host response to similar pathobionts. The host and microbial signatures of a number of disease states are currently being examined to identify potential correlations. How the oral microbiome interacts with inflammation and the immune system to cause disease remains an area of active research. In this review, we summarize recent advancements in understanding the role of oral microbiota in mediating inflammation and altering systemic health and disease. In line with these findings, it is possible that existing conditions may be resolved by targeting specific immune-microbial markers in a positive way.

scholarly journals Investigating the demographic history of Japan using ancient oral microbiota

2020 ◽  
Vol 375 (1812) ◽  
pp. 20190578 ◽  
Author(s):  
Raphael Eisenhofer ◽  
Hideaki Kanzawa-Kiriyama ◽  
Ken-ichi Shinoda ◽  
Laura S. Weyrich
Keyword(s):  
Ancient Dna ◽  
Demographic History ◽  
Phylogenomic Analysis ◽  
Oral Microbiota ◽  
Dental Calculus ◽  
Oral Diseases ◽  
Edo Period ◽  
Deep Roots ◽  
History Of ◽  
Health And Disease

While microbial communities in the human body (microbiota) are now commonly associated with health and disease in industrialised populations, we know very little about how these communities co-evolved and changed with humans throughout history and deep prehistory. We can now examine these communities by sequencing ancient DNA preserved within calcified dental plaque (calculus), providing insights into the origins of disease and their links to human history. Here, we examine ancient DNA preserved within dental calculus samples and their associations with two major cultural periods in Japan: the Jomon period hunter–gatherers approximately 3000 years before present (BP) and the Edo period agriculturalists 400–150 BP. We investigate how human oral microbiomes have changed in Japan through time and explore the presence of microorganisms associated with oral diseases (e.g. periodontal disease, dental caries) in ancient Japanese populations. Finally, we explore oral microbial strain diversity and its potential links to ancient demography in ancient Japan by performing phylogenomic analysis of a widely conserved oral species— Anaerolineaceae oral taxon 439. This research represents, to our knowledge, the first study of ancient oral microbiomes from Japan and demonstrates that the analysis of ancient dental calculus can provide key information about the origin of non-infectious disease and its deep roots with human demography. This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.

scholarly journals Oral–Gut Microbiota and Arthritis: Is There an Evidence-Based Axis?

2019 ◽  
Vol 8 (10) ◽  
pp. 1753 ◽  
Author(s):  
Lorenzo Drago ◽  
Gian Vincenzo Zuccotti ◽  
Carlo Luca Romanò ◽  
Karan Goswami ◽  
Jorge Hugo Villafañe ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Treatment Strategies ◽  
Joint Inflammation ◽  
Oral Microbiota ◽  
Microbiome Composition ◽  
Inflammatory Conditions ◽  
New Findings ◽  
Novel Biomarkers ◽  
Health And Disease ◽  
Prevention Of Bone Loss

The gut microbiome appears to be a significant contributor to musculoskeletal health and disease. Recently, it has been found that oral microbiota are involved in arthritis pathogenesis. Microbiome composition and its functional implications have been associated with the prevention of bone loss and/or reducing fracture risk. The link between gut–oral microbiota and joint inflammation in animal models of arthritis has been established, and it is now receiving increasing attention in human studies. Recent papers have demonstrated substantial alterations in the gut and oral microbiota in patients with rheumatoid arthritis (RA) and osteoarthritis (OA). These alterations resemble those established in systemic inflammatory conditions (inflammatory bowel disease, spondyloarthritides, and psoriasis), which include decreased microbial diversity and a disturbance of immunoregulatory properties. An association between abundance of oral Porphyromonas gingivalis and intestinal Prevotella copri in RA patients compared to healthy controls has been clearly demonstrated. These new findings open important future horizons both for understanding disease pathophysiology and for developing novel biomarkers and treatment strategies. The changes and decreased diversity of oral and gut microbiota seem to play an important role in the etiopathogenesis of RA and OA. However, specific microbial clusters and biomarkers belonging to oral and gut microbiota need to be further investigated to highlight the mechanisms related to alterations in bones and joints inflammatory pathway.

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