scholarly journals Understanding Oral Diseases: Exploring Opportunities from Filipino Oral Microbiome Research

2021 ◽  
Author(s):  
Marilen P. Balolong ◽  
Michael Antonio F. Mendoza
Keyword(s):  
Soft Tissues ◽  
Selective Constraint ◽  
Current Control ◽  
Oral Microbiome ◽  
Policy Framework ◽  
Oral Microbiota ◽  
Oral Diseases ◽  
Microbiome Research ◽  
Health And Disease ◽  
And Function

The human mouth houses the second most diverse microbial community in the body, with almost 700 species of bacteria colonizing the hard surfaces of teeth and the soft tissues of the oral mucosa. To compete in the relatively exposed oral cavity, resident microbes must avoid being replaced by newcomers. This selective constraint, coupled with pressure on the host to cultivate a beneficial microbiome, has rendered a commensal oral microbiota that displays colonization resistance, protecting the human host from invasive species, including pathogens. Current control of dental plaque-related diseases is non-specific and is centered on the removal of plaque by mechanical means. Several new methods based on the modulation of the microbiome that aim at maintaining and re-establishing a healthy oral ecosystem have been developed and has greatly expanded our knowledge of the composition and function of the oral microbiome in health and disease. Promoting a balanced microbiome is therefore important to effectively maintain or restore oral health. This review provides an updated body of knowledge on oral microbiome in health and disease and discusses the implications for modern-day oral healthcare. Filipino Oral Microbiome Research to develop a policy framework for microbiome-based management of dental diseases and opportunities will be discussed.

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 Single-Cell Genomics and the Oral Microbiome

2020 ◽  
Vol 99 (6) ◽  
pp. 613-620 ◽  
Author(s):  
M. Balachandran ◽  
K.L. Cross ◽  
M. Podar
Keyword(s):  
Microbial Community ◽  
Single Cell ◽  
Single Cells ◽  
Oral Bacteria ◽  
Oral Microbiome ◽  
Oral Microbiota ◽  
Oral Diseases ◽  
Interspecies Interactions ◽  
Single Cell Genomics

The human oral cavity is one of the first environments where microbes have been discovered and studied since the dawn of microbiology. Nevertheless, approximately 200 types of bacteria from the oral microbiota have remained uncultured in the laboratory. Some are associated with a healthy oral microbial community, while others are linked to oral diseases, from dental caries to gum disease. Single-cell genomics has enabled inferences on the physiology, virulence, and evolution of such uncultured microorganisms and has further enabled isolation and cultivation of several novel oral bacteria, including the discovery of novel interspecies interactions. This review summarizes some of the more recent advances in this field, which is rapidly moving toward physiologic characterization of single cells and ultimately cultivation of the yet uncultured. A combination of traditional microbiological approaches with genomic-based physiologic predictions and isolation strategies may lead to the oral microbiome being the first complex microbial community to have all its members cultivable in the laboratory. Studying the biology of the individual microbes when in association with other members of the community, in controlled laboratory conditions and in vivo, should lead to a better understanding of oral dysbiosis and its prevention and reversion.

scholarly journals Characterization of the salivary microbiome in people with obesity

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4458 ◽  
Author(s):  
Yujia Wu ◽  
Xiaopei Chi ◽  
Qian Zhang ◽  
Feng Chen ◽  
Xuliang Deng
Keyword(s):  
High Throughput Sequencing ◽  
Periodontal Diseases ◽  
Illumina Miseq ◽  
Normal Weight ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Oral Diseases ◽  
And Function ◽  
Healthy Participants

Background The interactions between the gut microbiome and obesity have been extensively studied. Although the oral cavity is the gateway to the gut, and is extensively colonized with microbes, little is known about the oral microbiome in people with obesity. In the present study, we investigated the salivary microbiome in obese and normal weight healthy participants using metagenomic analysis. The subjects were categorized into two groups, obesity and normal weight, based on their BMIs. Methods We characterized the salivary microbiome of 33 adults with obesity and 29 normal weight controls using high-throughput sequencing of the V3–V4 region of the 16S rRNA gene (Illumina MiSeq). None of the selected participants had systemic, oral mucosal, or periodontal diseases. Results The salivary microbiome of the obesity group was distinct from that of the normal weight group. The salivary microbiome of periodontally healthy people with obesity had both significantly lower bacterial diversity and richness compared with the controls. The genus Prevotella, Granulicatella, Peptostreptococcus, Solobacterium, Catonella, and Mogibacterium were significantly more abundant in the obesity group; meanwhile the genus Haemophilus, Corynebacterium, Capnocytophaga, and Staphylococcus were less abundant in the obesity group. We also performed a functional analysis of the inferred metagenomes, and showed that the salivary community associated with obesity had a stronger signature of immune disease and a decreased functional signature related to environmental adaptation and Xenobiotics biodegradation compared with the normal weight controls. Discussion Our study demonstrates that the microbial diversity and structure of the salivary microbiome in people with obesity are significantly different from those of normal weight controls. These results suggested that changes in the structure and function of salivary microbiome in people with obesity might reflect their susceptibility to oral diseases.

scholarly journals Oral Microbiota Profile of Individuals Who Abuse Methamphetamine

2021 ◽  
Vol 11 ◽  
Author(s):  
Yongde Yang ◽  
Xuan Yu ◽  
Xue Yang ◽  
Kuan Zeng ◽  
Guangya Liu ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Treatment Strategies ◽  
Etiologic Agent ◽  
Oral Microbiome ◽  
Oral Disease ◽  
Control Group ◽  
Oral Microbiota ◽  
Microbiota Composition ◽  
Oral Diseases ◽  
Oral Disease Prevention

The poor oral health condition of individuals who abuse methamphetamine (MA) is well known. The roles of the oral and fecal microbiomes in addiction and nervous system diseases have been the focus of many studies. However, changes in the microbiota composition of MA users have not been reported. This was addressed in the present study in 20 MA users and 14 sex-matched healthy subjects. Saliva samples were collected and high-throughput 16S rRNA sequencing and bioinformatic analysis were performed to evaluate oral microbiome profiles. The results showed that species richness was significantly lower in the MA group than in the control group. Bacterial taxa that are known to be related to oral diseases such as Negativicutes, Veillonellaceae, Veillonella, and Selenomonadales had higher relative abundance in the MA group than in the control group, and the relative abundance of Prevotella melaninogenica—a putative etiologic agent of periodontal disease—was also higher. Avoiding MA use and improving oral hygiene practices over a short term (i.e., during hospitalization for 2 weeks) did not alter the oral microbiota composition of MA users. Although the causal relationship between changes in oral microbiome profile and MA abuse remains to be determined, our results suggest that oral disease prevention and treatment strategies are important for MA users.

Host Genetic Associations with Salivary Microbiome in Oral Cancer

2021 ◽  
pp. 002203452110519
Author(s):  
S.F. Yang ◽  
C.W. Lin ◽  
C.Y. Chuang ◽  
Y.C. Lee ◽  
W.H. Chung ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Meta Analysis ◽  
Genetic Effect ◽  
Oral Microbiome ◽  
Oral Microbiota ◽  
Oral Diseases ◽  
Genetic Associations ◽  
Β Diversity ◽  
Host Genetic ◽  
Discovery Stage

Despite the growing recognition of a host genetic effect on shaping gut microbiota composition, the genetic determinants of oral microbiota remain largely unexplored, especially in the context of oral diseases. Here, we performed a microbiome genome-wide association study in 2 independent cohorts of patients with oral squamous cell carcinoma (OSCC, n = 144 and 67) and an additional group of noncancer individuals ( n = 104). Besides oral bacterial dysbiosis and signatures observed in OSCC, associations of 3 loci with the abundance of genus-level taxa and 4 loci with β diversity measures were detected ( q < 0.05) at the discovery stage. The most significant hit (rs10906082 with the genus Lachnoanaerobaculum, P = 3.55 × 10–9 at discovery stage) was replicated in a second OSCC cohort. Moreover, the other 2 taxonomical associations, rs10973953 with the genus Kingella ( P = 1.38 × 10–9) and rs4721629 with the genus Parvimonas ( P = 3.53 × 10–8), were suggestive in the meta-analysis combining 2 OSCC cohorts. Further pathway analysis revealed that these loci were enriched for genes in regulation of oncogenic and angiogenic responses, implicating a genetic anchor to the oral microbiome in estimation of casual relationships with OSCC. Our findings delineate the role of host genotypes in influencing the structure of oral microbial communities.

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 Cryopreservation of a soil microbiome using a Stirling 1 cycle approach - a genomic assessment.

2021 ◽  
Author(s):  
Giovanni Cafa ◽  
Juan Miguel Bonnin ◽  
Nicola Holden ◽  
Jacob G. Malone ◽  
Tim H. Mauchline ◽  
...  
Keyword(s):  
Liquid Medium ◽  
Soil Sample ◽  
Soil Samples ◽  
Soil Microbiome ◽  
Similar Response ◽  
Before And After ◽  
Microbiome Research ◽  
Health And Disease ◽  
And Function

Abstract Soil microbiomes are dynamic systems that respond to biotic and abiotic environmental factors such as those presented at seasonal scales or due to long-term anthropogenic regime shifts. These can affect the composition and function of microbiomes. Investigation of microbiomes can uncover hidden microbial roles in health and disease and discover microbiome-based interventions. Collections of soil samples are kept by various institutions in either a refrigerated or occasionally frozen state, but conditions are not optimised to ensure the integrity of soil microbiome. In this manuscript, we describe cryopreservation with a controlled rate cooler and estimate the genomic content of an exemplar soil sample before and after cryopreservation. The first hypothesis was to test the genomic integrity of the microbiome. We also enriched the soil sample with a liquid medium to estimate the growth of bacteria and compared their growth before and after cryopreservation. Sequence-based rRNA metabarcoding was used to demonstrate that the controlled rate cooler maintains intact the DNA content of the microbiome. Two methods of cryopreservation were applied and compared with control aliquots of soil. An optimised cryopreservation of soil samples is essential for the development of microbiome research in order to retain stable, functionally intact microbiomes. Our results showed that metabarcoding of 16S and ITS rRNA were useful methods to estimate successful cryopreservation. The soil microbiome after enrichment with liquid medium exhibited a similar response of cryopreserved soil and this was estimated with the comparison of the ten most abundant bacterial taxa. These findings support a successful process of cryopreservation and are promising for future use of this technology. To the best of our knowledge, this study is the first report of cryopreservation of soil using a Stirling cycle cooling approach.

scholarly journals Future Prospective of Oral Microbiome Research

2021 ◽  
Vol 12 (1) ◽  
pp. 55
Author(s):  
Yoshiaki Nomura ◽  
Ayako Okada ◽  
Nobuhiro Hanada
Keyword(s):  
Older Adults ◽  
Human Health ◽  
Complex Structure ◽  
Oral Microbiome ◽  
Oral Diseases ◽  
Beneficial Bacteria ◽  
Concise Review ◽  
Microbiome Research

Oral microbiome has complex structure. It consisted of more than 700 species of bacteria. These bacteria contains pathogens for human health. In contrast, some beneficial bacteria were included. Perspective of oral microbiome is not still elucidated. In this paper, information regarding oral microbiome of health older adults and oral diseases are included. Additionally, concise review of oral microbiome are presented.

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 Effect of different sweeteners on the oral microbiota and immune system of Sprague Dawley rats

AMB Express ◽  
2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Xi Cheng ◽  
Xiurong Guo ◽  
Feihong Huang ◽  
Hui Lei ◽  
Quan Zhou ◽  
...  
Keyword(s):  
Immune System ◽  
High Throughput Sequencing ◽  
Pure Water ◽  
Structure And Function ◽  
Oral Microbiome ◽  
Oral Microbiota ◽  
Sprague Dawley ◽  
Sprague Dawley Rats ◽  
And Function

AbstractSucrose, xylose, and saccharin are commonly used beverage additives and long-term consumption of these compounds inevitably affects the oral immune system and the composition of oral microbiomes. In this study, we used 24 Sprague Dawley rats divided into four groups, i.e., sucrose, saccharin, xylose, or pure water treated over an eight week period to evaluate any changes in the composition, community structure, and function of the oral microbiomes. At the end of the treatment period, we collected oral microbiome samples from each animal and subjected them to high-throughput sequencing. We also used ELISA to determine the concentration of salivary immunoglobulin in these rats to reveal the effect of sweetener on the oral immune system. Sequencing results demonstrated that Firmicutes and Proteobacteria, remained the predominant phyla, but we found that the oral microbial diversity of rats drinking sucrose water was significantly higher than that of the other groups. Our results indicate that drinking water supplemented with sweeteners may influence oral immunity as well as the composition, metabolic function, and diversity of the oral microbiota, thereby disrupting the oral microbiome.

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