Construction of a caries diagnosis model based on microbiome novelty score / 华西口腔医学杂志

OBJECTIVES@#This study aimed to analyze the bacteria in dental caries and establish an optimized dental-ca-ries diagnosis model based on 16S ribosomal RNA (rRNA) data of oral flora.@*METHODS@#We searched the public databa-ses of microbiomes including NCBI, MG-RAST, EMBL-EBI, and QIITA and collected data involved in the relevant research on human oral microbiomes worldwide. The samples in the caries dataset (1 703) were compared with healthy ones (20 540) by using the microbial search engine (MSE) to obtain the microbiome novelty score (MNS) and construct a caries diagnosis model based on this index. Nonparametric multivariate ANOVA was used to analyze and compare the impact of different host factors on the oral flora MNS, and the model was optimized by controlling related factors. Finally, the effect of the model was evaluated by receiver operating characteristic (ROC) curve analysis.@*RESULTS@#1) The oral microbiota distribution obviously differed among people with various oral-health statuses, and the species richness and species diversity index decreased. 2) ROC curve was used to evaluate the caries data set, and the area under ROC curve was AUC=0.67. 3) Among the five hosts' factors including caries status, country, age, decayed missing filled tooth (DMFT) indices, and sampling site displayed the strongest effect on MNS of samples (P=0.001). 4) The AUC of the model was 0.87, 0.74, 0.74, and 0.75 in high caries, medium caries, low caries samples in Chinese children, and mixed dental plaque samples after controlling host factors, respectively.@*CONCLUSIONS@#The model based on the analysis of 16S rRNA data of oral flora had good diagnostic efficiency.

Microbioma oral: variabilidad entre regiones y poblaciones / Oral Microbiome: Variability Between Regions and Populations

Resumen De acuerdo con la Organización Mundial de la Salud (OMS), 3.58 billones de personas son afectadas por desórdenes orales, donde la caries, seguida de la enfermedad periodontal son las más frecuentes y las principales causas de daño al tejido pulpar y pérdida de órganos dentales. En México, el Sistema de Vigilancia Epidemiológica de Patologías Bucales (SIVEPAB) reportó que el 53% de la población se ve afectada por algún grado de enfermedad periodontal, mientras que en promedio la caries afecta al 93.3% de la población de entre 20 a 85 años y más, así como a alrededor del 50.0% de niños y adolescentes, por lo que ambos padecimientos son considerados un problema de salud pública importante en este país. Adicionalmente, se sabe que el microbioma oral humano está asociado con la salud y la enfermedad bucodental. Entre los géneros bacterianos que comúnmente habitan la cavidad oral humana destacan Streptococcus spp., Lactobacillus spp. y Porphyromonas spp. que, a través del desequilibrio del microbioma oral (disbiosis), se asocian con la caries o la enfermedad periodontal. En vista de que estamos constantemente expuestos a este tipo de infecciones crónicas inflamatorias, se sabe que las bacterias orales se trasladan a otras partes del cuerpo contribuyendo al desarrollo y exacerbación de la inflamación sistémica y otras enfermedades. Ya que existen factores como la ubicación geográfica, además de la disbiosis, la edad, la dieta y la genética, que influyen en la variabilidad del microbioma humano. Es importante analizar la diversidad del microbioma oral desde esta perspectiva, ya que el conocimiento que se tiene hasta el momento aún es escaso; por lo anterior se realizó una búsqueda de artículos publicados entre 2010 y 2020 en poblaciones de Asia, África, América y Europa, con el fin de responder la siguiente pregunta: ¿el factor geográfico tiene un impacto en la composición de la variabilidad del microbioma oral humano?

Abstract According to the World Health Organization (WHO), 3.58 billion people were affected by oral disorders, where caries, followed by periodontal disease are the most frequent and the main causes of damage to pulp tissue and loss of dental organs. In Mexico, the Epidemiological Surveillance System for Oral Pathologies (SIVEPAB) reported that 53% of the population is affected by some degree of periodontal disease, while on average caries affects 93.3% of the population between 20 and 85 years old and older, as well as about 50.0% of children and adolescents, so both conditions are considered an important public health problem in this country. Additionally, the human oral microbiome is known to be associated with oral health and disease. An imbalance in the oral microbiome (dysbiosis) can result in the proliferation of Streptococcus mutans and Porphyromonas gingivalis, linked to caries and periodontal disease. The latter two conditions, the most prevalent oral diseases worldwide, are the main causes of damage to pulp tissue and loss of dental organs. In the presence of these pathologies, constant exposure to the corresponding inflammatory chronic infection could lead to the translocation of oral bacteria to other parts of the body, where they may contribute to the development and/or exacerbation of systemic inflammation and trigger disease. Since age, diet, genetics, and geographical location are known to influence the variability of the human microbiome, it is important to analyze differences in the oral microbiome between distinct populations. Up to now, little attention has been given to this task. The current review carried out for articles published between 2010 and 2020 and describes the human oral microbiome in populations of Asia, Africa, America and Europa, to explore whether geographical differences have an impact on the variability of the human oral microbiome.

Research progress on the relationship between orthodontic treatment and the oral microbiome / 口腔疾病防治

@#With the deepening of research in oral microbiomics, an important relationship between changes in the oral microbiome and orthodontic treatment has been found. Orthodontic treatment will have an impact on the oral and systemic microbiome. The presence of oral appliances can change the quantity and quality of the oral microbiometo and increase the risk of oral and even systemic diseases in patients undergoing orthodontic treatment. Compared with fixed orthodontic treatment, clear aligners will not have a harmful impact on the structure of the oral microbiome, which is more conducive to maintain oral health during the orthodontic treatment process. In addition, different bracket types and materials can lead to different changes in the oral microbiome, and the occurrence and development of orthodontic-related diseases, such as white spot lesions, dental caries, gingivitis and periodontitis, are also related to changes in the oral microbiome. At present, the role of the oral microbiome in the process of orthodontic treatment needs to be further studied. Whether a change in the oral microbiome caused by orthodontic treatment can be restored after orthodontic treatment is still uncertain and needs more research. This paper reviews the research progress on the application of microbiomics in orthodontics, including the impact of fixed appliances and clear aligners on the microbiome and the relationship between orthodontic-related diseases and the oral microbiome.

Efeito da colostroterapia e do leite materno no estabelecimento da microbiota de recém-nascidos prematuros / Effect of breast milk and oropharyngeal administration of colostrum on the establishment of the microbiota of preterm newborns

A colonização inicial da microbiota humana é de suma importância, desempenhando um papel fundamental no desenvolvimento imunológico, nutricional, metabólico e neurológico. Recémnascidos prematuros e de baixo peso muitas vezes precisam permanecer internados em unidades de terapia intensiva e frequentemente a dieta enteral trófica é limitada, devido à imaturidade do sistema digestivo ou estado clínico do recém-nascido. Nesse contexto, a amamentação é importante para o desenvolvimento do recém-nascido e para a colonização inicial do trato gastrointestinal. Além disso, a administração de colostro como imunoterapia oral já foi descrita como uma terapia segura, viável e bem tolerável por recém-nascidos. Sendo assim, este projeto avaliou o efeito da administração de leite materno, seja através da dieta ou colostroterapia, no desenvolvimento da microbiota oral e intestinal de recém-nascidos prematuros. Foi realizado um estudo longitudinal e observacional, onde foram recrutados 20 neonatos prematuros para a análise da microbiota oral e 56 para a análise da microbiota intestinal. Foram coletadas amostras de saliva e fezes dos neonatos, e leite materno das mães destes neonatos, e realizado sequenciamento do gene 16S rRNA destas amostras, além da dosagem de imunoglobulina A (IgA) nas fezes dos recém-nascidos. Para análise estatística, foi utilizado o software SPSS e R Studio, adotando significância de 5% para os testes. O leite materno de mães de recém-nascidos prematuros apresenta composição que muda ao longo do tempo, com aumento de Staphylococcus e Streptococcus e diminuição de Corynebacterium 1. A colostroterapia possui efeito benéfico sobre a microbiota oral, com aumento de gêneros como Staphylococcus, Bifidobacterium e Bacteroides. Adicionalmente, existe diferença na microbiota intestinal quando diferentes proporções de leite materno são oferecidas durante a primeira semana de vida, além de maiores níveis de IgA total nas amostras de fezes de neonatos que receberam maiores proporções de leite materno

The initial colonization of the human microbiota is of paramount importance, playing a fundamental role in immunological, nutritional, metabolic, and neurological development. Premature and low-birth-weight newborns often need to remain hospitalized in intensive care units and often enteral trophic diet is limited due to the immaturity of the digestive system or the newborn's clinical status. In this context, breastfeeding is important for the newborn's development and for the initial colonization of the gastrointestinal tract. Furthermore, the administration of colostrum as oral immunotherapy has been described as a safe, viable and well-tolerable therapy for newborns. Therefore, this project evaluated the effect of administering breast milk, either through diet or administration of colostrum, on the development of the oral and intestinal microbiota of preterm newborns. A longitudinal and observational study was carried out, where 20 premature neonates were recruited for the analysis of the oral microbiota and 56 for the analysis of the intestinal microbiota. Samples of saliva and feces were collected from the newborns, and breast milk from the mothers of these newborns, and 16S rRNA gene sequencing was performed from these samples, in addition to the dosage of immunoglobulin A (IgA) in the feces of the newborns. For statistical analysis, SPSS and R Studio software were used, adopting a significance of 5% for the tests. Breast milk from mothers of premature newborns has a composition that changes over time, with an increase in Staphylococcus and Streptococcus and a decrease in Corynebacterium 1. Administration of colostrum has a beneficial effect on the oral microbiota, with an increase in genera such as Staphylococcus, Bifidobacterium and Bacteroides. Additionally, there is a difference in the intestinal microbiota when different proportions of breast milk are offered during the first week of life, in addition to higher levels of total IgA in stool samples from newborns who received higher proportions of breast mil

A preliminary study on bacterial composition in the subgingival plaque of woman with periodontitis during pregnancy and menopause

Aim: The aim of the present study was to explore the bacterial composition in subgingival plaque of females with periodontitis during pregnancy and menopause stages using 16S ribosomal RNA (rRNA) gene pyrosequencing approach.Methodology: Subgingival plaque was collected from four woman volunteers (healthy, periodontitis, periodontitis at pregnancy and periodontitis at menopause). The microbial community composition was analyzed by 454/Roche GS FLX chemistry pyrosequencing approach using the variable (V1-V3) region of the 16S rRNA gene. Pyrosequencing reads were sorted to get the clean reads that were annotated against the EzBioCloud data base for taxonomic classification. Operational Taxonomic Units (OTUs) were assigned and shared, and subsequently identified using CLCOMMUNITY software. Results: Pyrosequencing yielded 13,939 sequences comprising of 13 phyla, 124 genera, and 372 species. The predominant microbial phyla in subgingival plaque of all woman volunteers included Firmicutes, Actinobacteria, Fusobacteria, Bacteroidetes, and Proteobacteria. In the healthy volunteer, Streptococcus (52.4%) formed the predominant genus while in woman with periodontitis Streptococcus (24.6%) and Fusobacterium (11.7%) predominated. In the periodontitis volunteer with pregnancy, the predominant genus included Streptococcus (25.8%) and Fusobacterium (22.4%), whereas volunteer with menopause, the gingivitis was associated with genus Alloprevotella (19.5%), Leptotrichia (14.3%), Fusobacterium (12.3%), and Porphyromonas (12.0%). Interpretation: This study proves on preliminary basis that the subgingival microbiome of woman with periodontitis at pregnancy or menopause tend to differ from that of healthy woman, and these species included certain periodontal pathogens such as Fusobacterium nucleatum and Porphyromonas gingivalis

Factors influencing the structure of the oral microbiome / 口腔疾病防治

@#The oral microbiome has been identified as one of the most diverse microbial communities in the human body, and the ecological imbalance of the oral microbiome can not only induce a variety of oral diseases, such as dental caries, pulpitis, apical periodontitis, and periodontal diseases, but also is closely related to cardiovascular diseases, diabetes and other systemic diseases. The structure of the oral microbiome is affected by multiple factors. This paper reviews and summarizes the effects of genetics, the environment, diet and systemic diseases. Literature reviews have shown that environmental factors play an important role in the structure of the oral microbiome, while the influence of genetic and dietary factors is still controversial. In addition, systemic diseases may also affect the oral microbial community. High-throughput sequencing studies have identified some “core microbiota”, and “core microbiota” in different environments and in different genetic backgrounds will be the next research direction.

Assessment of the oral microbiome in the development of recurrent oral aphthae in patients with gastrointestinal pathology

Chronic recurrent oral aphthae in residents living in an ecologically unfavourable region are characterized by a permanent course and prolonged recovery processes of regeneration of pathological elements of the oral mucosa. Using the microbiological method and modern test systems, it has been found that on the surface of aphthae an extremely diverse state of the oral microbiota is determined and its types are diverse. Trigger mechanisms have been determined. The role of representatives of various types of microorganisms - enterococci, staphylococci, streptococci, yeast-like fungi of the genus Candida (C. albicans) and obligate-anaerobes in the development of recurrent oral aphthae has been established. The data obtained can serve as an indication for the development of modern treatment and preventive measures regarding this category of patients.

Diversity of Oral Microflora in Oral and Systemic Diseases: A Brief Review

The oral cavity contains rich and diverse microflora, known as oral microflora. Oral microflora usually presents within the biofilms attached to the various soft and hard tissue surfaces of the oral cavity. Oral microflora is beneficial to us and plays an important role in the normal development of the physiology. It also contributes to host defense; however, it can also have severe adverse effects for overall health. The present article aims to review the information regarding oral microflora in health and diseases. Recent updates regarding the oral microflora contribution in several common oral and systemic diseases are also briefly discussed.

Potential application of human microbiomes in the diagnosis and treatment of type 2 diabetes mellitus / 华西口腔医学杂志

Human microbiome refers to the total microorganism genetic information of human body surface and internal, which is closely related to human health and disease. Oral and gut microbiomes are the most diverse microbial communities, which can interact and play a role in the development of the disease, and can reflect the health and disease state in real time. Type 2 diabetes mellitus is a metabolic disorder caused by both genetic and environmental factors. Recent research has shown a link between microbes and diabetes. This article reviewed the latest research on the changes of oral and gut microbiomes in type 2 diabetes mellitus patients, which expects to provide a reference for exploring the development of the disease model for prediction, diagnosis and prognosis of type 2 diabetes mellitus based on human microbiome characteristics.

Research progress on carbohydrate active enzymes of human microbiome / 华西口腔医学杂志

A massive variety of microorganisms live in and on the human body, especially at oral, skin, vaginal, gastroin-testinal, and respiratory sites. The complicated metabolic activities of microorganisms assist human digestive function and participate in a series of physiological and pathogenetic processes. Carbohydrate-active enzymes (CAZymes) are a series of enzymes that function in degradation, modification, and formation of glycoside bonds. Microbes regulate the physiological and pathogenetic processes of human body by producing various CAZymes to degrade and modify complex carbohydrates and generate signal molecules for further utilization in human cells. Here, we reviewed the mechanisms of complex carbohy-drate metabolism and related microbial CAZymes, especially in digestive tract and oral cavity. We also summarized the rela-tionship between microbial CAZymes and human health, and proposed potential applications.

Microbial Profile of Supragingival and Subgingival Plaque of Patients With Glycogen Storage Disease

Abstract Patients with glycogen storage disease (GSD) are either orally fed (ORF) or gastronomy-tube fed (GTF) with cornstarch to maintain normal glucose levels. It is not known whether the use of cornstarch affects the microbiological oral profile of patients with GSD. Thus, the purpose of this study was to compare supragingival and subgingival plaque samples collected from 53 participants with GSD (2-56 years)—29 ORF and 24 GTF. The 16S sequence bacterial profiles of plaque DNA were obtained and a total of 768 probes were detected across the plaque groups. Orally fed patients showed higher means of cariogenic species and periodontal health-associated species, whereas GTF patients showed higher means of periopathogenic species (P < .05). Orally fed patients exhibited high levels of caries pathogens and lower levels of periodontal pathogens possibly due to the acidic environment created by their cornstarch diet, when compared to GTF patients.

Avances en el Estudio de la Diversidad Bacteriana Oral Asociada a Caries Dental Mediante el Estudio Genómico / Advances in the Study of Oral Bacterial Diversity Associated with Dental Caries by Genomic Study

La caries es una enfermedad infecciosa, transmisible y multifactorial, que conduce a la pérdida de minerales reversible o irreversible de los tejidos duros susceptibles del diente, por acción de productos ácidos provenientes de la fermentación de los hidratos de carbono de la dieta por la actividad metabólica del biofilm adherido a la superficie dentaria. Aunque tradicionalmente se ha considerado al Streptococcus mutans como el responsable de la enfermedad, actualmente otras bacterias, denominadas no mutans, se han asociado con el inicio, progresión y actividad de la enfermedad en esmalte, dentina y cemento radicular. Para profundizar el estudio de la diversidad bacteriana oral asociada a caries dental se han aplicado diversas metodologías, dentro de las cuales destaca el estudio del metagenoma oral. Este nos permite estudiar comunidades bacterianas completas mediante el análisis del DNA, en un determinado ambiente sin necesidad de aislar y cultivar las especies, entregando información sobre la diversidad taxonómica y filogenética de estas comunidades. Existen diferentes métodos de análisis de la diversidad bactariana, entre los que tenemos el análisis del ARNr 16S mediante electroforésis, PCR, microarreglos, secuenciamiento de última generación, entre otros. El estudio del metagenoma oral ha permitido identificar especies que no han podido ser aisladas por métodos convencionales, además de identificar su presencia o ausencia en las distintas etapas del desarrollo de la enfermedad de caries dental, permitiendo un mejor conocimiento del desarrollo de esta patología. El estudio basado en el metagenoma ha dado a conocer una diversidad microbiana oral inesperada, dando información relevante para la actualización de los conocimientos y así identificar nuevos objetivos terapéuticos. El propósito de esta revisión bibliográfica es exponer los principales resultados que ha aportado el estudio del metagenoma sobre la diversidad microbiana, aplicado específicamente a la comunidad bacteriana oral.

Dental caries is an infectious, transmissible and multifactorial disease, which leads towards a reversible and irreversible loss of minerals found in hard tissues of a tooth, caused by acids from carbohydrates fermentation due to metabolic activity of the biofilm attached to the tooth surface. Although Streptococcus mutans has been thought to be responsible for tooth decay, another bacterium named no mutans has been linked to the beginning, progression and activity of the disease in the enamel, dentine and cement. One of the methodologies put into practice to deepen the study of oral bacteria diversity related to carious cavities is oral metagenome. This methodology allows the study of whole bacterial groups by the analysis of DNA in a particular environment without the need of isolating and cultivating species, providing information about the taxonomical and phylogenetic diversity of these groups. There are different methods to study the bacterial diversity, including 16 S rRNA analysis through electrophoresis, PCR, microarrays, next generation sequence (NGS). The metagenome tool permits to recognize species that have not been able to be isolated by conventional methods. As well as identify its presence or absence in the different stages of the dental caries development, which allows a better understanding of development of the disease. The metagenome-based study has revealed an unexpected oral microbial diversity, giving information relevant to the updating of knowledge and identifies new therapeutic targets. The purpose of this review is to present the main results has brought the study of the metagenome on microbial diversity, applied specifically to the oral bacterial community in health and caries disease.

Comparison of DNA Extraction Methods for Human Oral Microbiome Research.

The oral micro biome is highly diverse and its composition is associated with oral disease and potentially diseases at other sites. Our objective is to evaluate DNA extraction methods potentially suitable for population-based investigations on the oral human microbiome and disease risk. Six commonly used microbial DNA extraction kits, employing either enzymatic methods or mechanical bead beating for cell lysis, were evaluated for the following aspects total DNA yield and quality and 16s rRNA DNA product and representation of microbial diversity. All analyses were carried out using a pooled and homogenized sample from one study subject. 16s rRNA gene sequence data were processed using the QIIME pipeline. One way ANOVA and Kruskal-Wallis tests were used to compare the different DNA extraction methods. We found that enzymatic extraction kits produced higher human genomic DNA, compared with mechanical extraction kits, however, phylogenic diversity in oral microbiome community structure from 16s rRNA gene sequence reads revealed no important differences between kit types. Enzymatic and mechanical bead beating kits provide alternative approaches for DNA extraction of oral microbiome DNA from oral wash samples. Greater total DNA yields are found in enzymatic approaches but microbial diversity can be similarly well characterized by either enzymatic or mechanical bead beating approaches.