Metagenomic analysis of dental plaque on pit and fissure sites with and without caries among adolescents
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ABSTRACT:
PROVIDER: PRJEB47564 | ENA |
REPOSITORIES: ENA
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Project description:Caries is one of the most prevalent infectious diseases worldwide and is driven by the dysbiosis of dental biofilms adhering to tooth surfaces. The pits and fissured surfaces are the most susceptible sites of caries. However, information on the taxonomic composition and functional characteristics of the plaque microbiota in the pit and fissure sites is very limited. This study aimed to use metagenomic sequencing analyses to investigate the relationship between the plaque microbiome in the pit and fissure site and caries in adolescents. A total of 20 adolescents with active pit and fissure surface caries were involved as well as 20 age-matched, caries-free teenagers for control tests. Plaque samples were collected from the pit and fissure site and were subjected to metagenomic analyses, in which the microbial communities were investigated. Our results showed that the microbiota diversity was similar between those two groups. At the species level, the relative abundances of A. gerencseriae, P. acidifaciens, P. multisaccharivorax, S. oralis, S. mutans, and P. denticolens were higher in the caries-active group. N. elongata, C. hominis, and A. johnsonii were relatively more abundant in the caries-free groups. Functional analysis suggested that the metabolic pathway was the most abundant pathway, and the functional traits of the level 2 pathways included amino acid metabolism, metabolism of cofactors, and vitamins and carbohydrate metabolism. Our results also revealed that the caries group displayed several alterations in metabolic pathways, including enriched functions in carbohydrate digestion and absorption. This study suggested that in addition to the specific anatomical structures of the pit and fissured surfaces, the fundamental differences in the plaque microbiome may also be related to the susceptibility of pit and fissure caries.
| S-EPMC8579706 | biostudies-literature
Project description:The study aims to assess gene expression in plaque samples collected from twin pairs that are both concordant and discordant with respect to dental Caries diagnosis. File Naming Conventions are as follows: Patient ID : 4 digit identifier Diagnosis : Caries Negative(CN) or Caries Positive(CP) Type of Twin: Monozygotic(MZ)or Dizygotic(DZ) Pair to xxxx: 4 digit twin identifier maps to the Patient ID E.g: 2126_CP_MZ_PairTo_2125_fastqc - 2126 is a caries positive patient and pairs to monozygotic twin pair 2125. Plaque samples from twin pairs that are both concordant and discordant with respect to dental Caries diagnosis are enriched for bacterial messenger RNA to study the gene expression differences in the samples. RNA was extracted from RNAprotect (Qiagen, In c.) treated dental plaque scrapings from 38 patients. Amplified cDNA was created and rRNA sequence was removed by subtractive hybridization. Individual patient samples were run on a single lane of an Illumina Genome Analyzer.
2011-09-26 | E-GEOD-31439 | biostudies-arrayexpress
Project description:The study aims to assess gene expression in plaque samples collected from twin pairs that are both concordant and discordant with respect to dental Caries diagnosis. File Naming Conventions are as follows: Patient ID : 4 digit identifier Diagnosis : Caries Negative(CN) or Caries Positive(CP) Type of Twin: Monozygotic(MZ)or Dizygotic(DZ) Pair to xxxx: 4 digit twin identifier maps to the Patient ID E.g: 2126_CP_MZ_PairTo_2125_fastqc - 2126 is a caries positive patient and pairs to monozygotic twin pair 2125. Plaque samples from twin pairs that are both concordant and discordant with respect to dental Caries diagnosis are enriched for bacterial messenger RNA to study the gene expression differences in the samples.
2011-09-26 | GSE31439 | GEO
Project description:The aims of this study were to assess the prevalence of dental caries and the DMFT index, as well as the distribution pattern of pit and fissure sealants on permanent teeth in a Portuguese sample of adolescents, and to assess whether the existing usage of sealants and socio-demographic factors are correlated to caries prevalence on the examined sample.A cross-sectional study was designed with a sample of 447 adolescents aged 12 to 18 years old, attending a public school in Sátão, Portugal. A self-administered questionnaire with questions about oral health behaviours and socio-economic status was answered by adolescents in the classroom. Clinical examination of oral health status and assessment of fissure sealants were accomplished by only one trained member of the research team.We obtained a DMFT index of 3.32 (2.92), which indicates a moderate level of prevalence of dental caries. When considering a DMFT = 0, we found significant statistical differences between the parents' level of education (≤ 4th grade = 26.3 vs 5th-12th grade = 18.8 vs <12th grade = 43.3, p = 0.001), gender (male = 27.3 vs female = 19.6, p = 0.04), age (≤ 15 years = 27.1 vs <15 years = 18.5, p = 0.02), presence of fissure sealants (yes = 30.6 vs no = 13.5, p = 0.001) and experience of dental pain (no = 25.4 vs yes = 16.8, p = 0.02). When analyzing the prevalence of fissure sealants, we verified that 58.8% of adolescents had at least one fissure sealant applied. Significant statistical differences were found when analyzing the presence of fissure sealants related with parents' educational level (<9th grade, OR = 1.56 CI95% = 1.05-2.54), gender (female, OR = 1.86 CI95% = 1.19-2.98), experience of dental pain (yes, OR = 0.62 CI95% = 0.39-0.97) and presence of dental caries (yes, OR = 0.35 CI95% = 0.19-0.65).The moderate level of caries prevalence reveals the need of improvement of primary prevention interventions among Portuguese adolescents. The establishment of a more targeted preventive program with better and more effective oral health education is essential, having into account socio-demographic aspects.
| S-EPMC4372347 | biostudies-other
Project description:Incomplete fusion of the optic fissure leads to ocular coloboma, a congenital eye defect that affects up to 7.5 per 10,000 births and accounts for up to 10 percent of childhood blindness. The molecular and cellular mechanisms that facilitate optic fissure fusion remain elusive. We have profiled global gene expression during optic fissure morphogenesis by transcriptome analysis of tissue dissected from the margins of the zebrafish optic fissure and the opposing dorsal retina before (32 hours post fertilisation, hpf), during (48 hpf) and after (56 hpf) optic fissure fusion. Differential expression analysis between optic fissure and dorsal retinal tissue resulted in the detection of several known and novel developmental genes. The expression of selected genes was validated by qRT-PCR analysis and localisation investigated using in situ hybridisation. We discuss significantly overrepresented functional ontology categories in the context of optic fissure morphogenesis and highlight interesting transcripts from hierarchical clustering for subsequent analysis. We have identified netrin1a (ntn1a) as highly differentially expressed across optic fissure fusion, with a resultant ocular coloboma phenotype following morpholino antisense translation-blocking knockdown and downstream disruption of atoh7 expression. To support the identification of candidate genes in human studies, we have generated an online open-access resource for fast and simple quantitative querying of the gene expression data. Our study represents the first comprehensive analysis of the zebrafish optic fissure transcriptome and provides a valuable resource to facilitate our understanding of the complex aetiology of ocular coloboma.
2020-10-22 | GSE159822 | GEO