Ontology highlight
ABSTRACT:
PROVIDER: PRJEB41041 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR4778630.fastq.gz | Fastqsanger.gz | |||
| ERR4778640.fastq.gz | Fastqsanger.gz | |||
| ERR4778650.fastq.gz | Fastqsanger.gz | |||
| ERR4778660.fastq.gz | Fastqsanger.gz | |||
| ERR4778670.fastq.gz | Fastqsanger.gz |
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Project description:The composition of the salivary microbiota has been reported to differentiate between patients with periodontitis, dental caries and orally healthy individuals. Thus, the purpose of the present investigation was to compare metaproteomic profiles of saliva in oral health and disease. Stimulated saliva samples were collected from 10 patients with periodontitis, 10 patients with dental caries and 10 orally healthy individuals. Samples were analyzed by means of shotgun proteomics. 4161 different proteins were recorded out of which 1946 and 2090 were of bacterial and human origin respectively. The human proteomic profile displayed significant overexpression of the complement system and inflammatory mediators in periodontitis and dental caries. Bacterial proteomic profiles and functional annotation were very similar in health and disease. Data revealed multiple potential salivary proteomic biomarkers of oral disease. In addition, comparable bacterial functional profiles were observed in periodontitis, dental caries and oral health, which suggest that the salivary microbiota predominantly thrives in a planktonic state expressing no characteristic disease-associated metabolic activity. Future large-scale longitudinal studies are warranted to reveal the full potential of proteomic analysis of saliva as a biomarker of oral health and disease.
2016-08-15 | PXD004319 | Pride
Project description:Human saliva microbiota is phylogenetically divergent among host individuals yet their roles in health and disease are poorly appreciated. We employed a microbial functional gene microarray, HuMiChip 1.0, to reconstruct the global functional profiles of human saliva microbiota from ten healthy and ten caries-active adults. Saliva microbiota in the pilot population featured a vast diversity of functional genes. No significant distinction in gene number or diversity indices was observed between healthy and caries-active microbiota. However, co-presence network analysis of functional genes revealed that caries-active microbiota was more divergent in non-core genes than healthy microbiota, despite both groups exhibited a similar degree of conservation at their respective core genes. Furthermore, functional gene structure of saliva microbiota could potentially distinguish caries-active patients from healthy hosts. Microbial functions such as Diaminopimelate epimerase, Prephenate dehydrogenase, Pyruvate-formate lyase and N-acetylmuramoyl-L-alanine amidase were significantly linked to caries. Therefore, saliva microbiota carried disease-associated functional signatures, which could be potentially exploited for caries diagnosis. The DMFT INDEX (Decayed, Missing, Filled [DMF] teeth index used in dental epidemiology) values are provided for each sample
2013-08-15 | GSE49875 | GEO
Project description:Human saliva microbiota is phylogenetically divergent among host individuals yet their roles in health and disease are poorly appreciated. We employed a microbial functional gene microarray, HuMiChip 1.0, to reconstruct the global functional profiles of human saliva microbiota from ten healthy and ten caries-active adults. Saliva microbiota in the pilot population featured a vast diversity of functional genes. No significant distinction in gene number or diversity indices was observed between healthy and caries-active microbiota. However, co-presence network analysis of functional genes revealed that caries-active microbiota was more divergent in non-core genes than healthy microbiota, despite both groups exhibited a similar degree of conservation at their respective core genes. Furthermore, functional gene structure of saliva microbiota could potentially distinguish caries-active patients from healthy hosts. Microbial functions such as Diaminopimelate epimerase, Prephenate dehydrogenase, Pyruvate-formate lyase and N-acetylmuramoyl-L-alanine amidase were significantly linked to caries. Therefore, saliva microbiota carried disease-associated functional signatures, which could be potentially exploited for caries diagnosis. The DMFT INDEX (Decayed, Missing, Filled [DMF] teeth index used in dental epidemiology) values are provided for each sample We employed a microbial functional gene microarray, HuMiChip 1.0, to reconstruct the global functional profiles of human saliva microbiota from ten healthy and ten caries-active adults.
2013-08-15 | E-GEOD-49875 | biostudies-arrayexpress
Project description:The composition of the salivary microbiota has been reported to differentiate between patients with periodontitis, dental caries and orally healthy individuals. Thus, the purpose of the present investigation was to compare metaproteomic profiles of saliva in oral health and disease. Stimulated saliva samples were collected from 10 patients with periodontitis, 10 patients with dental caries and 10 orally healthy individuals. Samples were analyzed by means of shotgun proteomics. 4161 different proteins were recorded out of which 1946 and 2090 were of bacterial and human origin respectively. The human proteomic profile displayed significant overexpression of the complement system and inflammatory mediators in periodontitis and dental caries. Bacterial proteomic profiles and functional annotation were very similar in health and disease. Data revealed multiple potential salivary proteomic biomarkers of oral disease. In addition, comparable bacterial functional profiles were observed in periodontitis, dental caries and oral health, which suggest that the salivary microbiota predominantly thrives in a planktonic state expressing no characteristic disease-associated metabolic activity. Future large-scale longitudinal studies are warranted to reveal the full potential of proteomic analysis of saliva as a biomarker of oral health and disease.
2017-03-29 | MSV000080763 | MassIVE
Project description:Saliva is a rich-bodily fluid with recognized clinical diagnosis roles and this research aimed at investigating if there is any change in the salivary proteome signatures of MIH children with distinct degrees of severity. Fifty schoolers (6-10 years) were equally assigned into the following groups: Group 1 (Control group - Healthy teeth), Group 2 (Mild MIH with white/creamy opacity and free of caries), Group 3 (Mild MIH with yellow/brown opacity and free of caries), Group 4 (Severe MIH with white/creamy, yellow/brown opacities including post-eruptive fracture and free of caries), Group 5 (Severe MIH with white/creamy, yellow/brown opacities, post-eruptive fracture, and caries). Unstimulated saliva samples were collected and later explored using mass spectrometry analysis. In total, 6,471 proteins were found, 5,073 exclusively from MIH children, and 778 overlapping among the different degrees of the disturb. The Biological Pathways displayed distinct patterns among the groups, being different according to the degrees of MIH. Gene-Odontology differences might not be verified regarding the biological processes and cellular components. Conversely, with respect to molecular function, alterations among groups were evident, with the presence of proteins that would contribute to MIH in children with the severe condition (i.e, calcium ion binding, microtubule binding, platelet-derived growth factor binding). In conclusion, the results of this study support important salivary proteomic changes in MIH children, according to distinct degrees of severity, reinforcing the interplay between the clinical aspects of hypomineralization (white/yellow opacities/enamel breakdown) and changes in the salivary proteome.
2024-08-18 | PXD044610 | JPOST Repository
Project description:The lesions of enamel caries can be considered as the outcome of dysbiotic changes in the biofilm community of supragingival dental plaque. Demineralization occurs as the cumulative outcome of repeated shifts towards a less diverse microbiota that produces and tolerates a low pH environment in tooth sites that are sheltered from protective factors in host saliva. Although the etiology of caries is multifactorial, frequent consumption of foods rich in fermentable carbohydrates, notably sucrose, appears to be one of the major factors driving the microbiota in the direction of dysbiosis, particularly in the case of otherwise healthy children with normal salivary flow. Streptococcus mutans and closely related species (such as Streptococcus sobrinus) have long been considered to play a primary etiological role in dental caries. S. mutans responds to sucrose by producing large quantities of lactic acid. It is very tolerant of low pH, and produces an insoluble extracellular polysaccharide that may sequester acid at tooth surfaces. The mechanisms behind those putative virulence factors have been intensively studied in monoculture, and recently in simple multi-species consortia. Much less is known of other species that may also contribute to or protect against dysbiosis driven by dietary carbohydrates. Some strains of “non-mutans” streptococci produce and tolerate acid at levels comparable to S. mutans, while others show increased ariginolytic capabilities, which may act to raise pH within the biofilm matrix. S. mutans tends to be a minority species even in caries-active children, and carious lesions likewise can occur in children with no detectable S. mutans. 16S rDNA-based metagenomic comparisons of caries-active and caries-free subjects have detected associations between caries and a variety of oral species, including not only non-mutans streptococci, but also members of other genera, such as Scardovia and Bifidobacterium. Caries associations have not been consistent between studies. Moreover, different taxonomic clusters have been defined as subgroups within the same study. This raises an important point. Although caries-associated communities are typically less diverse than healthy supragingival plaque overall, those dysbiotic communities still display considerable taxonomic diversity between affected individuals. That in turn raises the question of whether it is desirable to define biomarkers of dysbiosis that are less dependent on taxonomy. The Human Microbiome project generated comprehensive metagenomic data for a wide variety of body sites in healthy subjects, including supragingival plaque. Although most of that data was based on 16S rDNA sequencing, shotgun metagenomics was also used to catalog the functional potential of all microbial genes within a smaller subset of subjects. One of the key findings was that healthy sites from different people were broadly similar with respect to their functional profiles, even though there was extensive individual variation in their taxonomic profiles. It is possible that the “conservation of function” concept may also extend to dysbiotic communities. This would explain why microbial communities associated with caries still show considerable taxonomic variation. In that case, differential patterns of community-wide gene and/or protein expression might provide a more accurate indicator of dysbiosis than can be achieved by counting caries-associated species. Metatranscriptomic or metaproteomic approaches can be used to provide information on function. A recent metatranscriptomic comparison of subgingival plaque from healthy and periodontally diseased sites in three subjects has provided data that support the “conservation of function” concept. They observed that taxonomically diverse diseased sites shared conserved gene expression profiles [20]. By the same token, a recent metaproteomic comparison of gut microbiotas from healthy controls to Crohn’s disease patients found that major shifts in protein expression by function did not always correlate with changes in taxon relative abundance [21]. In this metaproteomic study, we found that sucrose–induced changes in protein expression patterns for pathways involving glycolysis, lactate production, aciduricity and ammonia/glutamate metabolism were likewise conserved in taxonomically diverse dysbiotic oral microcosm biofilm communities.
2016-01-04 | PXD003151 | Pride
Project description:Childhood caries is an extremely common childhood chronic disease, affecting 60–90% of children in industrialized countries. It results in lesions in both the primary and permanent dentitions, hospitalizations and emergency room visits, high treatment costs, loss of school days, diminished ability to learn increases the risk of caries in adulthood. Streptococcus mutans is a key bacteria in caries development. While multiple caries risk factors have been identified, significant interpersonal variability not explained by known risk factors still exists. The immune system generates a personal antibody repertoire that helps maintain a balanced and healthy oral microbiome. Using mass-spectrometry, we probed in an hypothesis-free manner which S. mutans proteins are identified by antibodies of children with low and high DMFT (decayed, missing, filled teeth) scores. We identified a core set of proteins, recognized by the immune system of most individuals. This set was enriched with proteins enabling bacterial adhesion, and included glucosyltransferases and glucan-binding proteins known to be important for S. mutans cariogenicity. To explore the physiological relevance of these findings, we tested the ability of saliva from caries free individuals in preventing S. mutans from binding to the tooth surface. Indeed, saliva from individuals with caries free prevented S. mutans binding to teeth. These findings map the S. mutans proteome targeted by the immune system and suggest that inhibiting tooth attachment is a primary mechanism used by the immune system to maintain oral balance and prevent caries. These findings provide new insights into the role of the immune system in maintaining oral health and preventing caries development.
2023-06-26 | PXD043103 | Pride
Project description:Saliva samples derived from children with severe caries disease and healthy children
2017-12-19 | MSV000081832 | GNPS
Project description:<p>Metabolites are important determinants of disease progression. In this study, we conducted a case-control study to explore permanent teeth caries-related differences in salivary metabolite profiles and related changes in the composition of the oral microbiota in 200 subjects including 100 caries-free individuals and 100 with moderate-to-severe caries with good homogeneity through widely targeted metabolomics and 16S rRNA deep sequencing technologies. We found that: 1) 822 metabolites were detectable in salivary samples from these participants, of which 4-acetamidobutyric acid and adipic acid were respectively enriched in healthy individuals and individuals with caries, exhibited the greatest area under the curve (AUC) values of > 0.970; 2) less diversity was observed in individuals with dental caries relative to caries-free individuals, and significant differences in the dominant taxa were evident between the two groups. For example, the healthy oral microbiome is enriched for <em>Rothia aeria</em> and <em>Neisseria perflava</em>, whereas <em>Prevotella melaninogenica</em>, <em>Streptococcus salivarius</em>, <em>Streptococcus parasanguinis</em> and <em>Prevotella histicola</em>, and <em>Streptococcus mutans</em> were enriched in individuals with caries; 3) <em>Prevotella histicola</em>, <em>Oribacterium asaccharolyticum </em>and<em> Rothia aeria</em> were the top 3 species being required to differentiate caries from caries free population; 4) adipic acid and 4-acetamidobutyric acid derived from microbiota and host-microbiota co-metabolism, respectively. A negative correlation was observed between the microbes enriched in caries individuals (such as <em>Prevotella histicola</em>) and 4-acetamidobutyric acid. Moreover, the upstream regulatory factor ALDH of 4-acetamidobutyric acid is expressed throughout the entire process of tooth development including the differentiation of tooth bud, ameloblasts and odontoblasts. Together, these results suggest that 4-acetamidobutyric acid and adipic acid are important targets for future caries-focused research, offering insight into cariogenic activity or risk assessment in moderate or severe cases.</p>
2024-05-14 | MTBLS4569 | MetaboLights