Ontology highlight
ABSTRACT:
PROVIDER: PRJNA768619 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR16202522_1.fastq.gz | Fastqsanger.gz | |||
| SRR16202522_2.fastq.gz | Fastqsanger.gz | |||
| SRR16202523_1.fastq.gz | Fastqsanger.gz | |||
| SRR16202523_2.fastq.gz | Fastqsanger.gz | |||
| SRR16202524_1.fastq.gz | Fastqsanger.gz |
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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:Gut microbiota were assessed in 540 colonoscopy-screened adults by 16S rRNA gene sequencing of stool samples. Investigators compared gut microbiota diversity, overall composition, and normalized taxon abundance among these groups.
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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.
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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.
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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>
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