Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1091815 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28471900_1.fastq.gz | Fastqsanger.gz | |||
| SRR28471900_2.fastq.gz | Fastqsanger.gz | |||
| SRR28472000_1.fastq.gz | Fastqsanger.gz | |||
| SRR28472000_2.fastq.gz | Fastqsanger.gz | |||
| SRR28472100_1.fastq.gz | Fastqsanger.gz |
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Project description:The supragingival plaque microbiota of pre-school children.
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Project description:The present study focuses on the use of a metaproteomic approach to analyse Black Extrinsic Tooth Stains, a specific type of pigmented extrinsic substance, in a cohort of 96 Children. Metaproteomics is a powerful emerging technology that successfully enabled human protein and bacterial identification of this specific dental biofilm using mass spectrometry. 1600 bacterial proteins were identified in black stains (BS) samples and 2058 proteins in dental plaque (DP) samples whereas 607 and 582 human proteins identified in (BS and DP, respectively). 132 genera bacteria in black stains and dental plaque were identified using phylopeptidomic analysis, showing prevalence of Rothia, Kingella, Nesseria and Pseudopropionibatcterium in black stains samples. We additionally confirmed the metaproteomic approach by performing 16S rRNA. In this work, we showed an interesting diversity of the microbiota and proteome including significant difference between Black stain and dental plaque samples.
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Project description:We used a DNA microarray chip covering 369 resistance types to investigate the relation of antibiotic resistance gene diversity with humans’ age. Metagenomic DNA from fecal samples of 123 healthy volunteers of four different age groups, i.e. pre-school Children (CH), School Children (SC), High School Students (HSS) and Adults (AD) were used for hybridization. The results showed that 80 different gene types were recovered from the 123 individuals gut microbiota, among which 25 were present in CH, 37 in SC, 58 in HSS and 72 in AD. Further analysis indicated that antibiotic resistance genes in groups of CH, SC and AD can be independently clustered, and those ones in group HSS are more divergent. The detailed analysis of antibiotic resistance genes in human gut is further described in the paper DNA microarray analysis reveals the antibiotic resistance gene diversity in human gut microbiota is age-related submitted to Sentific Reports
2014-01-16 | GSE54070 | GEO
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:We used a DNA microarray chip covering 369 resistance types to investigate the relation of antibiotic resistance gene diversity with humansM-bM-^@M-^Y age. Metagenomic DNA from fecal samples of 123 healthy volunteers of four different age groups, i.e. pre-school Children (CH), School Children (SC), High School Students (HSS) and Adults (AD) were used for hybridization. The results showed that 80 different gene types were recovered from the 123 individuals gut microbiota, among which 25 were present in CH, 37 in SC, 58 in HSS and 72 in AD. Further analysis indicated that antibiotic resistance genes in groups of CH, SC and AD can be independently clustered, and those ones in group HSS are more divergent. The detailed analysis of antibiotic resistance genes in human gut is further described in the paper DNA microarray analysis reveals the antibiotic resistance gene diversity in human gut microbiota is age-related submitted to Sentific Reports The antibiotic resistance gene microarray is custom-designed (Roche NimbleGen), based on a single chip containing 3 internal replicated probe sets of 12 probes per resistance gene, covering the whole 315K 12-plex platform spots.
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