Ontology highlight
ABSTRACT:
PROVIDER: PRJNA739092 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14871500_1.fastq.gz | Fastqsanger.gz | |||
| SRR14871500_2.fastq.gz | Fastqsanger.gz | |||
| SRR14871600_1.fastq.gz | Fastqsanger.gz | |||
| SRR14871600_2.fastq.gz | Fastqsanger.gz | |||
| SRR14871501.fastq.gz | Fastqsanger.gz |
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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: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:In this paper, we first report that EC smoking significantly increases the odds of gingival inflammation. Then, we seek to identify and explain the mechanism that underlies the relationship between EC smoking and gingival inflammation via the oral microbiome. We performed mediation analyses to assess if EC smoking affects the oral microbiome, which in turn affects gingival inflammation. For this, we collected saliva and subgingival samples from EC users and non-users and profiled their microbial compositions via 16S rRNA amplicon sequencing. We then performed α-diversity, β-diversity, and taxonomic differential analyses to survey the disparity in microbial composition between EC users and non-users. We found significant increases in α-diversity in EC users and disparities in β-diversity between EC users and non-users.
2022-12-09 | GSE201949 | GEO
Project description:We investigated daily oscillations in salivary miRNA and microbial RNA to explore relationships between these components of the gut-brain-axis and their implications in human health. Nine subjects provided 120 saliva samples at designated times, on repeated days. Samples were divided into three sets for exploration and cross-validation. Identification and quantification of host miRNA and microbial RNA was performed using next generation sequencing. Eleven miRNAs and 11 microbial RNAs demonstrated consistent diurnal oscillation across the first 2 sample sets and accurately predicted collection time in the hold-out set based on multivariate logistic regression modeling. Associations among five circadian miRNAs and four circadian microbial RNAs were observed.
2018-07-06 | GSE116686 | GEO
Project description:Human saliva has been commonly used as protein source in in vitro microbiological and biological assays to mimic the protein pellicle formation, termed acquired salivary pellicle, that precedes microbial and cell adhesion on surfaces exposed to the oral environment. However, saliva requires previous processing to remove food debris, microorganisms, and other molecules prior its use in microbiological and biological in vitro assays. For this purpose, 0.22 μm filtration, 0.45 μm filtration, and pasteurization methods have been commonly used, but the effect of these processing methods on the proteomic profile of saliva has not been tested experimentally. Stimulated human saliva was collected from 8 healthy volunteers and submitted to the following processes: non-processing (control), 0.22 μm filtration, 0.45 μm filtration, and pasteurization. The proteomic profile of non-processed saliva was compared with 0.22 μm filtered-, 0.45 μm filtered-, and pasteurized-saliva by liquid chromatography-mass spectrometry. The effect of processed saliva in microbial adhesion was tested using bacterial and fungus species, and in biological cell behavior using HaCaT immortalized human keratinocytes. Two hundred seventy-eight proteins were identified in non-processed saliva, 54 proteins (≈19%) were exclusive. Saliva processing reduced identified proteins to 222 (≈80%) for the 0.22 μm filtered saliva, 219 (≈79%) for the 0.45 μm filtered saliva, and 201 (≈72%) for the pasteurized saliva, compared to non-processed saliva. Although there were slight differences in the protein composition, the proteomic profile showed similar molecular functions and biological processes. The different saliva processing methods did not alter microbial adhesion (ANOVA, p>0.05). Interestingly, pasteurized saliva reduced keratinocytes cell viability. Saliva processing methods tested reduced the proteomic profile diversity of saliva, but maintained similar molecular functions and biological processes mediated by remaining proteins, not interfering on microbial adhesion and cell viability, except for pasteurization, which reduced cell viability.
2023-03-11 | PXD039248 | Pride
Project description:Background: The differential abundance of cell-free RNAs in bodily fluids is emerging as a promising tool for the non-invasive molecular diagnosis of cancer. Human saliva is considered a promising source of non-invasive biomarkers of diagnostic value for oral cancer detection. This study aims to identify diagnostic potent salivary RNAs in oral squamous cell carcinoma (OSCC)-patients by RNA-Sequencing. Method: Unstimulated saliva was collected from 5 normal control (NC) individuals and 9 OSCC patients (PS) with prior consent and ethical committee approvals. Total RNA isolated from cell-free saliva (CFS) supernatant was used to prepare small RNA libraries and sequenced on the Ion Torrent S5 platform. The sequencing reads were aligned to the human genome (hg19) using Bowtie 2, and the differential expression analysis was performed using RUVSeq and DESeq2. Mapped reads were screened across miRBase (v22) annotations for miRNAs and Gencode (v19) annotation for other RNAs. Reads were quantified by the Featurecount (v1.4.6) module of the R-package. The microbial-RNA enrichment analysis was determined using the One Codex platform. Result: RNA-sequencing detected protein-coding transcripts (PCTs), long-intergenic RNAs (lincRNAs), microRNAs (miRNAs), small nuclear RNAs (snRNAs), transfer RNAs (tRNAs) and pseudogenes from the saliva of PS and HC samples. Transcriptome analyses revealed 89 PCTs, 18 lincRNAs and 6 miRNAs differentially expressed between PS and HC with a log2fold change ≥ 1 or ≤ -1 and p-value < 0.05. Gene ontology and pathway enrichment analyses indicated a significant correlation of the identified PCTs and miRNAs to various cancer-related pathways that may have implications in the pathogenesis of OSCC. Interestingly, unmapped non-human reads aligned to the microbial reference genomes. Further analyses of these microbial sequence reads revealed a significant microbial dysbiosis differentiating PS from HC. Metabolic pathways and functional analysis of the identified microbial phylotypes showed gene ontologies associated with inflammation, cell proliferation, ROS generation, and a range of metabolic processes. Conclusion: We report novel panels of differentially expressed PCTs, miRNAs and lincRNAs distinguishing PS from HC. Importantly, our results also provide evidence for oral microbial dysbiosis that appears to have pathological implications in OSCC. Summarily, this study provides a comprehensive landscape of salivary RNAs that can be exploited as non-invasive biomarkers for OSCC detection.
2023-01-30 | GSE176077 | GEO
Project description:Samples of oil and production water were collected from five wells of the Qinghai Oilfield, China, and subjected to GeoChip hybridization experiments for microbial functional diversity profiling. Unexpectedly, a remarkable microbial diversity in oil samples, which was higher than that in the corresponding water samples, was observed, thus challenging previously believed assumptions about the microbial diversity in this ecosystem. Hierarchical clustering separated oil and water samples, thereby indicating distinct functional structures in the samples. Genes involved in the degradation of hydrocarbons, organic remediation, stress response, and carbon cycling were significantly abundant in crude oil, which is consistent with their important roles in residing in oil. Association analysis with environmental variables suggested that oil components comprising aromatic hydrocarbons, aliphatic hydrocarbons, and a polar fraction with nitrogen-, sulfur-, and oxygen-containing compounds were mainly influential on the structure of the microbial community. Furthermore, a comparison of microbial communities in oil samples indicated that the structures were depth/temperature-dependent. To our knowledge, this is the first thorough study to profile microbial functional diversity in crude oil samples.
2016-04-01 | GSE55293 | GEO
Project description:Genome-wide DNA methylation profiling of human blood and saliva samples. The Illumina Infinium HumanMethylation 450k BeadChip was used to obtain DNA methylation profiles across approximately 480,000 CpGs in blood and saliva samples provided from 22 persons, and saliva samples from 3 persons.
2020-03-31 | GSE130153 | GEO
Project description:Interventions: Group 1: Surgical patients undergoing surgery for colorectal cancer: immunophenotyping by PBMCs and metagenomic analyses from stool, mucosa, and saliva samples perioperatively and during oncologic follow-up.
Group 2: oncologic patients with chemo- / immune therapy without recent surgery:
Immunophenotyping by PBMCs and metagenomic analyses from stool, mucosa and saliva samples during therapy and oncological follow-up.
Group 3: healthy controls:
Immunophenotyping by PBMCs and metagenomic analyses from stool, mucosa, and saliva samples at the time of screening colonoscopy.
Primary outcome(s): Difference in the differential abundance of the colonic mucosa of patients with CRC vs. healthy controls for evaluation as diagnostic biomarkers based on metagenomic analyzes (microbial pattern)
Study Design: Allocation: ; Masking: ; Control: ; Assignment: ; Study design purpose: diagnostic
| 2439680 | ecrin-mdr-crc