Ontology highlight
ABSTRACT:
PROVIDER: PRJNA453979 | ENA |
REPOSITORIES: ENA
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Project description:The molecular genetic mechanisms used by bacteria to persist in humans are poorly understood. Group A Streptococcus (GAS) causes the majority of bacterial pharyngitis cases in humans and is prone to persistently inhabit the upper respiratory tract. To gain information about how GAS survives in and infects the oropharynx, we analyzed the transcriptome of a serotype M1 strain grown in saliva. The dynamic pattern of changes in transcripts of genes [spy0874/0875, herein named sptR and sptS (sptR/S), for saliva persistence] encoding a two-component gene regulatory system of unknown function suggested that SptR/S contributed to persistence of GAS in saliva. Consistent with this idea, an isogenic nonpolar mutant strain (DeltasptR) was dramatically less able to survive in saliva compared with the parental strain. Iterative expression microarray analysis of bacteria grown in saliva revealed that transcripts of several known and putative GAS virulence factor genes were decreased significantly in the DeltasptR mutant strain. Compared with the parental strain, the isogenic mutant strain also had altered transcripts of multiple genes encoding proteins involved in complex carbohydrate acquisition and utilization pathways. Western immunoblot analysis and real-time PCR analysis of GAS in throat swabs taken from humans with pharyngitis confirmed the findings. We conclude that SptR/S optimizes persistence of GAS in human saliva, apparently by strategically influencing metabolic pathways and virulence factor production. The discovery of a genetic program that significantly increased persistence of a major human pathogen in saliva enhances understanding of how bacteria survive in the host and suggests new therapeutic strategies.
2009-05-16 | GSE16124 | GEO
Project description:The molecular genetic mechanisms used by bacteria to persist in humans are poorly understood. Group A Streptococcus (GAS) causes the majority of bacterial pharyngitis cases in humans and is prone to persistently inhabit the upper respiratory tract. To gain information about how GAS survives in and infects the oropharynx, we analyzed the transcriptome of a serotype M1 strain grown in saliva. The dynamic pattern of changes in transcripts of genes [spy0874/0875, herein named sptR and sptS (sptR/S), for saliva persistence] encoding a two-component gene regulatory system of unknown function suggested that SptR/S contributed to persistence of GAS in saliva. Consistent with this idea, an isogenic nonpolar mutant strain (DeltasptR) was dramatically less able to survive in saliva compared with the parental strain. Iterative expression microarray analysis of bacteria grown in saliva revealed that transcripts of several known and putative GAS virulence factor genes were decreased significantly in the DeltasptR mutant strain. Compared with the parental strain, the isogenic mutant strain also had altered transcripts of multiple genes encoding proteins involved in complex carbohydrate acquisition and utilization pathways. Western immunoblot analysis and real-time PCR analysis of GAS in throat swabs taken from humans with pharyngitis confirmed the findings. We conclude that SptR/S optimizes persistence of GAS in human saliva, apparently by strategically influencing metabolic pathways and virulence factor production. The discovery of a genetic program that significantly increased persistence of a major human pathogen in saliva enhances understanding of how bacteria survive in the host and suggests new therapeutic strategies. We determined the transcriptome of SptR (spy0874) in human saliva by comparing expression microarray date for parental wild-type strain MGAS5005 and its delta-spy0874 isogenic mutant strain. 4 replicates of each strain were grown to mid-exponential and stationary growth phases in human saliva. RNA was isolated, converted to cDNA, labeled and hybridized to a custom-made Affymetrix GeneChip. Data was analyzed using GCOS.
2010-05-19 | E-GEOD-16124 | biostudies-arrayexpress
Project description:Anopheline mosquito saliva bacteria
| PRJEB59447 | ENA
Project description:In this study, small RNAs were isolated from individual donations of eight forensically relevant biological fluids (blood, semen, vaginal fluid, menstrual blood, saliva, urine, feces, and perspiration) and subjected to next generation sequencing using the Illumina® Hi-Seq platform. Sequencing reads were aligned and annotated against miRbase release 21, resulting in a list of miRNAs and their relative expression levels for each sample analyzed. Body fluids with high bacterial loads (vaginal fluid, saliva, and feces) yielded relatively low annotated miRNA counts, likely due to oversaturation of small RNAs from the endogenous bacteria. Both body-fluid specific and potential normalization miRNAs were identified for further analysis as potential body fluid identification tools for each body fluid.
2016-08-20 | GSE85830 | GEO
Project description:Total DNA was extracted from saliva and stool of the patients, amplified to collect amplicons of variable V3–V4 regions of the bacterial 16s rRNA gene and sequenced with MiSeq (2x300bp) Illumina platform.
2023-05-31 | GSE206765 | GEO
Project description:Saliva is a convenient non-invasive source of liquid biopsy to monitor human health and diagnose diseases. In particular, extracellular vesicles (EVs) in saliva can potentially reveal clinically relevant information for systemic health. Recent studies have shown that RNA in saliva EVs could be exploited as biomarkers for disease diagnosis. However, there is no standardized protocol for profiling RNA in saliva EV nor clear guideline on selecting saliva fractions for biomarker analysis. To address these issues, we established a robust protocol for small RNA profiling from fractionated saliva. With this method, we performed comprehensive small RNA sequencing of four saliva fractions, including cell-free saliva (CFS), EV-depleted saliva (EV-D), exosome (EXO), and microvesicle (MV) from ten healthy volunteers. Methods: To address these issues, we established a robust protocol for small RNA profiling from fractionated saliva. With this method, we performed comprehensive small RNA sequencing of four saliva fractions, including cell-free saliva (CFS), EV-depleted saliva (EV-D), exosome (EXO), and microvesicle (MV) from ten healthy volunteers.
2023-01-07 | GSE222014 | GEO
Project description:To shed light on the molecular bases of B-lineage acute lymphoblastic leukemia lacking known rearrangements (B-NEG ALL) and the differences between children and adults, we analyzed 168 B-NEG ALLs - including children, adolescents/young adults (AYA) and adults by genome-wide technologies, namely Next-generation sequencing and copy number aberration (CNA). Affymetrix SNP array analysis was performed according to the manufacturer's directions on DNA extracted from bone marrow sampled at diagnosis and paired germline DNA extracted from peripheral blood/bone marrow at complete remission or saliva.
2016-03-01 | GSE67405 | GEO
Project description:DNA extracted from saliva for methylation studies of psychiatric traits
| PRJNA261780 | ENA
Project description:Purpose The role of intestinal flora in carcinogenesis and chemotherapy efficacy has been increasingly studied; however, comparisons between oral and intestinal flora remain limited. This study aimed to identify the microbial changes in urothelial carcinoma (UC) by analyzing oral saliva and stool samples from healthy individuals and patients. We also examined the association between microbial composition and immune checkpoint inhibitor (ICI) response. Methods A total of 20 healthy individuals and 38 patients with UC were analyzed. Among them, 27 patients with UC underwent ICI treatment. Oral saliva and stool samples were analyzed for 16S rRNA sequences to assess bacterial composition. Operational taxonomic units were generated, and phylogenetic analysis was performed using the 16S Metagenomics app whithin the Illumina BaseSpace Sequence Hub. Results Patients with UC showed higher Veillonellaceae and Prevotellaceae levels in saliva and stool, with lower levels of these bacteria associated with more prolonged overall survival and progression-free survival, particularly Veillonellaceae in stool. A higher neutrophil-to-lymphocyte ratio correlated with increased levels of these bacteria. Conclusion Veillonellaceae and Prevotellaceae are potential microbial biomarkers of survival outcomes and ICI efficacy in patients with UC. Non-invasive oral microbial sampling may facilitate personalized cancer treatment strategies.
2025-05-28 | GSE293354 | GEO