Streptococcus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA358614 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR5167871_subreads.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Genome sequencing of oral streptococci
| PRJNA1366903 | ENA
Project description:Oral commensal streptococci play a large role in mediating microbial homeostasis. Our published findings have demonstrated that hydrogen peroxide (H2O2) produced by oral commensal streptococci can react with salivary nitrite (NO2) and generate peroxynitrite (ONOO-), a potent antimicrobial. We have shown that the combinatorial antimicrobial effects of NO2 and H2O2 produced from the commensal Streptococcus parasanguinis, inhibit the colonization and pathogenesis of oral pathogens to promote homeostasis. Remarkably, S. parasanguinis is highly resistant to the NO2 and ONOO-. However, it remains unclear how S. parasanguinis copes in the presence of nitrosative stress. The goal of this study was to identify mechanisms used by S. parasanguinis to resist NO2-mediated nitrosative stress using a transcriptomics approach. Transcriptomic analysis showed that the competence response regulator, comE, is upregulated in the presence of NO2. Loss of comE resulted in a decrease in biofilm development, H2O2 production, increased acid tolerance and sensitivity to ONOO- compared to wild-type S. parasanguinis. Our data show that ComE is critical for key aspects of S. parasanguinis physiology and potentially impacts this commensal's ability to colonize and modulate homeostasis in the oral cavity.
2026-02-01 | GSE284166 | GEO
Project description:Genomic characterization of diverse oral streptococci
| PRJNA480251 | ENA
Project description:BACKGROUND: Hundreds of bacterial species coexist within the human oral cavity, where complex interactions can occur. Recent evidence has shown that the commensal oral streptococci that populate supragingival biofilms on the tooth surface produce extracellular proteases that degrade cell-cell signaling molecules of their disease-causing competitors, Streptococcus mutans. To further explore these interactions, we performed transcriptome analysis of S. mutans cocultured with different oral streptococci and found that cell-cell signaling was complety inhibited, but only when the bacteria were directly cocultured together. METHODS: RNA-Seq was utilized to compare the transcriptomes of S. mutans wild-type strain UA159 cocultured in its own supernatant (3 replicates), UA159 cocultured in S. sp. A12 supernatant (3 replicates) and directly cocultured with S. sp. A12 (3 replicates). Strains were grown to OD600 nm = 0.5 in CDM medium before harvest. Deep sequencing was performed at the University of Florida ICBR facilities (Gainesville, FL). Approximately 15 million short-reads were obtained for each sample. After removing adapter sequences from each short-read and trimming of the 3’-ends by quality scores, the resulting sequences were mapped onto the reference genome of strain UA159 (GenBank accession no. AE014133) using the short-read aligner. Mapped short-read alignments were then converted into readable formats using SAMTOOLS. RESULTS: Using an optimzed data analysis workflow, we mapped 13-16 million reads per sample to the genome of UA159. For viewing of the mapped reads aligned to the genome, .bam files were uploaded into the Integrative Genomics Viewer (IGV – version 2.3.55). A .csv file containing raw read counts for each replicate (3) was then uploaded to Degust (http://degust.erc.monash.edu/) and edgeR analysis performed to determine Log2 fold change and a false discovery rate (FDR). When comparing the growth of S. mutans in its own spent supernatant against competitor spent supernatants, we found 88 genes differentially expressed (Log2 fold change > (-)1.5, -log10 P-value > 4) which included upregulation of the zinc transport system and several amino acid ABC transporters, along with downregulation of the TnSmu1 genomic island. A more substantial effect was seen when we compared growth of S. mutans in competitor spent supernatant compared to growth directly with a competitor. Here, 140 genes were differentially expressed and included upregulation of one of the CRISPR genetic clusters as well as downregulation of the entire genetic competence regulon, as expected. Principal component analysis (PCA) of transcriptome data from these three conditions displayed a wide variation and separation among the tested groups, further confirming a unique transcriptome response for S. mutans between growth in the supernatant of a competitor and directly with a competitor. CONCLUSIONS: We believe that these measured transcriptomic changes represent a conserved S. mutans response to competitors that has not been previously captured in RNA-Seq experiments of monocultures alone. Together, these results highlight a previously undocumented transcriptomic alteration by S. mutans when challenged by health-associated oral streptococci.
2020-03-24 | GSE147421 | GEO
Project description:The human oral cavity harbors a diverse microbial community, with oral streptococci, particularly the Streptococcus mitis group, playing a pivotal role in biofilm formation and oral health. Among these, Streptococcus oralis is a key early colonizer that stabilizes oral biofilms. Here, we identify two mucin-degrading proteases, MdpS and MdpS2, that enable S. oralis to degrade MUC5B, the sole gel-forming mucin in saliva. Despite low sequence similarity, these enzymes share a high degree of tertiary structural resemblance and exhibits complementary biological functions. Their activity leads to extensive MUC5B degradation influencing biofilm dynamics by promoting biofilm dispersal and altering MUC5B and/or MUC5AC BCi mucus gels properties, with MdpS2 displaying specificity for MUC5B gels. Our findings reveal a specialized role in biofilm structural remodeling, offering potential avenues for clinical applications in biofilm modulation and mucus degradation.
2025-11-10 | PXD062603 | Pride
Project description:Streptococcus sanguinis is a major component of the oral flora and an important cause of infective endocarditis. The genome sequence of S. sanguinis strain SK36 was recently determined. A number of foreign genes acquired by natural transformation were detected, as well as orthologs of competence genes previously identified in other species. However, significant differences in the S. sanguinis competence system relative to that of other streptococci were noted. We sought to examine S. sanguinis genetic competence, to characterize the global transcriptional response to competence induction, and to compare our results with those obtained from previous analyses of other streptococci. A mutant possessing an in-frame deletion in the comC gene encoding the competence-stimulating peptide was created and confirmed to have the expected phenotype. Studies indicated that competence could be induced in this strain by addition of competence-stimulating peptide, and determined the optimal conditions to employ for this purpose. Expression was monitored by microarray analysis at multiple time points from 2.5 to 30 min after induction. Over 200 genes were identified whose expression was altered at least two-fold in at least one time point, with the majority upregulated. The “late” response was typical of that seen in previous studies. However, comparison of the “early” response in S. sanguinis with that of other streptococci revealed unexpected heterogeneity with regard to the number of genes induced, the nature of these genes, and their putative upstream regulatory sequences. S. sanguinis possesses a comparatively limited early response, which may define a minimal competence regulatory circuit.
2011-01-21 | GSE21619 | GEO
Project description:Streptococcus sanguinis is a major component of the oral flora and an important cause of infective endocarditis. The genome sequence of S. sanguinis strain SK36 was recently determined. A number of foreign genes acquired by natural transformation were detected, as well as orthologs of competence genes previously identified in other species. However, significant differences in the S. sanguinis competence system relative to that of other streptococci were noted. We sought to examine S. sanguinis genetic competence, to characterize the global transcriptional response to competence induction, and to compare our results with those obtained from previous analyses of other streptococci. A mutant possessing an in-frame deletion in the comC gene encoding the competence-stimulating peptide was created and confirmed to have the expected phenotype. Studies indicated that competence could be induced in this strain by addition of competence-stimulating peptide, and determined the optimal conditions to employ for this purpose. Expression was monitored by microarray analysis at multiple time points from 2.5 to 30 min after induction. Over 200 genes were identified whose expression was altered at least two-fold in at least one time point, with the majority upregulated. The M-bM-^@M-^\lateM-bM-^@M-^] response was typical of that seen in previous studies. However, comparison of the M-bM-^@M-^\earlyM-bM-^@M-^] response in S. sanguinis with that of other streptococci revealed unexpected heterogeneity with regard to the number of genes induced, the nature of these genes, and their putative upstream regulatory sequences. S. sanguinis possesses a comparatively limited early response, which may define a minimal competence regulatory circuit. Transcriptional analysis of S. sanguinis strain JFP41 cells 0 to 30 min after treatment with CSP. Biological replicates: 3 replicates each independently grown and harvested. 4 technical replicates per array
2011-01-21 | E-GEOD-21619 | biostudies-arrayexpress
Project description:Our group recently transcriptomically characterized coculture growth between Streptococcus mutans and several species of commensal streptococci (Rose et al, 2023; Choi et al 2024). One interaction that stood out was with Streptococcus mitis ATCC 49456, which completely inhibited the growth of S. mutans during biofilm formation. This is due to abudant hydrogen peroxide production by S. mitis ATCC 49456, 3-5x higher than other oral commensal streptococci we have worked with. To understand how the transcriptome of S. mutans is modified in coculture with a high hydrogen peroxide producer, we evaluated the transcriptome during monoculture or coculture growth between the two strains. Our results show differential gene expression (DEGs) in S. mutans that follows other trends we have documented previously with other commensal Streptococcus species, as well as DEGs specific to the interaction with S. mitis.
2024-08-02 | GSE273140 | GEO
Project description:Oral streptococci, including Streptococcus gordonii, and Actinomyces naeslundii, are consistently found to be the most abundant bacteria in the early stages of dental plaque accumulation. These organisms interact physically (coaggregate) in vitro and in vivo. We hypothesized that coaggregation between S. gordonii and A. naeslundii leads to changes in gene expression in the partner organisms. Furthermore, we predicted that coaggregation-induced changes in phenotype contribute to the success of streptococci and actinomyces in dental plaque. To assess the responses of S. gordonii to coaggregation with A. naeslundii, RNA was extracted from S. gordonii cells 3 h after inducing coaggregation with A. naeslundii or from equivalent S. gordonii monocultures. The two RNA populations were reverse transcribed and compared by competitive hybridization with an S. gordonii genomic microarray. The most striking feature of the response to coaggregation was a profound change in expression of S. gordonii genes involved in arginine biosynthesis and transport. Subsequent experiments demonstrated that coaggregation with A. naeslundii stabilizes arginine biosynthesis in S. gordonii and enables growth under low-arginine conditions, such as those present in human saliva. Keywords: Cell-cell interaction
2008-06-02 | GSE9478 | GEO
Project description:Streptococcus agalactiae (group B streptococci) genome sequencing and assembly
| PRJNA551699 | ENA