Transcriptomes of Streptococcus anginosus KH1 in artificial saliva medium and modified serum medium
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PROVIDER: PRJNA1206156 | ENA |
REPOSITORIES: ENA
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Project description:The transcriptomes of S. anginosus KH1 under conditions mimicking either the oral cavity or the bloodstream were determined to identify loci that are highly regulated by culture media.
2025-07-30 | GSE285825 | GEO
Project description:S. anginosus, S. aureus LMG 10147 and P. aeruginosa DK2 are often co-isolated in sputum samples from cystic fibrosis patients. We found that S. anginosus LMG 14502 becomes less suceptible towards treatment with several antibiotics when it's grown together with S. aureus LMG 10147 and P. aeruginosa DK2, compared to when it's grown alone. In order to elucidate the molecular mechanisms responsible, we performed RNA-seq of an S. anginosus monospecies biofilm and of a multispecies bioiflm of S. anginosus, S. aureus and P. aeruginosa. First, biofilms of S. anginosus alone or in combination with S. aureus and P. aeruginosa were grown. Next, RNA was isolated. Subsequently, a Truseq stranded RNA library preparation kit (Illumina) was used to create strand specific libraries. After a quality and concentration control, the libraries were equimolarly pooled and sequenced using an Illumina NextSeq 500, generating 75bp unpaired reads.
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Project description:Follow-up study of 9 year old IVF children who underwent embryo culture in G3 (Vitrolife) or K-SICM (Cook) medium. Genome-wide DNA methylation profiling of 9 year old IVF children (saliva samples) who had undergone embryo culture in G3 medium (Vitrolife) or K-SICM medium (Lonza). The EPIC array was used to profile the methylome at approximately 850,000 CpG sites across the human genome.
2022-09-01 | GSE196432 | GEO
Project description:We performed transcriptome sequencing to profile gene expressions upon the treatment of vancomycin in two Streptococcus anginosus strains.
2022-12-01 | GSE163717 | GEO
Project description:Pseudomonas aeruginosa airway infection is the leading cause of morbidity and mortality in cystic fibrosis (CF) patients. In vitro models that closely mimic CF sputum are needed to improve understanding of the pathobiology of P. aeruginosa in the CF airway. We developed an artificial sputum medium (ASMDM) that more closely resembles the composition of CF sputum than current media. In order to validate the utility of ASMDM, we used GeneChip microarrays to compare expression data of P. aeruginosa UCBPP-PA14 (PA14) in ASMDM with published data for this strain grown under the same conditions in an artificial medium containing 10% (v/v) CF sputum. Thirty-seven of 39 nutrition-related genes were differentially expressed in the same manner in both media. However, 24 quorum-sensing (QS) genes, 23 Type III secretion system and several anaerobic respiration genes were more highly expressed in ASMDM than in sputum-containing medium. When grown to stationary phase in ASMDM, PA14 differentially expressed about 50 biologically significant genes compared to stationary phase growth in Luria Broth; genes involved in iron acquisition (pfeA, fepC) and in assimilatory nitrate reduction (nasC, nirD) were upregulated, while 24 QS genes, including the regulator rhlR, lasA, rsaL, aprADEI and phenazine genes phzC2DD2EG2 were downregulated. Downregulation of QS-regulated virulence genes has been noted in chronic P. aeruginosa infection. ASMDM thus appears highly suitable for studies on gene expression of (i) P. aeruginosa strains from acutely and chronically infected CF patients and (ii) established biofilms that are a hallmark of advanced CF lung disease.
2010-05-31 | GSE18594 | GEO
Project description:Streptococcus anginosus is an important cause of brain and liver abscesses, meningitis, appendicitis, female genital tract infection, neonatal sepsis, and bacteremia. Recent studies show that S. anginosus is responsible for around 30% of streptococci associated purulent infections of internal organs. Genome sequencing of S. anginosus identified a phage-like chromosomal island (SanCI) integrated into the DNA mismatch repair operon. In S. pyogenes, related chromosomal islands (SpyCI) integrated into the same operon confer a mutator phenotype as well as alter global gene regulation, including the increased expression of many virulence factors. We hypothesized that SanCI will also alter global transcription patterns and virulence in S. anginosus. The SanCI from strain F0211 was introduced into a SanCI-free S. anginosus strain (J4211) by natural transformation. To provide a selectable marker for transformation, gene strA, encoding a predicted transcriptional regulator, was replaced in F0211 with the gene conferring erythromycin resistance (ermB), which after transfer created strain OKSan3. A functional copy of strA was then returned to this derivative of J4211, creating strain OKSan4. RNA sequencing (RNA-seq) of strains J4211, OKSan4 and OKSan3 confirmed that the addition of the SanCI altered S. anginosus global transcription patterns with increased expression of virulence, stress response and competence factors in a growth phase dependent manner. Virulence studies using Galleria mellonella as an acute infection model showed significantly increased inflammation and mortality in larvae challenged with strains OKSan4 and OKSan3 as compare to SanCI-free strain J4211. qRT-PCR analysis supported these results, revealing that antimicrobial factors of G. mellonella were more highly expressed after infection with OKSan4 compare to J4211 infection. Further, RNA-seq suggested that SanCI-encoded gene strA may encode one of the factors responsible for altered global transcriptional changes. The result of this study along with our previous studies in S. pyogenes demonstrate that streptococcal chromosomal islands are a unique class of virulence factors that improve the fitness of their host cell by altering global transcription patterns and increasing virulence.
2018-12-21 | GSE124234 | GEO
Project description:Our group recently transcriptomically characterized coculture growth between Streptococcus mutans and several species of commensal streptococci (Rose et al, 2023). However, these experiments were carried out in our lab-based experimental medium, tryptone and yeast extract (TY-). To understand whether culturing these species within a medium that more closely mimics their natural environment alters the interaction, we evaluated both monoculture and coculture growth between the dental caries pathogen Streptococcus mutans and oral commensal species Streptococcus oralis in a half TY- / half human saliva mix that was optimally chosen based on our initial characterization of oral streptococci behaviors in medium mixes containing saliva. Our results surprising show that inclusion of saliva enhances the competition of Streptococcus mutans against commensal streptococci through upregulation of carbohydrate uptake and glycolytic pathways.
2023-08-22 | GSE239483 | GEO
Project description:We combined RT-LAMP with deep sequencing to detect as few as 5–10 virions of SARS-CoV-2 in unprocessed human saliva. Based on a multi-dimensional barcoding strategy, COV-ID can be used to test thousands of samples overnight in a single sequencing run with limited labor and laboratory equipment. The sequencing-based readout allows COV-ID to detect multiple amplicons simultaneously, including key controls such as host transcripts and artificial spike-ins, as well as multiple pathogens. Here we demonstrate this flexibility by simultaneous detection of 4 amplicons in contrived saliva samples: SARS-CoV-2, influenza A, human STATHERIN, and an artificial SARS spike-in. The approach was validated on clinical saliva samples, where it showed 100% agreement with RT-qPCR. COV-ID can also be performed directly on saliva adsorbed on filter paper, simplifying collection logistics and sample handling.
2021-04-15 | GSE172118 | GEO
Project description:Streptococcus anginosus genome sequencing
| PRJNA1320968 | ENA