Glycerol metabolism supports oral commensal interactions.
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA961761 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24302366_1.fastq.gz | Fastqsanger.gz | |||
| SRR24302366_2.fastq.gz | Fastqsanger.gz | |||
| SRR24302367_1.fastq.gz | Fastqsanger.gz | |||
| SRR24302367_2.fastq.gz | Fastqsanger.gz | |||
| SRR24302368_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
Similar Datasets
Project description:To understand what molecular mechanisms determine the unique interspecies interactions between two predominant oral commensals Streptococcus sanguinis and Corynebacterium durum in the healthy oral cavity. We further investigated the regulatory connection between lipid metabolism and chain elongation based on the global gene expression profiling of the dual species cultures, as well as characterized S. sanguinis glycerol kinase (glpK) as a key gene involved in the interspecies interactions.
2023-04-26 | GSE230560 | GEO
Project description:Transcriptional profiling was utilized to define the biological pathways of gingival epithelial cells modulated by co-culture with the oral commensal S. gordonii and the opportunistic commensal F. nucleatum. We used microarrays to detail the global programme of gene expression underlying infection and identified distinct classes of up- and down-regulated genes during this process. Experiment Overall Design: Gingival epithelial HIGK cells were sham infected (CTRL) and infected with either the oral commensal S. gordonii (Sg) or the opportunistic commensal F. nucleatum (Fn). These samples were hybridized to Affymetrix microarrays. Understanding how host cells have adapted to commensals, and how barrier cells respond to limit their impact, provides a mechanistic biological basis of health in the mixed bacterial-human ecosystem of the oral cavity.
2009-04-28 | E-GEOD-6927 | biostudies-arrayexpress
Project description:Transcriptional profiling was utilized to define the biological pathways of gingival epithelial cells modulated by co-culture with the oral commensal S. gordonii and the opportunistic commensal F. nucleatum. We used microarrays to detail the global programme of gene expression underlying infection and identified distinct classes of up- and down-regulated genes during this process. Keywords: infection state
2007-06-21 | GSE6927 | GEO
Project description:Listeria monocytogenes is able to efficiently utilize glycerol as carbon source. In a defined minimal medium the growth rate is similar (during balanced growth) in presence of glycerol as in presence of glucose or cellobiose. Comparative transcriptome analyses of L. monocytogenes showed in the presence of glycerol (compared to glucose and/or cellobiose) high transcriptional upregulation of the known genes involved in glycerol uptake and metabolism (glpFK, glpD). Expression of the genes encoding a second putative glycerol uptake facilitator (GlpF-2) and a second putative glycerol kinase (GlpK-2) was less enhanced under these conditions. GlpK-1 but not GlpK-2 was essential for glycerol catabolism in L. monocytogenes under extracellular conditions, while loss of GlpK-1 affected replication in Caco-2 cells less than loss of GlpK-2 and GlpD. Additional genes whose transcription was higher in presence of glycerol than in presence of glucose and cellobiose included those for two dihydroxyacetone (Dha) kinases and many genes that are under carbon catabolite repression (CCR) control. Transcriptional down-regulation in the presence of glycerol (compared to glucose and cellobiose) was observed for several genes and operons that are positively regulated by glucose, including genes involved in glycolysis, N-metabolism and biosynthesis of branched chain amino acids. The highest transcriptional up-regulation was observed for all PrfA-dependent genes during early and late logarithmic growth in glycerol. Under these conditions a low level of HPr-Ser-P and a high level of HPr-His-P was present in the cells, suggesting that all EIIA (B) components of the PTS permeases expressed will be phosphorylated. These and other data reported suggest that the phosphorylation state of PTS permeases correlates with PrfA activity. Keywords: Response of Listeria monocytogenes to different carbon sources
2008-05-30 | GSE11459 | GEO
Project description:Transcriptional profiling was utilized to define the biological pathways of gingival epithelial cells modulated by mono- and complex co-culture with oral commensal S. gordonii and pathogenic P. gingivalis. We used microarrays to detail the global programme of gene expression underlying infection and identified distinct classes of up- and down-regulated genes during this process. Keywords: infection state
2009-07-14 | GSE12121 | GEO
Project description:Listeria monocytogenes is able to efficiently utilize glycerol as carbon source. In a defined minimal medium the growth rate is similar (during balanced growth) in presence of glycerol as in presence of glucose or cellobiose. Comparative transcriptome analyses of L. monocytogenes showed in the presence of glycerol (compared to glucose and/or cellobiose) high transcriptional upregulation of the known genes involved in glycerol uptake and metabolism (glpFK, glpD). Expression of the genes encoding a second putative glycerol uptake facilitator (GlpF-2) and a second putative glycerol kinase (GlpK-2) was less enhanced under these conditions. GlpK-1 but not GlpK-2 was essential for glycerol catabolism in L. monocytogenes under extracellular conditions, while loss of GlpK-1 affected replication in Caco-2 cells less than loss of GlpK-2 and GlpD. Additional genes whose transcription was higher in presence of glycerol than in presence of glucose and cellobiose included those for two dihydroxyacetone (Dha) kinases and many genes that are under carbon catabolite repression (CCR) control. Transcriptional down-regulation in the presence of glycerol (compared to glucose and cellobiose) was observed for several genes and operons that are positively regulated by glucose, including genes involved in glycolysis, N-metabolism and biosynthesis of branched chain amino acids. The highest transcriptional up-regulation was observed for all PrfA-dependent genes during early and late logarithmic growth in glycerol. Under these conditions a low level of HPr-Ser-P and a high level of HPr-His-P was present in the cells, suggesting that all EIIA (B) components of the PTS permeases expressed will be phosphorylated. These and other data reported suggest that the phosphorylation state of PTS permeases correlates with PrfA activity. Keywords: Response of Listeria monocytogenes to different carbon sources A total of four independently isolated RNA samples from each condition at each growth phase were used for the analysis. RNA from two isolations were pooled and hybridized onto two microarray slides with dye swap. Another two microarray slides were hybridized using the same principle. In total, we used four RNAs and four microarray slides to generate 16 replicate expression values for each combination except for the comparison between glucose and cellobiose, phase B where data generated from three microarray slides were used for further analysis
2008-05-30 | E-GEOD-11459 | biostudies-arrayexpress
Project description:RNA-Seq was used to compare the transcriptome of Streptococcus mutans UA159 during growth alone in monoculture, in coculture with Streptococcus gordonii DL1, Streptococcus sanguinis SK36 or Streptococcus oralis 34, and in a quadculture containing all four species. Individual cultures of commensal species Streptococcus gordonii DL1, Streptococcus sanguinis SK36 and Streptococcus oralis 34 were sequenced as well. This revealed a common transcriptome pattern in S. mutans when grown in mixed-species culture, indepenedent of the species identity that S. mutans was cultured with. Additionally, transcriptome changes in the commensal species could also be determined when undergoing competition from S. mutans. RNA-Seq was used to compare the transcriptome of Streptococcus mutans UA159 during growth alone in monoculture or in coculture with Streptococcus sobrinus NIDR 6715, Lactobacillus casei ATCC 4646 or Corynebacterium matruchotii ATCC 14266. These data were compared to previous coculture and quadculture RNA-Seq data with commensal streptococci (GSE209925). These data confirmed a common transcriptome pattern in S. mutans when grown in mixed-species culture with commensal streptococci that is not present with non-commensal streptococci, indepenedent of the species identity that S. mutans was cultured with.
2022-08-03 | GSE209925 | GEO
Project description:<p>Bacterial metabolism in oral biofilms is comprised of complex networks of nutritional chains and biochemical regulations. These processes involve both intraspecies and interspecies networks as well as interactions with components from host saliva, gingival crevicular fluid, and dietary intake. In a previous paper, a large salivary glycoprotein, mucin MUC5B, was suggested to promote a dental health-related phenotype in the oral type strain of <em>Streptococcus gordonii</em> DL1, by regulating bacterial adhesion and protein expression. In this study, nuclear magnetic resonance-based metabolomics was used to examine the effects on the metabolic output of monospecies compared to dual species early biofilms of two clinical strains of oral commensal bacteria, <em>S. gordonii</em> and <em>Actinomyces naeslundii</em>, in the presence of MUC5B. The presence of <em>S. gordonii</em> increased colonization of <em>A. naeslundii</em> on salivary MUC5B, and both commensals were able to utilize MUC5B as a sole nutrient source during early biofilm formation. The metabolomes suggested that the bacteria were able to release mucin carbohydrates from oligosaccharide side chains as well as amino acids from the protein core. Synergistic effects were also seen in the dual species biofilm metabolome compared to the monospecies, indicating that <em>A. naeslundii</em> and <em>S. gordonii</em> cooperated in the degradation of salivary MUC5B. A better understanding of bacterial interactions and salivary-mediated regulation of early dental biofilm activity is meaningful for understanding oral biofilm physiology and may contribute to the development of future prevention strategies for biofilm-induced oral disease.</p>
2023-10-30 | MTBLS8370 | MetaboLights
Project description:This SuperSeries is composed of the following subset Series: GSE11860: The impact of glycerol on the metabolism of Lactobacillus reuteri - Exploratory experiment GSE11861: The impact of glycerol on the metabolism of Lactobacillus reuteri - Main experiment Refer to individual Series
2010-05-20 | E-GEOD-11885 | biostudies-arrayexpress
Project description:Lactobacillus reuteri is a heterofermentative lactic acid bacterium best known for its ability to co-ferment glucose and glycerol. Its genome sequence has recently been deduced enabling the implementation of genome-wide analysis. In this study we developed a dedicated cDNA microarray platform and a genome-scale metabolic network model of L. reuteri and use them to revisit the co-fermentation of glucose and glycerol. The model was used to simulate experimental conditions and to visualize and integrate experimental data in particular the global transcriptional response of L. reuteri to the presence of glycerol. We show how the presence of glycerol affects cell physiology and triggers specific regulatory mechanisms allowing simultaneously a better yield and more efficient biomass formation. Furthermore we were able to predict and demonstrate for this well-studied condition the involvement of previously unsuspected metabolic pathways for instance related to amino acids and vitamins. These could be used as leads in future studies aiming at the increased production of industrially relevant compounds such as vitamin B12 or 1 3- propanediol. Keywords: cell type comparison
2008-09-15 | GSE11861 | GEO