Commensal Microbial Interactions Alter Streptococcus mutans Transcriptome Profile and Cell-Cell Signaling
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ABSTRACT:
PROVIDER: PRJNA614532 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11395900.fastq.gz | Fastqsanger.gz | |||
| SRR11395901.fastq.gz | Fastqsanger.gz | |||
| SRR11395902.fastq.gz | Fastqsanger.gz | |||
| SRR11395903.fastq.gz | Fastqsanger.gz | |||
| SRR11395904.fastq.gz | Fastqsanger.gz |
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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:Interactions with Commensal or Non-commensal Streptococci Alter Streptococcus mutans Transcriptome and Behaviors
| PRJNA862955 | 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:We use high-throughput sequencing to profile the response of oral commensal pathogen Streptococcus mutans to mucins protein polymers (human MUC5B mucins) and soluble mucin glycans (human MUC5B glycans and porcine MUC5AC glycans). We find that mucins and their glycans alter the regulation of dozens of S. mutans genes, specifically downregulating competence-associated quorum sensing genes. The transcriptional responses induced by MUC5B mucins, MUC5B glycans, and MUC5AC glycans are highly correlated.
2021-01-01 | GSE163258 | GEO
Project description:Amino sugars, particularly glucosamine (GlcN) and N-acetylglucosamine (GlcNAc) are abundant carbon and nitrogen sources that are continually supplied in host secretions and the diet to biofilms colonizing the human mouth. Evidence is emerging that these amino sugars may provide an ecological advantage to beneficial commensals over oral pathobionts. Here we performed transcriptome analysis on Streptococcus mutans and Streptococcus gordonii growing in single-species or dual-species cultures with glucose, GlcN or GlcNAc as the primary carbohydrate source. Compared to glucose, GlcN caused drastic transcriptomic shifts in each bacterium when they were cultured alone. Likewise, co-cultivation in the presence of GlcN yielded transcriptomic profiles that were dramatically different than the single-species results from GlcN-grown cells. In contrast, GlcNAc elicited only minor changes in the transcriptome of either organism, in both single- and dual-species cultures. Interestingly, genes involved in pyruvate metabolism were among the most significantly affected by GlcN in both species, and these changes were consistent with measurements of pyruvate in culture supernates. Differing a previous report, growth of S. mutans alone with GlcN inhibited expression of multiple operons required for mutacin production. Co-cultivation with S. gordonii consistently increased the expression by S. mutans of two manganese transporter operons (slo and mntH) and decreased expression of mutacin genes. Conversely, S. gordonii appeared to be less affected by the presence of S. mutans, but did show increases in genes for biosynthetic processes in the co-cultures. In conclusion, amino sugars profoundly altered the interactions between the pathogen and the commensal, likely by reprogramming their central metabolism.
2020-06-09 | GSE152021 | GEO
Project description:Glycerol metabolism supports oral commensal interactions.
| PRJNA961761 | ENA
Project description:Interspecies commensal interactions have nonlinear impacts on host immunity
| PRJNA742544 | ENA
Project description:AMINO SUGARS RESHAPE INTERACTIONS BETWEEN STREPTOCOCCUS MUTANS AND STREPTOCOCCUS GORDONII
| PRJNA638112 | ENA
Project description:Arginine metabolism via the arginine deiminase system (ADS) of oral bacteria generates ammonia, which can increase the pH of oral biofilms and decrease the risk for dental caries. Antagonistic interactions between ADS-positive and cariogenic bacteria in oral biofilms may be an important ecological determinant of caries. This study investigated the antagonistic potential and mechanisms of clinical isolates of arginolytic streptococci on and by Streptococcus mutans UA159, a well-characterized cariogenic human isolate. Low-passage isolates of Streptococcus gordonii, Streptococcus sanguinis, Streptococcus parasanguinis, Streptococcus australis, and Streptococcus cristatus inhibited the growth of S. mutans to various degrees when they were inoculated on growth media first or simultaneously with S. mutans. The antagonistic effects of arginolytic strains against S. mutans and the production of H2O2 by these strains were enhanced during growth in a less-rich medium or when galactose was substituted for glucose as the primary carbohydrate source. Pyruvate oxidase was the dominant pathway for H2O2 production by arginolytic strains, but lactate oxidase activity was also detected in some strains of S. gordonii and S. cristatus. UA159 inhibited the growth of all tested arginolytic strains when inoculated first, especially in aerobic conditions. However, the antagonistic effects of S. mutans on certain strains of S. gordonii and S. australis were not observed during anaerobic growth in the presence of arginine. Thus, arginolytic commensal streptococci may have a synergistically positive impact on the ecology of oral biofilms by moderating biofilm pH while antagonizing the growth and virulence of caries pathogens.
| S-EPMC5828942 | biostudies-literature
Project description:Nucleotide signaling pathways are found in all kingdoms of life and are utilized to coordinate a rapid response to changes in the environment. One more recently discovered signaling nucleotide is the secondary messenger cyclic diadenosine monophosphate (c-di-AMP), which is widely distributed among bacteria and is also found in several archaea. This cyclic nucleotide has been shown to involve in several important cellular processes, including maintenance of DNA integrity, cell wall metabolism, stress tolerance, transcription regulation and virulence. However, the mechanisms by which c-di-AMP modulates these physiological changes have remained largely unknown.In the present study, we identified and characterized a c-di-AMP synthase (CdaA) in S. mutans UA159. Furthermore, we investigated the role of CdaA in S. mutans cell physiology and global gene expression by utilizing cdaA gene in-frame deletion mutant. Our findings suggest that CdaA is an important global modulator of optimal growth and environmental adaption in this pathogen. Streptococcus mutans UA159 whole-genome arrays (8 x 15 K) were obtained from Agilent and included 1998 probes for S. mutans transcripts. For microarray analysis, S. mutans UA159 and S. mutans ?cdaA cells were routinely grown at 37°C anaerobically (90% N2, 5% CO2, 5% H2) in brain heart infusion broth (BHI; Difco, Sparks, MD, USA) to an optical density at 600 nm (OD600) of 0.5. Four RNA samples isolated from four independent cultures of UA159 and cdaA mutant strains were hybridized to the arrays and analyzed.
2015-04-06 | E-GEOD-65511 | biostudies-arrayexpress