Dental biofilm bacteria. Genome sequencing and assembly
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ABSTRACT:
PROVIDER: PRJNA887960 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:DENTAL SUPRAGINGIVAL BIOFILM Raw sequence reads
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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:Dental biofilm microbiota during allogeneic hematopoietic stem cell transplantation
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Project description:Early biofilm forming bacteria Metagenome
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Project description:Microbial composition of oral biofilm in dental plaque of dogs
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Project description:Biofilms are matrix-encased microbial communities that increase the environmental fitness and infectivity of many human pathogens including Vibrio cholerae. Biofilm matrix assembly is essential for biofilm formation and function. Known components of the V. cholerae biofilm matrix are the polysaccharide VPS, matrix proteins RbmA, RbmC, Bap1, and extracellular DNA, but the majority of the protein composition is uncharacterized. This study comprehensively analyzed the biofilm matrix proteome and revealed the presence of outer membrane proteins (OMPs). Outer membrane vesicles (OMVs) were also present in the V. cholerae biofilm matrix and were associated with OMPs and many biofilm matrix proteins suggesting that they participate in biofilm matrix assembly. Consistent with this, OMVs had the capability to alter biofilm structural properties depending on their composition. OmpU was the most prevalent OMP in the matrix, and its absence altered biofilm architecture by increasing VPS production. Using single-cell force spectroscopy, we further showed that OmpU, the matrix proteins RbmA, RbmC, and Bap1, and VPS contribute to cell-surface adhesion forces, which are critical for biofilm formation. Our findings provide new insights into the molecular mechanisms underlying biofilm matrix assembly in V. cholerae, which may open up new opportunities to develop inhibitors that specifically alter biofilm matrix properties and, thus, affect either the environmental survival or pathogenesis of Vibrio cholerae.
2023-07-14 | MSV000092446 | MassIVE
Project description:Biofilms are matrix-encased microbial communities that increase the environmental fitness and infectivity of many human pathogens including Vibrio cholerae. Biofilm matrix assembly is essential for biofilm formation and function. Known components of the V. cholerae biofilm matrix are the polysaccharide VPS, matrix proteins RbmA, RbmC, Bap1, and extracellular DNA, but the majority of the protein composition is uncharacterized. This study comprehensively analyzed the biofilm matrix proteome and revealed the presence of outer membrane proteins (OMPs). Outer membrane vesicles (OMVs) were also present in the V. cholerae biofilm matrix and were associated with OMPs and many biofilm matrix proteins suggesting that they participate in biofilm matrix assembly. Consistent with this, OMVs had the capability to alter biofilm structural properties depending on their composition. OmpU was the most prevalent OMP in the matrix, and its absence altered biofilm architecture by increasing VPS production. Single-cell force spectroscopy revealed that proteins critical for biofilm formation, OmpU, the matrix proteins RbmA, RbmC, Bap1, and VPS, contribute to cell-surface adhesion forces at differing efficiency, with VPS showing the highest efficiency whereas Bap1 showing the lowest efficiency. Our findings provide new insights into the molecular mechanisms underlying biofilm matrix assembly in V. cholerae, which may provide new opportunities to develop inhibitors that specifically alter biofilm matrix properties and, thus, affect either the environmental survival or pathogenesis of V. cholerae.
2023-12-12 | MSV000093650 | MassIVE
Project description:To combat dental implant-associated infections, there is a need for novel materials which effectively inhibit bacterial biofilm formation. In the present study, a titanium surface functionalization based on the “slippery liquid-infused porous surfaces” (SLIPS) principle was analyzed in an oral flow chamber system. The immobilized liquid layer was stable over 13 days of continuous flow. With increasing flow rates, the surface exhibited a significant reduction in attached biofilm of both the oral initial colonizer Streptococcus oralis and an oral multi-species biofilm composed of S. oralis, Actinomyces naeslundii, Veillonella dispar and Porphyromonas gingivalis. Using single cell force spectroscopy, reduced bacterial adhesion forces on the lubricant layer could be measured. Gene expression patterns in biofilms on SLIPS, on control surfaces and planktonic cultures were also compared. For this purpose, the genome of S. oralis strain ATCC® 9811TM was sequenced using PacBio Sequel technology. Even though biofilm cells showed clear changes in gene expression compared to planktonic cells, no differences could be detected between bacteria on SLIPS and on control surfaces. Therefore, it can be concluded that the ability of liquid-infused titanium to repel biofilms is solely due to weakened bacterial adhesion to the underlying liquid interface.
2020-05-10 | GSE129981 | GEO