The Effect of Oral Care Product Ingredients on Oral Pathogenic Bacteria Transcriptomics Through RNA-Seq
<p>Heatmap of treatment-induced total bacterial RNA yield fold change compared to untreated control indicated that stannous and hydrogen peroxide down-regulated RNA synthesis in all tested oral bacteria.</p> "> Figure 2
<p>Heatmap of treatment-induced differential expressed gene ratio (DEGR) showed stannous compounds induced strong gene expression changes in all tested oral bacteria.</p> "> Figure 3
<p>Microbial transcriptomics response to oral hygiene product ingredients is used to evaluate and rank material for treatment effect, indicating that stannous is the top treatment for these groups of tested bacteria. (<b>a</b>) Heatmap of log2 fold change of all the 12,546 genes from the six tested bacteria strains. (<b>b</b>) PCA plot of the combined gene expression data from all the 12,546 genes, showing all the tested materials and their relative distance to the control samples. (<b>c</b>) The rank treatment effect of different materials based on the normalized distance to control based on the PCA plot indicated that the stannous compounds are a top treatment for disturbing microbial gene expression, and the color matches the PCA plot.</p> "> Figure 4
<p>Treatment-induced transcriptomics changes in genes involved in LPS biosynthesis. (<b>a</b>) Heatmap of log2 fold change of <span class="html-italic">P. gingivalis</span> genes involved in LPS biosynthesis (Lipid A, Core, O-Antigen, or APS biosynthesis) and LPS export compared to no-treatment controls. (<b>b</b>) KEGG pathway mapping of the first four genes of <span class="html-italic">P. gingivalis</span> LPS biosynthesis pathway highlights gene expression changes induced by ArgB, H<sub>2</sub>O<sub>2</sub>, SnCl<sub>2</sub>_L, and SnF<sub>2</sub>_L, showing that stannous compounds down-regulated LPS biosynthesis. ArgB up-regulated LPS biosynthesis. (<b>c</b>) Bar plot of the log2 fold change of <span class="html-italic">P. gingivalis LpxA</span> gene, the first step for Lipid A biosynthesis, a critical component for LPS biosynthesis. (<b>d</b>) Bar plot of the log2 fold change of <span class="html-italic">P. gingivalis LpxC</span> gene, which is a rate-limiting gene for the LPS biosynthesis pathway. (<b>e</b>) Heat map of log2 fold change of <span class="html-italic">LpxA</span> and <span class="html-italic">LpxC</span> genes from all four tested Gram-negative bacteria. The standard error is shown as an error bar in all bar figures; a single star indicates <span class="html-italic">p</span>-value ≤ 0.05, and double stars indicate fdr-adjusted <span class="html-italic">p</span>-value ≤ 0.05.</p> "> Figure 5
<p>Treatment-induced transcriptomics changes in genes involved in <span class="html-italic">P. gingivalis</span> toxin translocation, secretion system, and infection (<b>a</b>) Heatmap of Log2 fold change of <span class="html-italic">P. gingivalis</span> genes involved in toxin translocation, secretion system, and infection (including Type 9 Secretion System (T9SS), <span class="html-italic">PPAD</span>, <span class="html-italic">gingipain</span>, <span class="html-italic">frimbrium</span>, <span class="html-italic">humY</span>-<span class="html-italic">tonB</span>, <span class="html-italic">VIM</span>, quorum sensing gene <span class="html-italic">LuxS</span>, <span class="html-italic">LuxR</span>, NO stress-associated gene <span class="html-italic">cdrH</span>, and infection-associated gene <span class="html-italic">hflX</span>) compared to untreated control from all tested bacteria strains. (<b>b</b>) Bar plot of the log2 fold change of <span class="html-italic">P. gingivalis</span> Type 9 Secretion System gene <span class="html-italic">PorQ</span> encoded by pgi:PG_0602. (<b>c</b>) Bar plot of the log2 fold change of <span class="html-italic">P. gingivalis fimbrium subunit C (fimC)</span> gene encoded by pgi:PG_1881. (<b>d</b>) Bar plot of the log2 fold change of <span class="html-italic">P. gingivalis VimF Glycosyltransferase</span> gene encoded by pgi:PG_0884, a key virulence modulating component. (<b>e</b>) Bar plot of the log2 fold change of <span class="html-italic">P. gingivalis hflX</span> gene encoded by pgi:PG_1886, a key virulence factor for infection and invasion. (<b>f</b>) Bar plot of the log2 fold change of <span class="html-italic">P. gingivalis peptidylarginine deiminase (PPAD)</span> gene encoded by pgi:PG_1424. (<b>g</b>) Bar plot of the log2 fold change of <span class="html-italic">P. gingivalis cdhR</span> gene encoded by pgi:PG_1237, also named <span class="html-italic">luxR</span> as a component of quorum sensing, regulating NO stress resistance. The standard error is shown as an error bar in all bar figures; a single star indicates <span class="html-italic">p</span>-value ≤ 0.05, and double stars indicate fdr-adjusted <span class="html-italic">p</span>-value ≤ 0.05.</p> "> Figure 6
<p>Treatment-induced transcriptomic responses of degradative enzymes including proteases, peptidases, and hemolysins. (<b>a</b>) Heatmap of log2 fold change of degradative enzymes, such as proteases, peptidases, and hemolysins, from all the tested bacteria strains compared to the no-treatment controls. (<b>b</b>) Gene number of the degradation enzymes in each bacteria genome and representational ratio towards all the genes encoded in the genome. (<b>c</b>) Bar plot of the log2 fold change of <span class="html-italic">P. gingivalis gingipain A</span> gene encoded by pgi:PG_2024. (<b>d</b>) Bar plot of the log2 fold change of <span class="html-italic">P. gingivalis gingipain B</span> gene encoded by pgi:PG_0506. (<b>e</b>) Bar plot of the log2 fold change of <span class="html-italic">P. gingivalis hemolysin</span> gene encoded by pgi:PG_1875. (<b>f</b>) Bar plot of the log2 fold change of <span class="html-italic">F. nucleatum</span> prtC <span class="html-italic">collagenase</span> gene encoded by PKHDFLHN_00556 [<a href="#B73-microorganisms-12-02668" class="html-bibr">73</a>]. The standard error is shown as an error bar in all bar figures; a single star indicates <span class="html-italic">p</span>-value ≤ 0.05, and double stars indicate fdr-adjusted <span class="html-italic">p</span>-value ≤ 0.05.</p> "> Figure 7
<p>Transcriptomic changes in genes that are regulated by major oral care ingredients and involved in biofilm development, adhesion to, and infection of host cells. (<b>a</b>). Genes in biofilm development and survival. (<b>b</b>). Genes in attachment to and initial interaction with host cells, such as gingival keratinocytes. (<b>c</b>). Genes encoding products that directly degrade the cellular structure of gingiva and facilitate bacterial survival and infection. The directions of gene expression changes are based on the results observed with SnF<sub>2</sub>, SnCl<sub>2</sub>, and CPC, which had the strongest activity. Blue arrows designate down-regulation, and red arrows designate up-regulation.</p> ">
Abstract
:1. Introduction
2. Materials and Methods
2.1. Bacteria and Culture Conditions
2.2. RNA Preparation and Sequencing
2.3. RNA-Seq Data Analysis
2.4. Bacterial Genome Analysis and Gene Annotation
3. Results
3.1. Microbial Transcriptomics Response to Oral Hygiene Product Functional Ingredients
3.1.1. The Impact of Different Treatments and Dosages on Microbial RNA Yield Revealed That SnF2, SnCl2, and H2O2 Exhibited the Most Significant Reduction in Bacterial RNA Synthesis
3.1.2. Compound and Dosage Effect Observed Based on the Differential Expressed Gene Ratio (DEGR)
3.1.3. Ranking Treatment Effects Based on Full Gene Expression Patterns: Stannous Compounds Led to the Strongest Gene Expression Changes
3.1.4. Transcriptomic Responses of LPS Biosynthesis and Transportation Demonstrated That Stannous Compounds Are Potent Inhibitors
3.1.5. Gene Expression Analysis of Key Factors Associated with P. gingivalis Infection: Pathogenic Protein’s Translocation and Secretion
3.1.6. Treatment Effect of Gene Expression for Degradative Enzymes Such as Proteases, Peptidases, and Hemolysins—Stannous Compounds Showed Potent Inhibition of These Types of Virulence Factors
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Bacterial Strain | ATCC |
---|---|
Prevotella pallens NCTC 13042 | 700821 [46] |
Streptococcus mutans NCTC 10449 | 25175 [47] |
Actinomyces viscosus MG1 | 43146 [48] |
Porphyromonas gingivalis W83 | BAA-308 [49] |
Fusobacterium nucleatum subsp. nucleatum VPI 4351 | 23726 |
Tannerella forsythia FDC 338 | 43037 [50] |
Compound | Concentration in Oral Care Products | High Estimated In-Use Concentration (Dilution of 1:2–1:10) | Low Estimated Post-Use Concentration (Dilution of 1:20–1:100) |
---|---|---|---|
Stannous Fluoride (SnF2) | 0.454% Dentifrice | 0.0908 (1:5) (SnF2_H) | 0.00908 (1:50) (SnF2_L) |
Sodium Fluoride (NaF) | 0.243% Dentifrice | 0.0908 (1:3) (NaF_H) | 0.00908 (1:30) (NaF_L) |
Sodium monofluorophosphate (MFP) | 1.14% Dentifrice | 0.114 (1:10) | - |
Cetylpyridinium Chloride monohydrate (CPC) | 0.1% Rinse | - | 0.002 (1:50) |
Hydrogen Peroxide (H2O2) | 3.0% Dentifrice | - | 0.06 (1:50) |
Zinc Phosphate (Zn) | 1.0% Dentifrice | 0.5 (1:2) (Zn_H) | 0.05 (1:20) (Zn_L) |
Stannous Chloride (SnCl2) | 0.5% Dentifrice | 0.09 (1:5) (SnCl2_H) | 0.09 (1:50) (SnCl2_L) |
Potassium Nitrate (KNO3) | 5.0% Dentifrice | 0.5 (1:10) | - |
Arginine Bicarbonate (ArgB) | 8.0% Dentifrice | 0.8 (1:10) | - |
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Hu, P.; Xie, S.; Shi, B.; Tansky, C.S.; Circello, B.; Sagel, P.A.; Schneiderman, E.; Biesbrock, A.R. The Effect of Oral Care Product Ingredients on Oral Pathogenic Bacteria Transcriptomics Through RNA-Seq. Microorganisms 2024, 12, 2668. https://doi.org/10.3390/microorganisms12122668
Hu P, Xie S, Shi B, Tansky CS, Circello B, Sagel PA, Schneiderman E, Biesbrock AR. The Effect of Oral Care Product Ingredients on Oral Pathogenic Bacteria Transcriptomics Through RNA-Seq. Microorganisms. 2024; 12(12):2668. https://doi.org/10.3390/microorganisms12122668
Chicago/Turabian StyleHu, Ping, Sancai Xie, Baochen Shi, Cheryl S. Tansky, Benjamin Circello, Paul A. Sagel, Eva Schneiderman, and Aaron R. Biesbrock. 2024. "The Effect of Oral Care Product Ingredients on Oral Pathogenic Bacteria Transcriptomics Through RNA-Seq" Microorganisms 12, no. 12: 2668. https://doi.org/10.3390/microorganisms12122668
APA StyleHu, P., Xie, S., Shi, B., Tansky, C. S., Circello, B., Sagel, P. A., Schneiderman, E., & Biesbrock, A. R. (2024). The Effect of Oral Care Product Ingredients on Oral Pathogenic Bacteria Transcriptomics Through RNA-Seq. Microorganisms, 12(12), 2668. https://doi.org/10.3390/microorganisms12122668