Replication Data for: Biofilm dysbiosis and caries activity: a surface or an individual issue?

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Replication Data for: Biofilm dysbiosis and caries activity: a surface or an individual issue?
Ev, Laís Daniela; Poloni, Joice Faria; Damé-Teixeira, Nailê; Corralo, Daniela Jorge; Henz, Sandra Liana; Do, Thuy; Maltz, Marisa; Parolo, Clarissa Cavalcanti Fatturi, 2023, "Replication Data for: Biofilm dysbiosis and caries activity: a surface or an individual issue?", https://doi.org/10.48331/scielodata.MT231Y, SciELO Data, V1
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Description
This study aimed to analyze the functional profile of supragingival biofilm from sound (CAs), active (CAa), and inactive (CAi) enamel caries lesions from caries-active individuals to provide insights into the diversity of biological processes regarding biofilm dysbiosis. A metatranscriptome analysis was performed in biofilm samples collected from five caries active individuals. Total RNA was extracted, and the microbial cDNAs were obtained and sequenced (Illumina HiSeq3000). Trimmed data were submitted to the SqueezeMeta pipeline in the co-assembly mode for functional analysis and further differential gene expression analysis (DESeq2). Bioinformatics analysis of mRNAs revealed a similar functional profile related to all analyzed conditions (CAa, CAi, and CAs). However, active and inactive surfaces share up-regulated genes (gtsA; qrtT; tqsA; pimB; EPHX1) related to virulence traits that were not overrepresented in sound surfaces. From a functional perspective, what matters most is the individual carious status rather than the surface condition. Therefore, pooling samples from various sites can be done in studies of naturally developed oral biofilms, but should preferentially include carious surfaces. (2023-09-24)
Subject Medicine, Health and Life Sciences
Keyword Dental Caries, Biofilms, Microbiota, Gene Expression Profiling
Related Publication Ev LD, Poloni JF, Damé-Teixeira N, Arthur RA, Corralo DJ, Henz SL, et al.Biofilm dysbiosis and caries activity: a surface or an individual issue? J App Oral Sci. 2023;31:e20230214. doi: 10.1590/1678-7757-2023-0214
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Figure_1.jpg
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Published Oct 18, 2023
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Variability in microbial composition among conditions (Fig.1a), and patients (Fig.1b) (R factoextra). The PCA plot Fig. 1.a separates samples according to caries status. The PCA plot Fig. 1.b separates samples according to subjects. Fig. 1a: Red represents biofilm samples from active non-cavitated caries lesions (CAa); green corresponds to arrested non-cavitated caries lesions (CAi), and blue to sound tooth surfaces (CAs). Fig. 1b: Red corresponds to all samples of CA1 patient (P1); olive green corresponds to all samples of CA2 patient (P2); green corresponds to all samples of CA3 patient (P3); blue corresponds to all samples of CA4 patient (P4), and purple corresponds to all samples of CA5 patient (P5). Ellipses represent 95% confidence interval.
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Figure_2.jpg
Figure_2.jpg
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Published Oct 18, 2023
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MD5: 22950c0a9bae8efa96b1abe00b38019b
Euclidean distance plot. Green shades represent patients (patient 1 (P1); patient 2 (P2); patient 3 (P3); patient 4 (P4); and patient 5 (P5)). Purple shades represent tooth surface clinical condition (active non-cavitated surfaces – CAa; arrested non-cavitated surfaces – CAi; and sound surfaces - CAs).
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Published Oct 18, 2023
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Venn diagram depicting the overlap between the differential expressed genes of the three different biofilm collected tooth surfaces (CAa – non-cavitated caries lesions surfaces; CAi – arrested non-cavitated lesions surfaces; CAs – sound tooth surfaces). Fig 3a represents genes up-regulated in CAa related to CAi (blue – 13 genes) and related to CAs (yellow – 19 genes); Fig 3b represents genes up-regulated in CAi related to CAa (blue – 15 genes) and related to CAs (yellow – 21 genes); Fig 3c represent genes up-regulated in CAs related to CAa (blue – 11 genes), related to CAi (yellow – 9 genes). Intersections between blue and yellow diagrams mean common differentially expressed genes between the comparisons.
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Published Oct 18, 2023
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Heatmap representing all genes up-regulated in one or more conditions and patient origin. Genes are grouped by bioprocess. P1 (patient 1); P2 (patient 2); P3 (patient 3); P4 (patient 4);P5 (patient 5). Conditions: CAa (non-cavitated caries lesions surfaces of caries-active patients); CAi (arrested non-cavitated lesions surfaces of caries-active patients); CAs (sound tooth surfaces of caries-active patients). Blue indicates negative correlation and red indicates positive correlation.
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ReadmeBiofilmdysbiosis.txt
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Published Oct 18, 2023
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Data description
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SupFig1.png
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Published Oct 18, 2023
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Supplementary Figure 1. Samples and condition correlations plot. Blue corresponds to a positive correlation, and red corresponds to a negative correlation. CAa correspond to non-cavitated active lesions surfaces (CAa_1; CAa_2; CAa_3; CAa_4; and CAa_5); CAi correspond to non-cavitated arrested lesions surfaces (CAi_1; CAi_2; CAi_3; CAi_4 and CAi_5); CAs correspond to sound surfaces (CAs_1; CAs_2; CAs_3; CAs_4; and CAs_5).
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supplementary1.csv
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Published Oct 18, 2023
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Supplementary Table 1. Up-regulated genes in CAa in relation to CAi and to CAs
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supplementary3.csv
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Supplementary Table 3. Up-regulated genes in CAs in relation to CAa and to CAi.
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supplemtary2.csv
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Published Oct 18, 2023
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Supplementary Table 2. Up-regulated genes in CAi in relation to CAa and to CAs.
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table1.xlsx
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Published Oct 18, 2023
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MD5: 55e7fccf8652e792b900dd37ad8cc6b5
Sociodemographic description of the samples.
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