Metatranscriptomic analysis unveils functional alterations in subgingival biofilm of young smokers with periodontitis

Version 1.0
Metatranscriptomic analysis unveils functional alterations in subgingival biofilm of young smokers with periodontitis
Casarin, Renato; Silva, Rafaela; Paz, Hélvis; Stolf, Camila; Carvalho, Lucas; Noronha, Melline; Sallum, Antonio; Monteiro, Mabelle, 2024, "Metatranscriptomic analysis unveils functional alterations in subgingival biofilm of young smokers with periodontitis", https://doi.org/10.48331/scielodata.XA1GIV, SciELO Data, V1, UNF:6:PGM/b92uI5cdyhtqOp+1xQ== [fileUNF]
Learn about Data Citation Standards.
Make Data Count (MDC) Metrics
since
0 Views
0 Downloads
0 Citations
Description
The objective was to assess the influence of smoking on the subgingival metatranscriptomic profile in young patients affected by stage III/IV and generalized periodontal disease. Six young patients affected by periodontitis, including both smokers and non-smokers (n=3/group), were selected, following STROBE (Strengthening the Reporting of Observational Studies in Epidemiology) guidelines for case-control reporting. Periodontal clinical measurements and subgingival biofilm samples were collected. RNA was extracted from biofilm and sequenced through Illumina HiSeq. Differential expression analysis utilized Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, and differentially expressed genes were identified using the Sleuth package in R with a statistical cutoff of ≤0.05. A total of 3351 KEGGs were identified in the subgingival biofilm of both groups, and smoking habits altered the functional behavior of the subgingival biofilm, resulting in 304 differentially expressed KEGGs between groups. Moreover, seven pathways were modulated: glycan degradation, galactose metabolism, glycosaminoglycan degradation, oxidative phosphorylation, peptidoglycan biosynthesis, butanoate metabolism, and glycosphingolipid biosynthesis. Besides, smoking also altered the Antibiotic Resistance Genes (ARGs) levels in subgingival biofilm through the significant over-expression of genes related to beta-lactamase, permeability, antibiotic efflux pumps, and antibiotic-resistant synthetases. Given the limitations of a small sample size, our data suggests that smoking may influence the functional behavior of the subgingival biofilm, modifying pathways that negatively impact the behavior of the subgingival biofilm, potentially leading to a more virulent community. (2024-07-12)
Subject Medicine, Health and Life Sciences
Keyword Smoking, Periodontitis, RNA-Seq, Host-Pathogen Interactions, Gene expression, Mouth
Related Publication Casarin RC, Silva RV, Paz HE, Stolf CS, Carvalho LM, Noronha MF, et al. Metatranscriptomic analysis shows functional alterations in subgingival biofilm in young smokers with periodontitis: a pilot study. J Appl Oral Sci. 2024;32:e20240031. doi: 10.1590/1678-7757-2024-0031
License/Data Use Agreement

CC BY 4.0

Filter by
1 to 10 of 11 Files
Figure_1.jpg
Figure_1.jpg
JPEG Image - 113.3 KB
Published Jul 16, 2024
0 Downloads
MD5: 935611e67e9d7de68bfc71101783b678
Heat-map analysis of bacterial KEGG Orthology identified in the metatranscriptomic analysis of subgingival biofilm of PerioCSmk and PerioCNSmk groups. According to their sequence similarities, the KEGGs cluster into three different clusters.
Preview "Figure_1.jpg"
Figure_2.jpg
Figure_2.jpg
JPEG Image - 311.2 KB
Published Jul 16, 2024
0 Downloads
MD5: 85e53005c348fa4ccd0253866ea14d40
Heat-map analysis of bacterial pathways identified though the values (TPM) of each KEGG in patient’s subgingival biofilm. A) Representation of the glycosaminoglycan degradation, glycosphingolipid biosynthesis, other glycan degradation and peptidoglycan biosynthesis pathways. B) Representation of the galactose metabolism pathway. C) Representation of the butanoate metabolism and oxidative phosphorylation pathways.
Preview "Figure_2.jpg"
README.txt
Plain Text - 3.3 KB
Published Jul 16, 2024
2 Downloads
MD5: f8c376d18cce5d6119a5a9a7489601b9
Preview "README.txt"
Supplementary_Table_1.tab
Tabular Data - 378.2 KB
Published Jul 16, 2024
1 Download
8 Variables, 3899 Observations UNF:6:CXoFPzCp97EnHayFc1XXUg==
Values (TPM) for total counts of each KEGG in both groups
Preview "Supplementary_Table_1.tab"
Supplementary_Table_2.tab
Tabular Data - 18.1 KB
Published Jul 16, 2024
1 Download
13 Variables, 324 Observations UNF:6:o+VbzrOErnX+SCAH/WHMhg==
KEGGs differentially expressed in both groups.
Preview "Supplementary_Table_2.tab"
Supplementary_Table_3.tab
Tabular Data - 45.5 KB
Published Jul 16, 2024
1 Download
17 Variables, 324 Observations UNF:6:vu2OgHdTAv9gs8leIqYZxA==
Values for total Orthology counts (up/down) of each pathway in both groups.
Preview "Supplementary_Table_3.tab"
Supplementary_Table_4.tab
Tabular Data - 452 B
Published Jul 16, 2024
1 Download
3 Variables, 10 Observations UNF:6:XPOoD29Qvj8z07zu4lCnCA==
Pathways significantly up and/or down regulated by orthologues in PerioCSmk group.
Preview "Supplementary_Table_4.tab"
Supplementary_Table_5.tab
Tabular Data - 646 B
Published Jul 16, 2024
1 Download
4 Variables, 6 Observations UNF:6:1yLLw9hhBSkd7EDmzgv15g==
Differentially expressed genes (DEG) of Antibiotic Resistance Genes (ARGs) subgingival biofilm of both groups. Positive fold change indicated increased expression in PerioCSmk group.
Preview "Supplementary_Table_5.tab"
Table_1.tab
Tabular Data - 567 B
Published Jul 16, 2024
0 Downloads
3 Variables, 10 Observations UNF:6:oJcx48FhYrXk9DbzGLCuHw==
Demographic and clinical data for PerioCSmk and PerioCNsmk groups.
Preview "Table_1.tab"
Table_2.tab
Tabular Data - 2.2 KB
Published Jul 16, 2024
0 Downloads
5 Variables, 10 Observations UNF:6:OHeiVCIU/xKiUTloDIpS7g==
Top 10 over-expressed genes in PerioCSmk group.
Preview "Table_2.tab"
Edit File

This file has already been deleted (or replaced) in the current version. It may not be edited.

Restrict Access

Restricting limits access to published files. People who want to use the restricted files can request access by default. If you disable request access, you must add information about access to the Terms of Access field.

Learn about restricting files and dataset access in the User Guide.

Enable access request
You must enable request access or add terms of access to restrict file access.
Save Changes
Edit Embargo

The selected file or files have already been published. Contact an administrator to change the embargo date or reason of the file or files.
Delete Files

The file will be deleted after you click on the Delete button.

Files will not be removed from previously published versions of the dataset.

Select File(s)

Please select one or more files.

Share Dataset

Share this dataset on your favorite social media networks.

Dataset Citations

Citations for this dataset are retrieved from Crossref via DataCite using Make Data Count standards. For more information about dataset metrics, please refer to the User Guide.

Sorry, no citations were found.
Restricted Files Selected

The selected file(s) may not be downloaded because you have not been granted access.

You may request access to the restricted file(s) by clicking the Request Access button.

Download Options

The files selected are too large to download as a ZIP.

You can select individual files that are below the 100.0 MB download limit from the files table, or use the Data Access API for programmatic access to the files.

Select File(s)

Please select a file or files to be downloaded.

Restricted Files Selected

The restricted file(s) selected may not be downloaded because you have not been granted access.

Click Continue to download the files you have access to download.

Delete Dataset

Are you sure you want to delete this dataset and all of its files? You cannot undelete this dataset.

Delete Draft Version

Are you sure you want to delete this draft version? Files will be reverted to the most recently published version. You cannot undelete this draft.

Unpublished Dataset Private URL

Private URL can only be used with unpublished versions of datasets.

Unpublished Dataset Private URL

Are you sure you want to disable the Private URL? If you have shared the Private URL with others they will no longer be able to use it to access your unpublished dataset.

Delete Files

The file(s) will be deleted after you click on the Delete button.

Files will not be removed from previously published versions of the dataset.

Compute

This dataset contains restricted files you may not compute on because you have not been granted access.

Deaccession Dataset

Are you sure you want to deaccession? This is permanent and the selected version(s) will no longer be viewable by the public.

Deaccession Dataset

Are you sure you want to deaccession this dataset? This is permanent an it will no longer be viewable by the public.

Version Differences Details

Please select two versions to view the differences.

Version Differences Details
 
Version:
Last Updated:
Version:
Last Updated:
Select File(s)

Please select a file or files for access request.

Select File(s)

Embargoed files cannot be accessed. Please select an unembargoed file or files for your access request.

Edit Tags

Select existing file tags or create new tags to describe your files. Each file can have more than one tag.

Request Access

  You need to Log In to request access.

Dataset Terms

This dataset is made available under the following terms. Please confirm and/or complete the information needed below in order to continue.

Our Community Norms as well as good scientific practices expect that proper credit is given via citation. Please use the data citation shown on the dataset page.

CC BY 4.0

Preview Guestbook

Upon downloading files the guestbook asks for the following information.

Account Information

Package File Download

Use the Download URL in a Wget command or a download manager to download this package file. Download via web browser is not recommended. User Guide - Downloading a Dataverse Package via URL

https://data.scielo.org/api/access/datafile/

Request Access

Please confirm and/or complete the information needed below in order to request access to files in this dataset.

Compute Batch
Clear Batch
Dataset Persistent Identifier Change Compute Batch
Compute Batch
Submit for Review

You will not be able to make changes to this dataset while it is in review.

Publish Dataset

Are you sure you want to republish this dataset?

Select if this is a minor or major version update.

Publish Dataset

This dataset cannot be published until Journal of Applied Oral Science is published by its administrator.

Publish Dataset

This dataset cannot be published until Journal of Applied Oral Science and SciELO Data are published.

Return to Author

Return this dataset to contributor for modification. The reason for return entered below will be sent by email to the author.