Integrated transcriptomic and network analysis identifies novel regulatory hubs driving biofilm formation in
4 affiliations
- 1Department of Prosthodontics, School of Dentistry, Shahrekord University of Medical Sciences, Shahrekord, Iran; Corresponding author.
- 2Department of Orthodontics, School of Dentistry, Shahrekord University of Medical Sciences, Shahrekord, Iran
- 3Department of Mathematics, University of Shahrekord, Shahrekord, Iran
- 4Department of Prosthodontics, School of Dentistry, Shahrekord University of Medical Sciences, Shahrekord, Iran
Abstract
Streptococcus mutans is a key cariogenic bacterium that forms robust biofilms on tooth surfaces, playing a central role in dental caries. Biofilm development is mediated by multiple genes, including adhesion factors ( spaP ), glucan synthesis enzymes ( gtfB , gtfC ), glucan-binding proteins ( gbpC ), and regulatory pathways such as the quorum sensing comCDE system, the two-component vicRK system, and the alternative sigma factor sigX . In this study, we performed a comparative transcriptomic analysis of publicly available RNA-Seq datasets derived from dental plaque samples of caries-active and healthy individuals (n = 14, NCBI SRA) to identify key gene expression changes and regulatory networks associated with cariogenic biofilm formation. A total of 412 differentially expressed genes (DEGs) were identified, including 237 upregulated and 175 downregulated in caries-active samples. Notably, canonical biofilm-associated genes were highly upregulated: spaP (log2FC = +3.14), gtfB (log2FC = +2.87), gtfC (log2FC = +2.54), and gbpC (log2FC = +2.96). Quorum sensing regulators comC (log2FC = +1.45) and comE (log2FC = +0.98) were induced, while comD (log2FC = −0.87) was moderately downregulated. Functional enrichment analysis revealed significant involvement of pathways in quorum sensing, two-component signaling, carbohydrate metabolism, and oxidative stress response. Weighted Gene Co-expression Network Analysis (WGCNA) identified a module strongly correlated with the caries phenotype (r = 0.85), containing SMU_RS10050 as a potential novel regulatory hub. These results provide a systems-level understanding of S. mutans biofilm regulatory mechanisms in clinical datasets and highlight potential molecular targets for therapeutic intervention against cariogenic biofilms.
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BibTeX
@article{hasanvand2026integrated,
title = {{Integrated transcriptomic and network analysis identifies novel regulatory hubs driving biofilm formation in}},
author = {Mohsen Kazemi Hasanvand and Darab Gholami Boroujeni and Maryam Khosropour and Hosein Alavi Eshkaftaki and Matin Karbasion},
journal = {The Microbe},
year = {2026},
month = oct,
doi = {10.1016/j.microb.2026.100808},
url = {https://doi.org/10.1016/j.microb.2026.100808},
note = {CC BY},
}
RIS
TY - JOUR
TI - Integrated transcriptomic and network analysis identifies novel regulatory hubs driving biofilm formation in
AU - Mohsen Kazemi Hasanvand
AU - Darab Gholami Boroujeni
AU - Maryam Khosropour
AU - Hosein Alavi Eshkaftaki
AU - Matin Karbasion
PY - 2026
DA - 2026/10/30
JO - The Microbe
DO - 10.1016/j.microb.2026.100808
UR - https://doi.org/10.1016/j.microb.2026.100808
AB - Streptococcus mutans is a key cariogenic bacterium that forms robust biofilms on tooth surfaces, playing a central role in dental caries. Biofilm development is mediated by multiple genes, including adhesion factors ( spaP ), glucan synthesis enzymes ( gtfB , gtfC ), glucan-binding proteins ( gbpC ), and regulatory pathways such as the quorum sensing comCDE system, the two-component vicRK system, and the alternative sigma factor sigX . In this study, we performed a comparative transcriptomic analysis of publicly available RNA-Seq datasets derived from dental plaque samples of caries-active and healthy individuals (n = 14, NCBI SRA) to identify key gene expression changes and regulatory networks associated with cariogenic biofilm formation. A total of 412 differentially expressed genes (DEGs) were identified, including 237 upregulated and 175 downregulated in caries-active samples. Notably, canonical biofilm-associated genes were highly upregulated: spaP (log2FC = +3.14), gtfB (log2FC = +2.87), gtfC (log2FC = +2.54), and gbpC (log2FC = +2.96). Quorum sensing regulators comC (log2FC = +1.45) and comE (log2FC = +0.98) were induced, while comD (log2FC = −0.87) was moderately downregulated. Functional enrichment analysis revealed significant involvement of pathways in quorum sensing, two-component signaling, carbohydrate metabolism, and oxidative stress response. Weighted Gene Co-expression Network Analysis (WGCNA) identified a module strongly correlated with the caries phenotype (r = 0.85), containing SMU_RS10050 as a potential novel regulatory hub. These results provide a systems-level understanding of S. mutans biofilm regulatory mechanisms in clinical datasets and highlight potential molecular targets for therapeutic intervention against cariogenic biofilms.
SN - 2950-1946
ER -