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The metagenome and metabolome signatures of dental biofilms associated with severe dental fluorosis

Ajrithirong, Penpitcha, Krasaesin, Annop, Sriarj, Wannakorn, Gavila, Patcharaporn, Chetruengchai, Wanna, Sriwattanapong, Kanokwan, Manaspon, Chawan, Samaranayake, Lakshman, Porntaveetus, Thantrira·2025·Journal of Oral Microbiology
DOI 10.1080/20002297.2025.2560591PMC PMC12459186
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Figure 1. Flow chart of the study design and clinical features of participants in this study. (A) The flow chart of study design in this study. (B–D) The clinical features of the SF group defined with discrete or confluent pitting, widespread brown stains which present as a corroded-like appearance whereas the control group (E–G) revealed shine smooth, glossy with translucent creamy-white color of the normal enamel. CT = control, SF = severe fluorosis.
Figure 1. Flow chart of the study design and clinical features of participants in this study. (A) The flow chart of study design in this study. (B–D) The clinical features of the SF group defined with discrete or confluent pitting, widespread brown stains which present as a corroded-like appearance whereas the control group (E–G) revealed shine smooth, glossy with translucent creamy-white color of the normal enamel. CT = control, SF = severe fluorosis.CC BY · PubMed Central
Figure 2. Bar graph of average relative abundance in different taxonomic levels found in both severe dental fluorosis (SF) and control (CT) group. (A) The average proportion of relative abundance at the phylum level which showed that Proteobacteria (39.70 ± 7.70%) was the most abundant phyla found in SF group while Actinobacteria (25.19 ± 11.78%) was the most frequent phyla found in the control group. (B) The most abundant genus in SF group was Neiserria (22.00 ± 4.76%) whereas Actinomyces (16.51 ± 7.27%) was the most frequent genus found in the controls. (C) At species levels, Neiserria sicca (13.47 ± 5.38%) was the most abundant in SF group and Actinomyces dentalis (6.60 ± 3.65%) was the most frequent species in the control.
Figure 2. Bar graph of average relative abundance in different taxonomic levels found in both severe dental fluorosis (SF) and control (CT) group. (A) The average proportion of relative abundance at the phylum level which showed that Proteobacteria (39.70 ± 7.70%) was the most abundant phyla found in SF group while Actinobacteria (25.19 ± 11.78%) was the most frequent phyla found in the control group. (B) The most abundant genus in SF group was Neiserria (22.00 ± 4.76%) whereas Actinomyces (16.51 ± 7.27%) was the most frequent genus found in the controls. (C) At species levels, Neiserria sicca (13.47 ± 5.38%) was the most abundant in SF group and Actinomyces dentalis (6.60 ± 3.65%) was the most frequent species in the control.CC BY · PubMed Central
Figure 3. Violin plot of alpha diversity indices and principal coordinates analysis (PCoA) with Bray–Curtis. (A–C) The alpha diversity based on Shannon, Simpson and Choa1 showed no significant differences between groups (p-value = 0.0149, 0.0650, and 0.7964, respectively). (D) The beta diversity, the PCoA plot based on Bray–Curtis showed a significant divergence between the SF group and control group (PERMANOVA, p-value = 0.0010). CT = control, SF = severe fluorosis.
Figure 3. Violin plot of alpha diversity indices and principal coordinates analysis (PCoA) with Bray–Curtis. (A–C) The alpha diversity based on Shannon, Simpson and Choa1 showed no significant differences between groups (p-value = 0.0149, 0.0650, and 0.7964, respectively). (D) The beta diversity, the PCoA plot based on Bray–Curtis showed a significant divergence between the SF group and control group (PERMANOVA, p-value = 0.0010). CT = control, SF = severe fluorosis.CC BY · PubMed Central
Figure 4. Heatmaps at each taxonomic level and a Venn diagram illustrating species distribution in the severe dental fluorosis (SF) and control (CT) groups. (A–C) Heatmap analysis illustrates the 20 most abundant microbial taxa in dental biofilms, comparing the SF and CT groups. Data are presented at the phylum, genus and species levels, with color intensity corresponding to relative abundance. (D) The Venn diagram shows the overlap and uniqueness of species detected in both groups. A total of 324 species were shared between SF and CT groups, while 17 species were exclusively found in the SF group and 13 species were unique to the CT group. CT = control, SF = severe fluorosis.
Figure 4. Heatmaps at each taxonomic level and a Venn diagram illustrating species distribution in the severe dental fluorosis (SF) and control (CT) groups. (A–C) Heatmap analysis illustrates the 20 most abundant microbial taxa in dental biofilms, comparing the SF and CT groups. Data are presented at the phylum, genus and species levels, with color intensity corresponding to relative abundance. (D) The Venn diagram shows the overlap and uniqueness of species detected in both groups. A total of 324 species were shared between SF and CT groups, while 17 species were exclusively found in the SF group and 13 species were unique to the CT group. CT = control, SF = severe fluorosis.CC BY · PubMed Central
Figure 5. Linear discriminant analysis effect size (LEfSe) of microbial composition in the severe dental fluorosis (SF) and control (CT) groups. LEfSe analysis at the species level identified microbial biomarkers with an LDA score (log₁₀) > 2 and p-value < 0.05. Four species were significantly enriched in the SF group: Neisseria sicca, Granulicatella elegans, Porphyromonas SGB2042 and Neisseria cinerea. In the control group, the five species with the highest LDA scores were Actinomyces dentalis, Tanner Ella sp. oral taxon HOT 286, Candidatus Nanosynsacchari sp. TM7 ANC 38.39 G1 1, Selenomonas noxia and Treponema sp OMZ 804. CT = control, SF = severe fluorosis.
Figure 5. Linear discriminant analysis effect size (LEfSe) of microbial composition in the severe dental fluorosis (SF) and control (CT) groups. LEfSe analysis at the species level identified microbial biomarkers with an LDA score (log₁₀) > 2 and p-value < 0.05. Four species were significantly enriched in the SF group: Neisseria sicca, Granulicatella elegans, Porphyromonas SGB2042 and Neisseria cinerea. In the control group, the five species with the highest LDA scores were Actinomyces dentalis, Tanner Ella sp. oral taxon HOT 286, Candidatus Nanosynsacchari sp. TM7 ANC 38.39 G1 1, Selenomonas noxia and Treponema sp OMZ 804. CT = control, SF = severe fluorosis.CC BY · PubMed Central
Figure 6. Heatmap analysis and volcano plot of metabolic pathway profiles. (A) Heatmap showing 58 significantly different pathways (FDR < 0.05) between the severe fluorosis (SF) and control (CT) groups. (B) Volcano plot highlighting dominant pathways in the SF and CT groups, defined by FDR < 0.05 and a fold change greater than two (|log2FC| > 1). (C) Log2 fold change of the eight most discriminative pathways, illustrating differential expression between groups. CT = control, SF = severe fluorosis.
Figure 6. Heatmap analysis and volcano plot of metabolic pathway profiles. (A) Heatmap showing 58 significantly different pathways (FDR < 0.05) between the severe fluorosis (SF) and control (CT) groups. (B) Volcano plot highlighting dominant pathways in the SF and CT groups, defined by FDR < 0.05 and a fold change greater than two (|log2FC| > 1). (C) Log2 fold change of the eight most discriminative pathways, illustrating differential expression between groups. CT = control, SF = severe fluorosis.CC BY · PubMed Central

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Metadata

Authors
Ajrithirong, P., Krasaesin, A., Sriarj, W., Gavila, P., Chetruengchai, W., Sriwattanapong, K., Manaspon, C., Samaranayake, L., & Porntaveetus, T.
Affiliations
  • Department of Pediatric Dentistry, Faculty of Dentistry, Chulalongkorn University
  • Department of Physiology, Faculty of Dentistry, Center of Excellence in Precision Medicine and Digital Health, Chulalongkorn University Implant and Esthetic Center, Chulalongkorn University
  • Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University
ORCID
Venue
Journal of Oral Microbiology
Publisher
Informa UK Limited
Published
2025-09-23
Volume
17
Issue
1
ISSN
2000-2297
DOI
10.1080/20002297.2025.2560591
PMC
PMC12459186
Cited by
12
References
5
Language
en
Licence
creativecommons.org/licenses/by/4.0/ (vor)
Funders
  • Faculty of Dentistry, Chulalongkorn University (DRF68_007)
  • Health Systems Research Institute (68-032, 68-056)
  • The Second Century Fund (C2F)
  • Thailand Science Research and Innovation (HEA_FF_68_008_3200_001)

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CoChat. (2026). Citation check: The metagenome and metabolome signatures of dental biofilms associated with severe dental fluorosis. https://app.cochat.ai/papers/10.1080/20002297.2025.2560591
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Ajrithirong, P., Krasaesin, A., Sriarj, W., Gavila, P., Chetruengchai, W., Sriwattanapong, K., Manaspon, C., Samaranayake, L., & Porntaveetus, T. (2025). The metagenome and metabolome signatures of dental biofilms associated with severe dental fluorosis. Journal of Oral Microbiology. https://doi.org/10.1080/20002297.2025.2560591