Structural changes in the oral microbiome of the adolescent patients with moderate or severe dental fluorosis
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Wang Q, Chen X, Hu H, Wei X, Wang X, Peng Z, Ma R, Zhao Q, Zhao J, Liu J, Deng F
Journal
Scientific reports
Year
2021
Dental fluorosis is a very prevalent endemic disease. Although oral microbiome has been reported to correlate with different oral diseases, there appears to be an absence of research recognizing any relationship between the severity of dental fluorosis and the oral microbiome. To this end, we investigated the changes in oral microbial community structure and identified bacterial species associated with moderate and severe dental fluorosis. Salivary samples of 42 individuals, assigned into Healthy (N = 9), Mild (N = 14) and Moderate/Severe (M&S, N = 19), were investigated using the V4 region of 16S rRNA gene. The oral microbial community structure based on Bray Curtis and Weighted Unifrac were significantly changed in the M&S group compared with both of Healthy and Mild. As the predominant phyla, Firmicutes and Bacteroidetes showed variation in the relative abundance among groups. The Firmicutes/Bacteroidetes (F/B) ratio was significantly higher in the M&S group. LEfSe analysis was used to identify differentially represented taxa at the species level. Several genera such as Streptococcus mitis, Gemella parahaemolysans, Lactococcus lactis, and Fusobacterium nucleatum, were significantly more abundant in patients with moderate/severe dental fluorosis, while Prevotella melaninogenica and Schaalia odontolytica were enriched in the Healthy group. In conclusion, our study indicates oral microbiome shift in patients with moderate/severe dental fluorosis. We identified several differentially represented bacterial species enriched in moderate and severe fluorosis. Findings from this study suggests that the roles of these bacteria in oral health and related diseases warrant more consideration in patients with moderate and severe fluorosis.
Experiment 1
Needs review
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Dental fluorosis dental fluorosis,fluorosis,Fluorosis, Dental,Intrinsic enamel discolouration of fluorosis,intrinsic enamel discolouration of fluorosis,Mottled teeth,mottled teeth,Mottling of enamel,mottling of enamel,Dental fluorosis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- M&S (Moderate/Severe)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group includes participants diagnosed with dental fluorosis according to the Dean’s Index, specifically those categorized as Code 4 (moderate) and Code 5 (severe). Code 4 (Moderate): Characterized by extensive brown or yellow-brown staining with mild enamel wear. Code 5 (Severe): Characterized by deep stains, obvious pits, and increased enamel brittleness.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 9
- Group 1 sample size Number of subjects in the case (exposed) group
- 19
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 6 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3.0
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 2
Needs review
Source: Figure 3C, 4A
Description: Significantly different bacterial species between Healthy and M&S group based on LEfSe analysis.
Abundance in Group 1: increased abundance in M&S (Moderate/Severe)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Fusobacterium nucleatum | ||
| Granulicatella elegans | ||
| Lactococcus lactis | ||
| Morococcus cerebrosus | ||
| Streptococcus mitis | ||
| Gemella parahaemolysans |
Revision editor(s): LiliGC, KateRasheed
Signature 3
Needs review
Source: Figure 3C, 4A
Description: Significantly different bacterial species between Healthy and M&S group based on LEfSe analysis.
Abundance in Group 1: decreased abundance in M&S (Moderate/Severe)
| NCBI | Quality Control | Links |
|---|---|---|
| Alloprevotella tannerae | ||
| Hoylesella shahii | ||
| Oribacterium parvum | ||
| Prevotella melaninogenica | ||
| Prevotella pallens | ||
| Schaalia odontolytica | ||
| Segatella salivae | ||
| Bacteroidota |
Revision editor(s): LiliGC, KateRasheed
Experiment 2
Experiment 3
Needs review
Differences from previous experiment shown
Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group includes participants diagnosed with dental fluorosis according to the Dean’s Index, specifically those categorized as Code 4 (moderate) and Code 5 (severe). Code 4 (Moderate): Characterized by extensive brown or yellow-brown staining with mild enamel wear. Code 5 (Severe): Characterized by deep stains, obvious pits, and increased enamel brittleness.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 14
Lab analysis
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Needs review
Source: Fig. 4C, 4E, 4G
Description: Significantly different bacterial species between Healthy and M&S group based on Wilcoxon analysis.
Abundance in Group 1: increased abundance in M&S (Moderate/Severe)
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus mitis | ||
| Gemella parahaemolysans | ||
| Lactococcus lactis |
Revision editor(s): KateRasheed
Signature 2
Needs review
Source: Fig. 4D, 4F
Description: Significantly different bacterial species between Healthy and M&S group based on Wilcoxon analysis.
Abundance in Group 1: decreased abundance in M&S (Moderate/Severe)
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella melaninogenica | ||
| Schaalia odontolytica |
Revision editor(s): KateRasheed
Experiment 4
Needs review
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Mild
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group includes participants diagnosed with dental fluorosis according to the Dean’s Index, specifically those categorized as Code 4 (moderate) and Code 5 (severe). Code 4 (Moderate): Characterized by extensive brown or yellow-brown staining with mild enamel wear. Code 5 (Severe): Characterized by deep stains, obvious pits, and increased enamel brittleness.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 19
- Group 1 sample size Number of subjects in the case (exposed) group
- 14
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Needs review
Source: Fig. 4D
Description: Significantly different bacterial species between Mild and M&S group based on Wilcoxon analysis.
Abundance in Group 1: decreased abundance in M&S (Moderate/Severe)
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella melaninogenica |
Revision editor(s): KateRasheed
Signature 2
Needs review
Source: Fig. 4C, 4E, 4G-H
Description: Significantly different bacterial species between Mild and M&S group based on Wilcoxon analysis.
Abundance in Group 1: increased abundance in M&S (Moderate/Severe)
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacterium nucleatum | ||
| Gemella parahaemolysans | ||
| Lactococcus lactis | ||
| Streptococcus mitis |
Revision editor(s): KateRasheed
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