Subgingival Microbiota during Healthy Pregnancy and Pregnancy Gingivitis
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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 Uniform resource identifier for web resources.
Authors
Balan P, Brandt BW, Chong YS, Crielaard W, Wong ML, Lopez V, He HG, Seneviratne CJ
Journal
JDR clinical and translational research
Year
2021
INTRODUCTION: Previous studies have largely explored the microbial composition and pathogenesis of pregnancy gingivitis. However, the patterns of microbial colonization during pregnancy in the absence of pregnancy gingivitis have rarely been studied. Characterization of the oral microbiome in pregnant women with healthy gingiva is an important initial step in understanding the role of the microbiome in progression to pregnancy gingivitis. OBJECTIVES: In this study, we compared the oral microbiome of pregnant women without gingivitis (healthy pregnancy) with pregnant women having gingivitis and nonpregnant healthy women to understand how pregnancy modifies the oral microbiome and induces progression to pregnancy gingivitis. METHODS: Subgingival plaque samples were collected from Chinese pregnant women with gingivitis (n = 10), healthy pregnant women (n = 10), and nonpregnant healthy women (n = 10). The Illumina MiSeq platform was used to perform 16S rRNA gene sequencing targeting the V4 region. RESULTS: The alpha and beta diversity was significantly different between pregnant and nonpregnant women, but minimal differences were observed between pregnant women with and without gingivitis. Interestingly, the oral bacterial community showed higher abundance of pathogenic taxa during healthy pregnancy as compared with nonpregnant women despite similar gingival and plaque index scores. However, when compared with overt pregnancy gingivitis, pathogenic taxa were less abundant during healthy pregnancy. PICRUSt analysis (phylogenetic investigation of communities by reconstruction of unobserved states) also suggested no difference in the functional capabilities of the microbiome during pregnancy, irrespective of gingival disease status. However, metabolic pathways related to amino acid metabolism were significantly increased in healthy pregnant women as compared with nonpregnant women. CONCLUSION: The presence of pathogenic taxa in healthy pregnancy and pregnancy gingivitis suggests that bacteria may be necessary for initiating disease development but progression to gingivitis may be influenced by the host environmental factors. More efforts are required to plan interventions aimed at sustaining health before the appearance of overt gingivitis. KNOWLEDGE TRANSFER STATEMENT: The results of this study draw attention to the importance of oral health maintenance during pregnancy, as women without any prenatal oral conditions are predisposed to the risk of developing pregnancy gingivitis. Hence, it is important to incorporate comprehensive assessment of oral health in the prenatal health care schedules. Pregnant woman should be screened for oral risks, counseled on proper oral hygiene and expected oral changes, and referred for dental treatment, when necessary.
Experiment 1
Reviewed Marked as Reviewed by Fatima on 2021/09/16
Subjects
- Location of subjects
- Singapore
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Subgingival dental plaque Subgingival plaque,Subgingival dental plaque
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- pregnancy Gestation,PREGN,Pregnancies,pregnancy
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- non pregnant women without gingivitis
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- pregnant women without gingivitis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Pregnant women sampled between 21 to 24 wk of gestation without gingivitis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
- 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
- Statistical test
- Mann-Whitney (Wilcoxon)
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- .05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
- Richness Number of species
- increased
Signature 1
Reviewed Marked as Reviewed by Fatima on 2021/09/16
Source: Appendix Figure 1, 2, text
Description: Phylum and Genera showing significant differential abundance in subgingival samples.
Abundance in Group 1: increased abundance in pregnant women without gingivitis
| NCBI | Links |
|---|---|
| Bacteroides | |
| Fusobacteriia | |
| Fusobacterium | |
| Spirochaetota | |
| Treponema | |
| Candidatus Saccharibacteria |
Signature 2
Reviewed Marked as Reviewed by Fatima on 2021/09/16
Source: Appendix Figure 2, text
Description: Phylum and Genera showing significant differential abundance in subgingival samples.
Abundance in Group 1: decreased abundance in pregnant women without gingivitis
| NCBI | Links |
|---|---|
| Bergeyella | |
| Gemella | |
| Haemophilus | |
| Streptococcus | |
| Terrahaemophilus |
Experiment 2
Reviewed Marked as Reviewed by Fatima on 2021/09/16
Subjects
- Location of subjects
- Singapore
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Subgingival dental plaque Subgingival plaque,Subgingival dental plaque
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- gingivitis acute gingivitis,chronic gingivitis,gingiva inflammation,gingivitis,inflammation of gingiva
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- pregnant women without gingivitis
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- pregnant women with gingivitis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
- 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
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- .05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Fatima on 2021/09/16
Source: Appendix Figure 1, 2, text
Description: Genera showing significant differential abundance in subgingival samples.
Abundance in Group 1: increased abundance in pregnant women with gingivitis
| NCBI | Links |
|---|---|
| Bacteroides | |
| Campylobacter | |
| Candidatus Saccharibacteria | |
| Filifactor ⚠ | |
| Fretibacterium | |
| Spirochaetota | |
| Tannerella | |
| Treponema |
Experiment 3
Subjects
- Location of subjects
- Singapore
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Subgingival dental plaque Subgingival plaque,Subgingival dental plaque
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- gingivitis acute gingivitis,chronic gingivitis,gingiva inflammation,gingivitis,inflammation of gingiva
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- pregnant women without gingivitis
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- pregnant women with gingivitis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
- 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
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- .05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 3, text
Description: Linear discriminant analysis effect size. Differentially abundant taxonomic profile of subgingival plaque (SGP) microbiota in pregnant women with gingivitis versus pregnant women without gingivitis
Abundance in Group 1: increased abundance in pregnant women with gingivitis
Revision editor(s): Tislam
Signature 2
Source: Figure 3, text
Description: Linear discriminant analysis effect size. Differentially abundant taxonomic profile of subgingival plaque (SGP) microbiota in pregnant women with gingivitis versus pregnant women without gingivitis
Abundance in Group 1: decreased abundance in pregnant women with gingivitis
Revision editor(s): Tislam
Experiment 4
Needs review
Subjects
- Location of subjects
- Singapore
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Subgingival dental plaque Subgingival plaque,Subgingival dental plaque
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- pregnancy Gestation,PREGN,Pregnancies,pregnancy
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- non pregnant women
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- pregnant women
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- pregnant women
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
- 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
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- .05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
Signature 1
Source: Figure 3, text
Description: Linear discriminant analysis effect size. pregnant women without gingivitis versus nonpregnant women without gingivitis
Abundance in Group 1: increased abundance in pregnant women
Revision editor(s): Tislam
Signature 2
Source: Figure 3, text
Description: pregnant women without gingivitis versus nonpregnant women without gingivitis
Abundance in Group 1: decreased abundance in pregnant women
| NCBI | Links |
|---|---|
| Bergeyella sp. oral taxon 322 | |
| Gemella morbillorum | |
| Haemophilus sp. | |
| Neisseria bacilliformis | |
| Rothia aeria | |
| Streptococcus sp. | |
| Terrahaemophilus aromaticivorans |
Revision editor(s): Tislam
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