Favorable subgingival plaque microbiome shifts are associated with clinical treatment for peri-implant diseases
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Subjects
- Location of subjects
- Italy
- 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
- Subgingival dental plaque Subgingival plaque,Subgingival dental plaque,subgingival dental plaque
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Peri-Implantitis Peri-Implantitis,peri-Implantitis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy group (case samples)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mucositis group (case samples)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Healthy species/ biomarkers enriched or significant in mucositis patients compared with healthy group patients who underwent surgical (n=9) or non-surgical treatment (n=22) as decided by clinical practitioners
- Group 0 sample size Number of subjects in the control (unexposed) group
- 32
- Group 1 sample size Number of subjects in the case (exposed) group
- 28
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- intake of systemic antibiotics within the past 6 months
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Experiment 2
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Peri-implantitis group (case samples)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Healthy species/ biomarkers enriched or significant in peri-implantitis patients compared with healthy group patients who underwent surgical (n=9) or non-surgical treatment (n=22) as decided by clinical practitioners
- Group 1 sample size Number of subjects in the case (exposed) group
- 31
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 2a and text (paragraph 4)
Description: LEFSE-identified healthy microbiome composition significantly enriched after treatment in healthy group patients compared with peri-implantitis patients
Abundance in Group 1: increased abundance in Peri-implantitis group (case samples)
NCBI | Quality Control | Links |
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Actinomyces oris | ||
Corynebacterium matruchotii | ||
Rothia aeria |
Experiment 3
Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Peri-implantitis species/ biomarkers enriched or significant in peri-implantitis patients compared with healthy group patients who underwent surgical (n=9) or non-surgical treatment (n=22) as decided by clinical practitioners
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 2c
Description: LEFSE-identified peri-implantitis biomarkers/microbiome composition significantly enriched after treatment in healthy group patients compared with peri-implantitis patients
Abundance in Group 1: decreased abundance in Peri-implantitis group (case samples)
NCBI | Quality Control | Links |
---|---|---|
Fusobacterium nucleatum | ||
Porphyromonas gingivalis | ||
unclassified Anaerolineaceae |
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy group (contralateral site samples)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mucositis group (contralateral site samples)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Healthy species/ biomarkers enriched or significant in mucositis patients compared with healthy group patients who underwent surgical (n=9) or non-surgical treatment (n=22) as decided by clinical practitioners
- Group 1 sample size Number of subjects in the case (exposed) group
- 28
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 2b
Description: LEFSE-identified healthy microbiome composition significantly enriched after treatment in mucositis patients compared with healthy group patients
Abundance in Group 1: decreased abundance in Mucositis group (contralateral site samples)
NCBI | Quality Control | Links |
---|---|---|
Streptococcus oralis |
Revision editor(s): Folakunmi
Experiment 5
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Peri-implantitis group (contralateral site samples)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Healthy species/ biomarkers enriched or significant in Peri-implantitis patients compared with healthy group patients who underwent surgical (n=9) or non-surgical treatment (n=22) as decided by clinical practitioners
- Group 1 sample size Number of subjects in the case (exposed) group
- 31
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 2b
Description: LEFSE-identified peri-implantitis biomarkers/microbiome composition significantly enriched after treatment in healthy group patients compared with peri-implantitis patients
Abundance in Group 1: decreased abundance in Peri-implantitis group (contralateral site samples)
NCBI | Quality Control | Links |
---|---|---|
Veillonella parvula |
Revision editor(s): Folakunmi
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy group (contralteral samples)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Peri-implantitis and mucositis groups (contralteral samples)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Peri-implantitis species/ biomarkers enriched or significant in peri-implantitis and mucositis patients compared with healthy group patients who underwent surgical (n=9) or non-surgical treatment (n=22) as decided by clinical practitioners
- Group 1 sample size Number of subjects in the case (exposed) group
- 59
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 2d
Description: LEFSE-identified peri-implantitis biomarkers/microbiome composition significantly enriched after treatment in healthy group patients compared with peri-implantitis and mucositis patients
Abundance in Group 1: increased abundance in Peri-implantitis and mucositis groups (contralteral samples)
NCBI | Quality Control | Links |
---|---|---|
Prevotella intermedia |
Revision editor(s): Folakunmi