Favorable subgingival plaque microbiome shifts are associated with clinical treatment for peri-implant diseases
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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
Bazzani D, Heidrich V, Manghi P, Blanco-Miguez A, Asnicar F, Armanini F, Cavaliere S, Bertelle A, Dell'Acqua F, Dellasega E, Waldner R, Vicentini D, Bolzan M, Tomasi C, Segata N, Pasolli E, Ghensi P
Journal
NPJ biofilms and microbiomes
Year
2024
We performed a longitudinal shotgun metagenomic investigation of the plaque microbiome associated with peri-implant diseases in a cohort of 91 subjects with 320 quality-controlled metagenomes. Through recently improved taxonomic profiling methods, we identified the most discriminative species between healthy and diseased subjects at baseline, evaluated their change over time, and provided evidence that clinical treatment had a positive effect on plaque microbiome composition in patients affected by mucositis and peri-implantitis.
Experiment 1
Reviewed Marked as Reviewed by Folakunmi on 2024-3-28
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
Reviewed Marked as Reviewed by Folakunmi on 2024-3-28
Differences from previous experiment shown
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
Reviewed Marked as Reviewed by Folakunmi on 2024-3-23
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 |
|---|---|---|
| Actinomyces oris | ||
| Corynebacterium matruchotii | ||
| Rothia aeria |
Experiment 3
Reviewed Marked as Reviewed by Folakunmi on 2024-3-28
Differences from previous experiment shown
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
Reviewed Marked as Reviewed by Folakunmi on 2024-3-23
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
Reviewed Marked as Reviewed by Folakunmi on 2024-3-28
Differences from previous experiment shown
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
Reviewed Marked as Reviewed by Folakunmi on 2024-3-28
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
Reviewed Marked as Reviewed by Folakunmi on 2024-3-28
Differences from previous experiment shown
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
Reviewed Marked as Reviewed by Folakunmi on 2024-3-28
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
Reviewed Marked as Reviewed by Folakunmi on 2024-3-28
Differences from previous experiment shown
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
Reviewed Marked as Reviewed by Folakunmi on 2024-3-28
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
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