Favorable subgingival plaque microbiome shifts are associated with clinical treatment for peri-implant diseases

From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2024-3-28
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

Curated date: 2024/03/23

Curator: Folakunmi

Revision editor(s): Folakunmi

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

Curated date: 2024/03/07

Curator: EniolaAde

Revision editor(s): EniolaAde, Folakunmi

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

Curated date: 2024/03/07

Curator: EniolaAde

Revision editor(s): EniolaAde, Folakunmi

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 ControlLinks
Actinomyces oris
Corynebacterium matruchotii
Rothia aeria

Revision editor(s): EniolaAde, Folakunmi

Experiment 3


Reviewed Marked as Reviewed by Folakunmi on 2024-3-28

Curated date: 2024/03/07

Curator: EniolaAde

Revision editor(s): EniolaAde, Folakunmi

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

Curated date: 2024/03/07

Curator: EniolaAde

Revision editor(s): EniolaAde, Folakunmi

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 ControlLinks
Fusobacterium nucleatum
Porphyromonas gingivalis
unclassified Anaerolineaceae

Revision editor(s): EniolaAde, Folakunmi

Experiment 4


Reviewed Marked as Reviewed by Folakunmi on 2024-3-28

Curated date: 2024/03/23

Curator: Folakunmi

Revision editor(s): Folakunmi

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

Curated date: 2024/03/23

Curator: Folakunmi

Revision editor(s): Folakunmi

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 ControlLinks
Streptococcus oralis

Revision editor(s): Folakunmi

Experiment 5


Reviewed Marked as Reviewed by Folakunmi on 2024-3-28

Curated date: 2024/03/23

Curator: Folakunmi

Revision editor(s): Folakunmi

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

Curated date: 2024/03/23

Curator: Folakunmi

Revision editor(s): Folakunmi

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 ControlLinks
Veillonella parvula

Revision editor(s): Folakunmi

Experiment 6


Reviewed Marked as Reviewed by Folakunmi on 2024-3-28

Curated date: 2024/03/28

Curator: Folakunmi

Revision editor(s): Folakunmi

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

Curated date: 2024/03/28

Curator: Folakunmi

Revision editor(s): Folakunmi

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 ControlLinks
Prevotella intermedia

Revision editor(s): Folakunmi