Non-Surgical Periodontal Therapy Modulates Oral Microbiome in Primary Immunodeficient Children

Study information

Needs review

study design

time series / longitudinal observational

Citation

PMID PubMed identifier for scientific articles.

40685148

DOI Digital object identifier for electronic documents.

https://doi.org/10.1111/jcpe.14201

URI Uniform resource identifier for web resources.

Authors

Stephen A.S., Worrall S., Somani C., Allaker R.P., Davies J., Nibali L., Donos N.

Journal

Journal of clinical periodontology

Year

2025

Keywords:

16S ribosomal RNA sequencing, microbiota, neutropenia, oral microbiome, periodontal therapy, primary immunodeficiency diseases, subgingival plaque

BACKGROUND AND AIM: Primary Immunodeficiencies (PIDs) arise from rare genetic defects affecting humoral and cellular immunity, which can lead to reduced dental plaque control. This study aimed to characterise the subgingival dental plaque microbiome in neutropenic PID children compared to healthy controls and assess their response to non-surgical periodontal therapy. METHODS: Subgingival plaque was collected from three first molars and one first incisor at baseline and 6 months post therapy from children with PID (n = 24) and systematically healthy control participants (n = 24) who were recruited from Great Ormond Street Hospital and Barts Health NHS Trust, respectively. The subgingival microbiome was profiled using an Illumina metabarcoding approach on the bacterial 16S rRNA gene V1-V2 region. RESULTS: Significant shifts in community structure were observed post therapy, as measured by alpha and beta diversities. An increase in Rothia spp., Neisseria spp. and Actinomyces spp. was noted in PID children post therapy, consistent with clinical improvements. Baseline blood absolute neutrophil counts in PID children were positively associated with Streptococcus cristatus and Gemella spp., and negatively with Saccharibacteria, Capnocytophaga and Porphyromonas spp., highlighting key host-microbial relationships. CONCLUSION: Non-surgical periodontal therapy modulated the subgingival microbiota in neutropenic PID children, revealing novel host-microbial interactions important for the oral microbiome in health.

Experiment 1

Edit History Delete Duplicate this Experiment Add a new Signature

incomplete

Curated date: 2025/10/21

Curator: Chyono2

Revision editor(s): Chyono2

Subjects

Location of subjects: United Kingdom

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: Primary immunodeficiency Primary immunodeficiency,primary immunodeficiency

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Healthy Children at baseline (received no therapy)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Primary Immunodeficiency(PID)children at baseline

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Subgingival plaque was collected from 3 first molars and 1 first incissor at baseline

Group 0 sample size Number of subjects in the control (unexposed) group: 24

Group 1 sample size Number of subjects in the case (exposed) group: 24

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: V1-V2

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: Linear Regression; PERMANOVA

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.005

Matched on Factors on which subjects have been matched on in a case-control study: age

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: decreased

Simpson Estimator of species richness and species evenness: more weight on species evenness: decreased

Richness Number of species: decreased

Experiment 2

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incomplete

Curated date: 2025/10/21

Curator: Chyono2

Revision editor(s): Chyono2

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Healthy Children at 6 months(no therapy)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Primary Immunodeficiency(PID)children at 6 months

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Subgingival plaque was collected from 3 first molars and 1 first incissor at 6 months of non-surgical periodontal therapy

Lab analysis

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: Not specified

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: decreased

Simpson Estimator of species richness and species evenness: more weight on species evenness: decreased

Richness Number of species: decreased

Experiment 3

Edit History Delete Duplicate this Experiment Add a new Signature

incomplete

Curated date: 2025/10/21

Curator: Chyono2

Revision editor(s): Chyono2

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Healthy Children baseline+6 months(no therapy)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Primary Immunodeficiency(PID)children baseline+6months with therapy

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Subgingival plaque was collected from 3 first molars and 1 first incissor at baseline and at 6 months with therapy

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: decreased

Simpson Estimator of species richness and species evenness: more weight on species evenness: decreased

Richness Number of species: decreased

Experiment 4

Edit History Delete Duplicate this Experiment Add a new Signature

incomplete

Curated date: 2025/10/21

Curator: Chyono2

Revision editor(s): Chyono2

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Healthy Children(no therapy) with microbiome stability at 6 months

Group 1 name Corresponds to the case (exposed) group for case-control studies: Primary Immunodeficiency(PID)children With therapy

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Primary Immunodeficiency(PID) children that shows microbiome changes induced by therapy