Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study

Study information

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study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

38745393

DOI Digital object identifier for electronic documents.

10.1111/jcpe.13998

URI

Authors

Bingöl M, Cardilli A, Bingöl AC, Löber U, Bang C, Franke A, Bartzela T, Beblo S, Mönch E, Stolz S, Schaefer AS, Forslund SK, Richter GM

Journal

Journal of clinical periodontology

Year

2024

Keywords:

16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque

AIM: The oral microenvironment contributes to microbial composition and immune equilibrium. It is considered to be influenced by dietary habits. Phenylketonuria (PKU) patients, who follow a lifelong low-protein diet, exhibit higher prevalence of oral diseases such as periodontitis, offering a suitable model to explore the interplay between diet, oral microbiota and oral health. MATERIALS AND METHODS: We conducted 16S rDNA sequencing on saliva and subgingival plaque from 109 PKU patients (ages 6-68 years) and 114 age-matched controls and correlated oral microbial composition and dental health. RESULTS: PKU patients exhibited worse dental health, reduced oral microbial diversity and a difference in the abundance of specific taxa, especially Actinobacteriota species, compared to controls. PKU patients with poor periodontal health exhibited higher alpha diversity than the orally healthy ones, marked by high abundance of the genus Tannerella. Notably, the observed taxonomic differences in PKU patients with normal indices of decayed/missing/filled teeth, plaque control record, gingival bleeding index and periodontal screening and recording index generally differed from microbial signatures of periodontitis. CONCLUSIONS: PKU patients' reduced microbial diversity may be due to their diet's metabolic challenges disrupting microbial and immune balance, thus increasing oral inflammation. Higher alpha diversity in PKU patients with oral inflammation is likely related to expanded microbial niches.

Experiment 1

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Curated date: 2024/06/24

Curator: MyleeeA

Revision editor(s): MyleeeA, Tosin, WikiWorks

Subjects

Location of subjects

Germany

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

Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology

Phenylketonuria Folling disease,Folling's disease,Folling's syndrome,Følling's disease,HPA, non-PKU mild,hyperphenylalaninemia, non-PKU mild,imbecilitus phenylpyruvica,oligophrenia Phenylpyruvica,oligophrenia phenylpyruvica,PAH deficiency,Pah deficiency,pah deficiency,Phenylalanine hydroxylase deficiency,phenylalanine hydroxylase deficiency,phenylalaninemia,phenylketonuria,phenylketonuria, maternal,phenylpyruvic oligophrenia,PKU,Phenylketonuria

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Control Saliva (Ctrl-S) patients

Group 1 name Corresponds to the case (exposed) group for case-control studies

Phenylketonuria Saliva (PKU-S) patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Patients diagnosed with Phenylketonuria (PKU) and who stimulated Saliva samples were gotten from.

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

114

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

109

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

Mann-Whitney (Wilcoxon)

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

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

age

Alpha Diversity

Pielou Quantifies how equal the community is numerically

increased

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

decreased

Richness Number of species

decreased

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample

decreased

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Source: Appendix Table 5, Figure 2D

Description: Differential abundant genera in Phenylketonuria (PKU-S) and Control (Ctrl-S) Saliva Patients.

Abundance in Group 1: increased abundance in Phenylketonuria Saliva (PKU-S) patients

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Campylobacter
Haemophilus
Veillonella

Revision editor(s): MyleeeA, Tosin, WikiWorks

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Source: Appendix Table 5, Figure 2D

Description: Differential abundant genera in Phenylketonuria (PKU-S) and Control (Ctrl-S) Saliva Patients.

Abundance in Group 1: decreased abundance in Phenylketonuria Saliva (PKU-S) patients

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Actinomyces
Alloprevotella
Arachnia
Cardiobacterium
Catonella
Olsenella
Peptococcus
Peptostreptococcus
Stomatobaculum
FO332FO332

Revision editor(s): MyleeeA, Tosin, WikiWorks

Experiment 2

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Curated date: 2024/06/24

Curator: MyleeeA

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Differences from previous experiment shown

Subjects

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

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Control Subgingival plaque (Ctrl-SP) patients

Group 1 name Corresponds to the case (exposed) group for case-control studies

Phenylketonuria Subgingival plaque (PKU-SP) patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Patients diagnosed with Phenylketonuria (PKU) and who stimulated Sub gingival plaque samples were gotten from.

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

113

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

96

Lab analysis

Statistical Analysis

Alpha Diversity

Pielou Quantifies how equal the community is numerically

decreased

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

decreased

Richness Number of species

decreased

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample

unchanged

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Source: Appendix Table 5, Figure 2D

Description: Differential abundant genera in Phenylketonuria (PKU-SP) and Control (Ctrl-SP) Subgingival Patients.

Abundance in Group 1: increased abundance in Phenylketonuria Subgingival plaque (PKU-SP) patients

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Actinomyces

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Source: Appendix Table 5, Figure 2D

Description: Differential abundant genera in Phenylketonuria (PKU-SP) and Control (Ctrl-SP) Subgingival Patients.

Abundance in Group 1: decreased abundance in Phenylketonuria Subgingival plaque (PKU-SP) patients

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Aggregatibacter
Capnocytophaga
Gemella
Leptotrichia

Revision editor(s): MyleeeA, Tosin, WikiWorks

Experiment 3

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Curated date: 2024/07/01

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Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology

Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Control Adults Saliva (Ctrl-Adults-S) patients

Group 1 name Corresponds to the case (exposed) group for case-control studies

Phenylketonuria Adults Saliva (PKU-Adults-S) patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Adult Patients diagnosed with Phenylketonuria (PKU) and who stimulated Saliva samples were gotten from.

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

52

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

50

Lab analysis

Statistical Analysis

Alpha Diversity

Pielou Quantifies how equal the community is numerically

unchanged

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

decreased

Richness Number of species

decreased

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample

decreased

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Source: Appendix Table 5, Figure 2D

Description: Differential abundant genera in Phenylketonuria (PKU-Adults-S) and Control (Ctrl-Adults-S) Adult Saliva patients.

Abundance in Group 1: decreased abundance in Phenylketonuria Adults Saliva (PKU-Adults-S) patients

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Actinomyces
Catonella
Peptococcus
Stomatobaculum

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Experiment 4

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Curated date: 2024/07/01

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Differences from previous experiment shown

Subjects

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

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Control Adults subgingival plaque (Ctrl-Adults-SP) patients

Group 1 name Corresponds to the case (exposed) group for case-control studies

Phenylketonuria Adults subgingival plaque (PKU-Adults-SP) patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Adult Patients diagnosed with Phenylketonuria (PKU) and who stimulated Sub gingival plaque samples were gotten from.

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

45

Lab analysis

Statistical Analysis

Alpha Diversity

Pielou Quantifies how equal the community is numerically

unchanged

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

unchanged

Richness Number of species

unchanged

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample

decreased

Signature 1

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Source: Appendix Table 5, Figure 2D

Description: Differential abundant genera in Phenylketonuria (PKU-Adults-SP) and Control (Ctrl-Adults-SP) Adults Subgingival plaque Patients.

Abundance in Group 1: increased abundance in Phenylketonuria Adults subgingival plaque (PKU-Adults-SP) patients

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Actinomyces

Revision editor(s): MyleeeA, Tosin, WikiWorks

Experiment 5

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Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology

Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Control Children Saliva (Ctrl-Ch-S) patients

Group 1 name Corresponds to the case (exposed) group for case-control studies

Phenylketonuria Children Saliva (PKU-Ch-S) patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Children Patients diagnosed with Phenylketonuria (PKU) and who stimulated Saliva samples were gotten from.

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

62

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

59

Lab analysis

Statistical Analysis

Alpha Diversity

Pielou Quantifies how equal the community is numerically

unchanged

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

unchanged

Richness Number of species

unchanged

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample

unchanged

Signature 1

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Source: Appendix Table 5 , Figure 2D

Description: Differential abundant genera in Phenylketonuria Children Saliva (PKU-Ch-S) and Control Children Saliva (Ctrl-Ch-S) Patients

Abundance in Group 1: increased abundance in Phenylketonuria Children Saliva (PKU-Ch-S) patients

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Haemophilus

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Signature 2

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Source: Appendix Table 5, Figure 2D

Description: Differential abundant genera in Phenylketonuria Children Saliva (PKU-Ch-S) and Control Children Saliva (Ctrl-Ch-S) Patients

Abundance in Group 1: decreased abundance in Phenylketonuria Children Saliva (PKU-Ch-S) patients

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Actinomyces
Arachnia
Olsenella
Peptococcus
Peptostreptococcus
Selenomonas
FO332FO332

Revision editor(s): MyleeeA, Tosin, WikiWorks

Experiment 6

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Curated date: 2024/07/31

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Differences from previous experiment shown

Subjects

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

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Control Children subgingival plaque (Ctrl-Ch-SP) patients

Group 1 name Corresponds to the case (exposed) group for case-control studies

Phenylketonuria Children subgingival plaque (PKU-Ch-SP) patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Children Patients diagnosed with Phenylketonuria (PKU) and who stimulated Sub gingival plaque samples were gotten from.

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

61

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

51

Lab analysis

Statistical Analysis

Alpha Diversity

Pielou Quantifies how equal the community is numerically

unchanged

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

unchanged

Richness Number of species

unchanged

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample

unchanged

Signature 1

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Source: Appendix Table 5 , Figure 2D

Description: Differential abundant genera in Phenylketonuria (PKU-Ch-SP) and Control (Ctrl-Ch-SP) Children Subgingival plague Patients.

Abundance in Group 1: increased abundance in Phenylketonuria Children subgingival plaque (PKU-Ch-SP) patients

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Actinomyces

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Signature 2

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Source: Appendix Table 5 , Figure 2D

Description: Differential abundant genera in Phenylketonuria (PKU-Ch-SP) and Control (Ctrl-Ch-SP) Children Subgingival plague Patients.

Abundance in Group 1: decreased abundance in Phenylketonuria Children subgingival plaque (PKU-Ch-SP) patients

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Aggregatibacter
Capnocytophaga
Gemella
Leptotrichia

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Experiment 7

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Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology

Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva

Group 0 name Corresponds to the control (unexposed) group for case-control studies

ChCtrlRel-S [related control children saliva (Healthy siblings of PKU patients)]

Group 1 name Corresponds to the case (exposed) group for case-control studies

ChCtrlUnrel-S (unrelated control children saliva) patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Control Children unrelated to Phenylketonuria (PKU) patients who stimulated saliva samples were gotten from.

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

12

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

26

Lab analysis

Statistical Analysis

Alpha Diversity

Pielou Quantifies how equal the community is numerically

decreased

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

increased

Richness Number of species

increased

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample

increased

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Source: Appendix Table 5, Figure 2D

Description: Differential abundant genera in ChCtrlRel-S (related control children saliva) and ChCtrlUnrel-S (unrelated control children saliva) to Phenylketonuria Patients.

Abundance in Group 1: decreased abundance in ChCtrlUnrel-S (unrelated control children saliva) patients

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Actinomyces

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Experiment 8

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Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies

ChPKU-S (PKU children saliva) patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Children diagnosed with Phenylketonuria (PKU) and who stimulated Saliva samples were gotten from.

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

59

Lab analysis

Statistical Analysis

Alpha Diversity

Pielou Quantifies how equal the community is numerically

unchanged

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

unchanged

Richness Number of species

unchanged

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample

unchanged

Experiment 9

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Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology

Oral cavity Bucca,Buccal cavity,Cavity of mouth,Oral cavity,oral cavity

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Control Saliva (Ctrl-S) patients

Group 1 name Corresponds to the case (exposed) group for case-control studies

Control Subgingival plaque (Ctrl-SP) patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Healthy Controls who stimulated Subgingival plaque samples were gotten from.

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

114

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

113

Lab analysis

Statistical Analysis

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Source: Appendix Table 10 , Figure 2D

Description: Differential abundant genera in Control Saliva (Ctrl-S) and Control Subgingival Plague (Ctrl-SP) patients

Abundance in Group 1: increased abundance in Control Subgingival plaque (Ctrl-SP) patients

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Alloprevotella
Atopobium
Gemella
Haemophilus
Lachnoanaerobaculum
Neisseria
Oribacterium
Peptostreptococcus
Porphyromonas
Prevotella
Rothia
Stomatobaculum
Streptococcus
Veillonella

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Signature 2

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Source: Appendix Table 10 , Figure 2D

Description: Differential abundant genera in Control Saliva (Ctrl-S) and Control Subgingival plague (Ctrl-SP) patients

Abundance in Group 1: decreased abundance in Control Subgingival plaque (Ctrl-SP) patients

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Aggregatibacter
Arachnia
Campylobacter
Capnocytophaga
Cardiobacterium
Corynebacterium
Fusobacterium
Kingella
Leptotrichia
Olsenella
Selenomonas
Tannerella
FO332FO332

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Experiment 10

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Control Adults Saliva (Ctrl-Adults-S) patients

Group 1 name Corresponds to the case (exposed) group for case-control studies

Control Adults Subgingival plaque (Ctrl-Adults-SP) patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Healthy Control adults who stimulated Sub gingival plaque samples were gotten from

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

52

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

52

Lab analysis

Statistical Analysis

Signature 1

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Source: Appendix Table 10 , Figure 2D

Description: Differential abundant genera in Control Adults Saliva (Ctrl-Adults-S) and Control Adults Subgingival plague (Ctrl-Adults-SP) patients

Abundance in Group 1: increased abundance in Control Adults Subgingival plaque (Ctrl-Adults-SP) patients

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Alloprevotella
Atopobium
Gemella
Haemophilus
Neisseria
Oribacterium
Peptostreptococcus
Porphyromonas
Prevotella
Rothia
Stomatobaculum
Streptococcus
Veillonella

Revision editor(s): MyleeeA, Tosin, WikiWorks

Signature 2

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Source: Appendix Table 10 , Figure 2D

Description: Differential abundant genera in Control Adults Saliva (Ctrl-Adults-S) and Control Adults Subgingival plague (Ctrl-Adults-SP) patients.

Abundance in Group 1: decreased abundance in Control Adults Subgingival plaque (Ctrl-Adults-SP) patients

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Aggregatibacter
Arachnia
Campylobacter
Capnocytophaga
Cardiobacterium
Corynebacterium
Fusobacterium
Selenomonas
Tannerella
F0332F0332

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Experiment 11

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Control Children Saliva (Ctrl-Ch-S) patients

Group 1 name Corresponds to the case (exposed) group for case-control studies

Control Children Subgingival plaque (Ctrl-Ch-SP) patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Healthy Control Children without PKU who stimulated Sub gingival plaque samples were gotten from.

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

62

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

61

Lab analysis

Statistical Analysis

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Source: Appendix Table 10, Figure 2D

Description: Differential abundant genera in Control Children Saliva (Ctrl-Ch-S) and Control children Subgingival plague (Ctrl-Ch-SP) patients.

Abundance in Group 1: increased abundance in Control Children Subgingival plaque (Ctrl-Ch-SP) patients

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Alloprevotella
Atopobium
Gemella
Haemophilus
Neisseria
Oribacterium
Peptostreptococcus
Porphyromonas
Prevotella
Rothia
Stomatobaculum
Streptococcus
Veillonella

Revision editor(s): MyleeeA, Tosin, WikiWorks

Signature 2

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Curated date: 2024/08/12

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Source: Appendix Table 10 , Figure 2D

Description: Differential abundant genera in Control Children Saliva (Ctrl-Ch-S) and Control children Subgingival plague (Ctrl-Ch-SP) patients.

Abundance in Group 1: decreased abundance in Control Children Subgingival plaque (Ctrl-Ch-SP) patients

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Aggregatibacter
Arachnia
Campylobacter
Capnocytophaga
Cardiobacterium
Corynebacterium
Fusobacterium
Selenomonas
Tannerella
FO332FO332

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Experiment 12

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Curated date: 2024/07/31

Curator: MyleeeA

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Phenylketonuria Saliva (PKU-S) patients

Group 1 name Corresponds to the case (exposed) group for case-control studies

Phenylketonuria Subgingival plaque (PKU-SP) patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Patients diagnosed with Phenylketonuria (PKU) and who stimulated Sub gingival plaque samples were gotten from.

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

109

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

96

Lab analysis

Statistical Analysis

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

Not specified

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Source: Appendix Table 10 , Figure 2D

Description: Differential abundant genera in PKU Saliva (PKU-S) and PKU Subgingival plague (PKU-SP) Patient s

Abundance in Group 1: increased abundance in Phenylketonuria Subgingival plaque (PKU-SP) patients

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Alloprevotella
Atopobium
Gemella
Haemophilus
Lachnoanaerobaculum
Neisseria
Oribacterium
Peptostreptococcus
Porphyromonas
Prevotella
Rothia
Stomatobaculum
Streptococcus
Veillonella

Revision editor(s): MyleeeA, Tosin, WikiWorks

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Source: Appendix Table 10 , Figure 2D

Description: Differneti abundant genera in PKU Saliva (PKU-S) and PKU Subgingival plague (PKU-SP) Patients.

Abundance in Group 1: decreased abundance in Phenylketonuria Subgingival plaque (PKU-SP) patients

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Actinomyces
Arachnia
Campylobacter
Capnocytophaga
Cardiobacterium
Corynebacterium
Fretibacterium
Fusobacterium
Kingella
Olsenella
Peptococcus
Selenomonas
Tannerella
FO332FO332

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Experiment 13

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Curated date: 2024/07/31

Curator: MyleeeA

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Phenylketonuria Adults Saliva (PKU-Adults-S)

Group 1 name Corresponds to the case (exposed) group for case-control studies

Phenylketonuria Adults Subgingival plaque (PKU-Adults-SP)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Adult Patients diagnosed with Phenylketonuria (PKU) and who stimulated Subgingival plaque samples were gotten from.

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

50

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

45

Lab analysis

Statistical Analysis

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Source: Appendix Table 10 , Figure 2D

Description: Differential abundant genera in PKU Adults Saliva (PKU-Adults-S) and PKU Subgingival plague (PKU-Adults-SP) patients.

Abundance in Group 1: increased abundance in Phenylketonuria Adults Subgingival plaque (PKU-Adults-SP)

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Alloprevotella
Atopobium
Gemella
Haemophilus
Lachnoanaerobaculum
Oribacterium
Peptostreptococcus
Prevotella
Rothia
Stomatobaculum
Streptococcus
Veillonella

Revision editor(s): MyleeeA, Tosin, WikiWorks

Signature 2

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Source: Appendix Table 10, Figure 2D

Description: Differential abundant genera in PKU Adults Saliva (PKU-Adults-S) and PKU Subgingival plague (PKU-Adults-SP) patients.

Abundance in Group 1: decreased abundance in Phenylketonuria Adults Subgingival plaque (PKU-Adults-SP)

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Actinomyces
Arachnia
Campylobacter
Capnocytophaga
Cardiobacterium
Corynebacterium
Fusobacterium
Olsenella
Selenomonas
Tannerella
FO332FO332

Revision editor(s): MyleeeA, Tosin, WikiWorks

Experiment 14

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Curated date: 2024/07/31

Curator: MyleeeA

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Phenylketonuria Children Saliva (PKU-Ch-S) patients

Group 1 name Corresponds to the case (exposed) group for case-control studies

Phenylketonuria Children subgingival plaque (PKU-Ch-SP) patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Children diagnosed with Phenylketonuria (PKU) and who stimulated Subgingival plaque samples were gotten from.

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

59

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

51

Lab analysis

Statistical Analysis

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Source: Appendix Table 10 , Figure 2D

Description: Differential abundant genera in PKU children Saliva (PKU-Ch-S) and PKU Children Subgingival plague (PKU-Ch-SP) patients

Abundance in Group 1: increased abundance in Phenylketonuria Children subgingival plaque (PKU-Ch-SP) patients

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Alloprevotella
Atopobium
Gemella
Haemophilus
Lachnoanaerobaculum
Neisseria
Oribacterium
Porphyromonas
Prevotella
Rothia
Streptococcus
Veillonella

Revision editor(s): MyleeeA, Tosin, WikiWorks

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Source: Appendix Table 10 , Figure 2D

Description: Differential abundant genera in PKU children Saliva (PKU-Ch-S) and PKU Children Subgingival plague (PKU-Ch-SP) patients

Abundance in Group 1: decreased abundance in Phenylketonuria Children subgingival plaque (PKU-Ch-SP) patients

NCBI	Quality Control	Links
Actinomyces
Arachnia
Campylobacter
Capnocytophaga
Cardiobacterium
Corynebacterium
Fretibacterium
Fusobacterium
Kingella
Olsenella
Selenomonas
Tannerella
FO332FO332

Revision editor(s): MyleeeA, Tosin, WikiWorks

Experiment 15

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Curated date: 2024/07/31

Curator: MyleeeA

Revision editor(s): WikiWorks, Tosin, MyleeeA

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology

Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Control No period (CTRL-S)

Group 1 name Corresponds to the case (exposed) group for case-control studies

Phenylketonuria No Period (PKU-S)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Patients diagnosed with Phenylketonuria (PKU) without suspected Periodontitis and who stimulated Saliva samples were gotten from.

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

Not specified

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

Not specified

Lab analysis

Statistical Analysis

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

age

Alpha Diversity

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample

decreased

Experiment 16

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Control Period (CTRL-S)

Group 1 name Corresponds to the case (exposed) group for case-control studies

Phenylketonuria Period (PKU-S)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Patients diagnosed with Phenylketonuria (PKU) with suspected Periodontitis and who stimulated Saliva samples were gotten from.

Lab analysis

Statistical Analysis

Alpha Diversity

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample

unchanged

Experiment 17

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Phenylketonuria No Period (PKU-S)

Lab analysis

Statistical Analysis

Alpha Diversity

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample

increased

Experiment 18

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Curated date: 2025/01/14

Curator: Tosin

Revision editor(s): Tosin, WikiWorks

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

CtrlRel-S (control related saliva)

Group 1 name Corresponds to the case (exposed) group for case-control studies

PKU-Rel-S (Phenylketonuria related saliva) patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Controls related to Phenylketonuria (PKU) patients who stimulated saliva samples were gotten from.

Lab analysis

Statistical Analysis

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Source: Appendix Table 4

Description: Differential abundant phylum between Ctrl-Rel-S (Control related saliva) patients and PKU-Rel-S (Phenylketonuria related saliva) patients

Abundance in Group 1: increased abundance in PKU-Rel-S (Phenylketonuria related saliva) patients

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Campylobacterota
Patescibacteria group
Spirochaetota

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Source: Appendix Table 4

Description: Differential abundant phylum between Ctrl-Rel-S (Control related saliva) patients and PKU-Rel-S (Phenylketonuria related saliva) patients.

Abundance in Group 1: decreased abundance in PKU-Rel-S (Phenylketonuria related saliva) patients

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Actinomycetota
Other_phylaOther_phyla

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Experiment 19

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Curated date: 2025/01/14

Curator: Tosin

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

CtrlRel-SP (control related subgingival plaque) patients

Group 1 name Corresponds to the case (exposed) group for case-control studies

PKU-Rel-SP (Phenylketonuria related subgingival plaque) patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Controls related to Phenylketonuria (PKU) patients who stimulated subgingival plaque samples were gotten from.

Lab analysis

Statistical Analysis

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Source: Appendix Table 4

Description: Differential abundant phylum between Ctrl-Rel-SP (Control related subgingival plaque) patients and PKU-Rel-SP (Phenylketonuria related subgingival plaque) patients.

Abundance in Group 1: increased abundance in PKU-Rel-SP (Phenylketonuria related subgingival plaque) patients

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Actinomycetota

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Source: Appendix Table 4

Description: Differential abundant phylum between Ctrl-Rel-SP (Control related subgingival plaque) patients and PKU-Rel-SP (Phenylketonuria related subgingival plaque) patients.

Abundance in Group 1: decreased abundance in PKU-Rel-SP (Phenylketonuria related subgingival plaque) patients

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Bacteroidota
Fusobacteriota

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