Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study
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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
- 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 (CTRL-S)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Phenylketonuria (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) 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
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- N/A
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
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
Signature 1
Source: Figure 2(D)
Description: Differential abundant genera in Phenylketonuria (PKU) and Control Saliva Patients.
Abundance in Group 1: increased abundance in Phenylketonuria (PKU-S)
| NCBI | Quality Control | Links |
|---|---|---|
| Campylobacter | ||
| Haemophilus | ||
| Lachnoanaerobaculum | ||
| Veillonella |
Revision editor(s): MyleeeA
Signature 2
Source: Figure 2(D)
Description: Differential abundant genera in Phenylketonuria (PKU) and Control Saliva Patients.
Abundance in Group 1: decreased abundance in Phenylketonuria (PKU-S)
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Arachnia | ||
| Cardiobacterium | ||
| Catonella | ||
| Fretibacterium | ||
| Olsenella | ||
| Peptococcus | ||
| Peptostreptococcus | ||
| Stomatobaculum | ||
| FO332FO332 |
Revision editor(s): MyleeeA
Experiment 2
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
- Controls (CTRL-SP)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Phenylketonuria (PKU-SP)
- 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
Signature 1
Source: Figure 2(D)
Description: Differential abundant genera in Phenylketonuria (PKU) and Control Subgingival Patients.
Abundance in Group 1: increased abundance in Phenylketonuria (PKU-SP)
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Fretibacterium |
Revision editor(s): MyleeeA
Signature 2
Source: Figure 2(D)
Description: Differential abundant genera in Phenylketonuria (PKU) and Control Subgingival Patients.
Abundance in Group 1: decreased abundance in Phenylketonuria (PKU-SP)
| NCBI | Quality Control | Links |
|---|---|---|
| Aggregatibacter | ||
| Capnocytophaga | ||
| Gemella | ||
| Leptotrichia | ||
| Peptostreptococcus |
Revision editor(s): MyleeeA
Experiment 3
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 (CTRL-S)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Phenylketonuria (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) 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
Signature 1
Source: Figure 2(D)
Description: Differential abundant genera in Phenylketonuria (PKU) and Control Saliva Adult Patients.
Abundance in Group 1: increased abundance in Phenylketonuria (PKU-S)
| NCBI | Quality Control | Links |
|---|---|---|
| Campylobacter | ||
| Capnocytophaga | ||
| Kingella |
Revision editor(s): MyleeeA
Signature 2
Source: Figure 2(D)
Description: Differential abundant genera in Phenylketonuria (PKU) and Control Saliva Adult Patients.
Abundance in Group 1: decreased abundance in Phenylketonuria (PKU-S)
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Arachnia | ||
| Catonella | ||
| Fretibacterium | ||
| Peptococcus | ||
| Stomatobaculum | ||
| FO332FO332 |
Revision editor(s): MyleeeA
Experiment 4
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 (CTRL-SP)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Phenylketonuria (PKU-SP)
- 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 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
Source: Figure 2(D)
Description: Differential abundant genera in Phenylketonuria (PKU) and Control Subgingival plaque Adults Patients
Abundance in Group 1: increased abundance in Phenylketonuria (PKU-SP)
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Fretibacterium | ||
| Kingella |
Revision editor(s): MyleeeA
Signature 2
Source: Figure 2(D)
Description: Differential abundant genera in Phenylketonuria (PKU) and Control Subgingival plaque Adults Patients
Abundance in Group 1: decreased abundance in Phenylketonuria (PKU-SP)
| NCBI | Quality Control | Links |
|---|---|---|
| Gemella | ||
| Peptostreptococcus | ||
| Stomatobaculum |
Revision editor(s): MyleeeA
Experiment 5
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 (CTRL-S)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Phenylketonuria (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) 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
Source: Figure 2(D)
Description: Differential abundant genera in Phenylketonuria (PKU) Children and Control Children Saliva Patients
Abundance in Group 1: increased abundance in Phenylketonuria (PKU-S)
| NCBI | Quality Control | Links |
|---|---|---|
| Haemophilus | ||
| Lachnoanaerobaculum | ||
| Oribacterium |
Revision editor(s): MyleeeA
Signature 2
Source: Figure 2(D)
Description: Differential abundant genera in Phenylketonuria (PKU) Children and Control Children Saliva Patients
Abundance in Group 1: decreased abundance in Phenylketonuria (PKU-S)
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Arachnia | ||
| Fretibacterium | ||
| Olsenella | ||
| Peptococcus | ||
| Stomatobaculum | ||
| Tannerella | ||
| FO332FO332 |
Revision editor(s): MyleeeA
Experiment 6
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 (CTRL-SP)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Phenylketonuria (PKU-SP)
- 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
- 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
Source: Figure 2(D)
Description: Differential abundant genera in Phenylketonuria (PKU) Children and Control Children Subgingival plague Patients
Abundance in Group 1: increased abundance in Phenylketonuria (PKU-SP)
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Atopobium | ||
| Fretibacterium | ||
| Kingella | ||
| Olsenella | ||
| Oribacterium | ||
| Selenomonas | ||
| Stomatobaculum |
Revision editor(s): MyleeeA
Signature 2
Source: Figure 2(D)
Description: Differential abundant genera in Phenylketonuria PKU Children and Control Children Subgingival plague Patients
Abundance in Group 1: decreased abundance in Phenylketonuria (PKU-SP)
| NCBI | Quality Control | Links |
|---|---|---|
| Aggregatibacter | ||
| Capnocytophaga | ||
| Gemella | ||
| Leptotrichia | ||
| Peptostreptococcus |
Revision editor(s): MyleeeA
Experiment 7
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
- Ch-CTRL-rel (Healthy siblings of PKU patients)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Ch-CTRL-unrel (unrelated control children)
- 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
- unchanged
- Richness Number of species
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Source: Figure 2(D)
Description: Differential abundant genera in Ch-CTRL-related and Ch-CTRL-unrelated to Phenylketonuria Patients.
Abundance in Group 1: increased abundance in Ch-CTRL-unrel (unrelated control children)
| NCBI | Quality Control | Links |
|---|---|---|
| Haemophilus | ||
| Lachnoanaerobaculum | ||
| Oribacterium |
Revision editor(s): MyleeeA
Signature 2
Source: Figure 2(D)
Description: Differential abundant genera in Ch-CTRL-related and Ch-CTRL-unrelated to Phenylketonuria Patients.
Abundance in Group 1: decreased abundance in Ch-CTRL-unrel (unrelated control children)
| NCBI | Quality Control | Links |
|---|---|---|
| Fretibacterium | ||
| Arachnia | ||
| FO332FO332 | ||
| Actinomyces | ||
| Atopobium | ||
| Lautropia | ||
| Peptostreptococcus |
Revision editor(s): MyleeeA
Experiment 8
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Ch CTRL rel (Healthy siblings of PKU patients)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Ch PKU (PKU children)
- 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
Signature 1
Source: Figure 2(D)
Description: Differential abundant genera in Ch-CTRL-related and Phenylketonuria (PKU-Ch) Saliva Patients.
Abundance in Group 1: increased abundance in Ch PKU (PKU children)
| NCBI | Quality Control | Links |
|---|---|---|
| Capnocytophaga | ||
| Peptostreptococcus | ||
| Peptococcus | ||
| Leptotrichia | ||
| Lachnoanaerobaculum | ||
| Porphyromonas | ||
| Aggregatibacter |
Revision editor(s): MyleeeA
Signature 2
Source: Figure 2(D)
Description: Differential abundant genera in Ch-CTRL-related and Phenylketonuria (PKU-Ch) Saliva Patients.
Abundance in Group 1: decreased abundance in Ch PKU (PKU children)
| NCBI | Quality Control | Links |
|---|---|---|
| Olsenella | ||
| Selenomonas | ||
| Atopobium | ||
| Actinomyces | ||
| FO332FO332 | ||
| Fretibacterium |
Revision editor(s): MyleeeA
Experiment 9
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Mouth Adult mouth,Cavital oralis,Cavitas oris,Cavum oris,Mouth cavity,Oral region,Oral vestibule,Regio oralis,Rima oris,Stoma,Stomatodaeum,Trophic apparatus,Vestibule of mouth,Vestibulum oris,Mouth,mouth
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control (CTRL-S)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Control (CTRL-SP)
- 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
Signature 1
Source: Figure 2(D)
Description: Differential abundant genera in Control Saliva and Control Subgingival Plague samples
Abundance in Group 1: increased abundance in Control (CTRL-SP)
| NCBI | Quality Control | Links |
|---|---|---|
| Veillonella | ||
| Streptococcus | ||
| Stomatobaculum | ||
| Peptostreptococcus | ||
| Haemophilus | ||
| Gemella | ||
| Atopobium | ||
| Alloprevotella | ||
| Neisseria | ||
| Porphyromonas | ||
| Oribacterium | ||
| Prevotella |
Revision editor(s): MyleeeA
Signature 2
Source: Figure 2(D)
Description: Differential abundant genera in Control Saliva and Control Subgingival plague
Abundance in Group 1: decreased abundance in Control (CTRL-SP)
| NCBI | Quality Control | Links |
|---|---|---|
| Aggregatibacter | ||
| Arachnia | ||
| Campylobacter | ||
| Capnocytophaga | ||
| Cardiobacterium | ||
| Corynebacterium | ||
| Fusobacterium | ||
| Kingella | ||
| Leptotrichia | ||
| Olsenella | ||
| Selenomonas | ||
| Tannerella | ||
| FO332FO332 |
Revision editor(s): MyleeeA
Experiment 10
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control Adults (CTRL-S)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Control Adults (CTRL-SP)
- 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
Source: Figure 2(D)
Description: Differential abundant genera in Control Saliva and Control Subgingival plague Adult samples
Abundance in Group 1: increased abundance in Control Adults (CTRL-SP)
| NCBI | Quality Control | Links |
|---|---|---|
| Veillonella | ||
| Streptococcus | ||
| Stomatobaculum | ||
| Peptostreptococcus | ||
| Haemophilus | ||
| Gemella | ||
| Atopobium | ||
| Alloprevotella | ||
| Neisseria | ||
| Porphyromonas | ||
| Oribacterium | ||
| Prevotella |
Revision editor(s): MyleeeA
Signature 2
Source: Figure 2(D)
Description: Differential abundant genera in Control Saliva and Control Subgingival plague Adult samples
Abundance in Group 1: decreased abundance in Control Adults (CTRL-SP)
| NCBI | Quality Control | Links |
|---|---|---|
| Aggregatibacter | ||
| Arachnia | ||
| Campylobacter | ||
| Capnocytophaga | ||
| Cardiobacterium | ||
| Corynebacterium | ||
| Fusobacterium | ||
| Kingella | ||
| Olsenella | ||
| Selenomonas | ||
| Tannerella | ||
| FO332FO332 |
Revision editor(s): MyleeeA
Experiment 11
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control Children (CTRL Ch-S)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Control Children (CTRL Ch-SP)
- 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
Signature 1
Source: Figure 2(D)
Description: Differential abundant genera in Control Saliva and Control Subgingival plague Children samples
Abundance in Group 1: increased abundance in Control Children (CTRL Ch-SP)
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella | ||
| Oribacterium | ||
| Porphyromonas | ||
| Neisseria | ||
| Alloprevotella | ||
| Atopobium | ||
| Gemella | ||
| Haemophilus | ||
| Peptostreptococcus | ||
| Stomatobaculum | ||
| Streptococcus | ||
| Veillonella |
Revision editor(s): MyleeeA
Signature 2
Source: Figure 2(D)
Description: Differential abundant genera in Control Saliva and Control Subgingival plague Children samples
Abundance in Group 1: decreased abundance in Control Children (CTRL Ch-SP)
| NCBI | Quality Control | Links |
|---|---|---|
| Capnocytophaga | ||
| Fusobacterium | ||
| Corynebacterium | ||
| Kingella | ||
| FO332FO332 | ||
| Arachnia | ||
| Cardiobacterium | ||
| Olsenella | ||
| Tannerella | ||
| Campylobacter | ||
| Fretibacterium |
Revision editor(s): MyleeeA
Experiment 12
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Phenylketonuria (PKU-S)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Phenylketonuria (PKU-SP)
- 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
Signature 1
Source: Figure 2(D)
Description: Differential abundant genera in PKU Saliva and PKU Subgingival plague Patient samples
Abundance in Group 1: increased abundance in Phenylketonuria (PKU-SP)
Revision editor(s): MyleeeA
Signature 2
Source: Figure 2(D)
Description: Differential abundant genera in PKU Saliva and PKU Subgingival plague Patients samples
Abundance in Group 1: decreased abundance in Phenylketonuria (PKU-SP)
Revision editor(s): MyleeeA
Experiment 13
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Phenylketonuria Adults (PKU-S)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Phenylketonuria Adults (PKU-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
Signature 1
Source: Figure 2(D)
Description: Differential abundant genera in PKU Saliva and PKU Subgingival plague Adult samples
Abundance in Group 1: increased abundance in Phenylketonuria Adults (PKU-SP)
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella | ||
| Rothia | ||
| Lachnoanaerobaculum | ||
| Alloprevotella | ||
| Atopobium | ||
| Gemella | ||
| Haemophilus | ||
| Stomatobaculum | ||
| Streptococcus | ||
| Veillonella |
Revision editor(s): MyleeeA
Signature 2
Source: Figure 2(D)
Description: Differential abundant genera in PKU Saliva and PKU Subgingival plague Adult samples
Abundance in Group 1: decreased abundance in Phenylketonuria Adults (PKU-SP)
| NCBI | Quality Control | Links |
|---|---|---|
| Campylobacter | ||
| Peptococcus | ||
| Olsenella | ||
| Cardiobacterium | ||
| Actinomyces | ||
| Selenomonas | ||
| FO332FO332 | ||
| Arachnia | ||
| Fretibacterium | ||
| Corynebacterium | ||
| Fusobacterium | ||
| Capnocytophaga |
Revision editor(s): MyleeeA
Experiment 14
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Phenylketonuria Ch (PKU-S)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Phenylketonuria Ch (PKU-SP)
- 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
Signature 1
Source: Figure 2(D)
Description: Differential abundant genera in PKU Saliva and PKU Subgingival plague Children samples
Abundance in Group 1: increased abundance in Phenylketonuria Ch (PKU-SP)
| NCBI | Quality Control | Links |
|---|---|---|
| Alloprevotella | ||
| Atopobium | ||
| Gemella | ||
| Haemophilus | ||
| Lachnoanaerobaculum | ||
| Neisseria | ||
| Peptostreptococcus | ||
| Porphyromonas | ||
| Prevotella | ||
| Streptococcus | ||
| Veillonella |
Revision editor(s): MyleeeA
Signature 2
Source: Figure 2(D)
Description: Differential abundant genera in PKU Saliva and PKU Subgingival plague Adult samples
Abundance in Group 1: decreased abundance in Phenylketonuria Ch (PKU-SP)
| NCBI | Quality Control | Links |
|---|---|---|
| Campylobacter | ||
| Tannerella | ||
| Peptococcus | ||
| Olsenella | ||
| Cardiobacterium | ||
| Actinomyces | ||
| Selenomonas | ||
| FO332FO332 | ||
| Kingella | ||
| Fretibacterium | ||
| Corynebacterium | ||
| Fusobacterium | ||
| Capnocytophaga | ||
| Arachnia |
Revision editor(s): MyleeeA
Experiment 15
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
Alpha Diversity
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Experiment 16
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Mouth Adult mouth,Cavital oralis,Cavitas oris,Cavum oris,Mouth cavity,Oral region,Oral vestibule,Regio oralis,Rima oris,Stoma,Stomatodaeum,Trophic apparatus,Vestibule of mouth,Vestibulum oris,Mouth,mouth
- 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
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
