Oral and Gut Microbial Diversity and Immune Regulation in Patients with HIV on Antiretroviral Therapy
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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
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- HIV infection [X]Human immunodeficiency virus disease,[X]Human immunodeficiency virus disease (disorder),[X]Unspecified human immunodeficiency virus [HIV] disease,[X]Unspecified human immunodeficiency virus [HIV] disease (disorder),HIV - Human immunodeficiency virus infection,HIV INFECT,HIV Infection,HIV infection,HIV Infections,HIV infectious disease,HTLV III INFECT,HTLV III Infections,HTLV III LAV INFECT,HTLV III LAV Infections,HTLV WIII INFECTIONS,HTLV WIII LAV INFECTIONS,HTLV-III Infection,HTLV-III Infections,HTLV-III-LAV Infection,HTLV-III-LAV Infections,HUMAN IMMUNO VIRUS DIS,human immunodeficiency virus,Human immunodeficiency virus [HIV] disease,HUMAN IMMUNOdeficiency VIRUS [HIV] INFECTION,Human immunodeficiency virus caused disease or disorder,Human immunodeficiency virus disease,Human immunodeficiency virus disease (disorder),Human immunodeficiency virus disease or disorder,Human immunodeficiency virus infection,Human immunodeficiency virus infection (disorder),Human immunodeficiency virus infection, NOS,Human immunodeficiency virus infectious disease,human immunodeficiency virus infectious disease,Infection, HIV,Infection, HTLV-III,Infection, HTLV-III-LAV,Infections, HIV,Infections, HTLV-III,Infections, HTLV-III-LAV,LYMPHOTROPIC VIRUS TYPE III INFECTIONS HUMAN T,T LYMPHOTROPIC VIRUS TYPE III INFECT HUMAN,T Lymphotropic Virus Type III Infections, Human,T-Lymphotropic Virus Type III Infections, Human,Unspecified human immunodeficiency virus [HIV] disease (disorder)
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- PLWH >50 years old with no/mild periodontitis
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- PLWH >50 years old with severe periodontitis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Periodontal disease severity categories as defined by the Centers for Disease Control and Prevention (CDC) and the American Academy of Periodontology (AAP)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 4
- Group 1 sample size Number of subjects in the case (exposed) group
- 22
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- 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
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- .05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, race, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Table S6 Supplemental Text
Description: Relative Abundance between severe and no/mild periodontal disease
Abundance in Group 1: increased abundance in PLWH >50 years old with severe periodontitis
NCBI | Quality Control | Links |
---|---|---|
Candida albicans | ||
Candida parapsilosis | ||
Filobasidiales |
Revision editor(s): Jacquelynshevin
Signature 2
Source: Table S6 Supplemental Text
Description: Relative Abundance between severe and no/mild periodontal disease
Abundance in Group 1: decreased abundance in PLWH >50 years old with severe periodontitis
NCBI | Quality Control | Links |
---|---|---|
Candida dubliniensis | ||
Exserohilum turcicum | ||
Tausonia pullulans | ||
Debaryomyces hansenii |
Revision editor(s): Jacquelynshevin
Signature 3
Source: Table S5 Supplemental Text
Description: Relative Abundance between severe and no/mild periodontal disease
Abundance in Group 1: increased abundance in PLWH >50 years old with severe periodontitis
NCBI | Quality Control | Links |
---|---|---|
Fusobacterium | ||
Kingella | ||
Prevotella | ||
Prevotella melaninogenica | ||
Rothia dentocariosa | ||
Rothia mucilaginosa | ||
Streptococcus | ||
Veillonella | ||
Veillonella dispar |
Revision editor(s): Jacquelynshevin
Signature 4
Source: Table S5 Supplemental Text
Description: Relative Abundance between severe and no/mild periodontal disease
Abundance in Group 1: decreased abundance in PLWH >50 years old with severe periodontitis
NCBI | Quality Control | Links |
---|---|---|
Megasphaera | ||
Veillonella dispar |
Revision editor(s): Jacquelynshevin
Signature 5
Source: Table S8 Supplemental Text
Description: Relative Abundance between severe and no/mild periodontal disease
Abundance in Group 1: increased abundance in PLWH >50 years old with severe periodontitis
NCBI | Quality Control | Links |
---|---|---|
Streptococcus |
Revision editor(s): Jacquelynshevin
Signature 6
Source: Table S8 Supplemental Text
Description: Relative Abundance between severe and no/mild periodontal disease
Abundance in Group 1: decreased abundance in PLWH >50 years old with severe periodontitis
NCBI | Quality Control | Links |
---|---|---|
Rothia mucilaginosa | ||
Neisseria |
Revision editor(s): Jacquelynshevin