Alterations in Oral Microbiota in HIV Are Related to Decreased Pulmonary Function
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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
- Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Human immunodeficiency virus AIDS virus,HIV,Human immunodeficiency virus
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HIV-uninfected individuals
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HIV+ individuals
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- People with HIV
- Group 0 sample size Number of subjects in the control (unexposed) group
- 93
- Group 1 sample size Number of subjects in the case (exposed) group
- 75
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 5 days
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- 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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2.0
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Figure 1 D
Description: Differential abundance in saliva of HIV- individuals vs HIV+ individuals
Abundance in Group 1: decreased abundance in HIV+ individuals
Revision editor(s): Joyessa, Claregrieve1
Signature 2
Source: Figure 1 D
Description: Differential microbial abundance in saliva of HIV- individuals vs HIV+ individuals
Abundance in Group 1: increased abundance in HIV+ individuals
NCBI | Quality Control | Links |
---|---|---|
Bifidobacterium | ||
Lactobacillus | ||
Rothia | ||
Streptococcus | ||
Veillonella |
Revision editor(s): Joyessa, Claregrieve1
Experiment 2
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- nicotine dependence , smoking behavior cigarette habituation, susceptibility to,Cigarette Smoking,Dependence, Nicotine,Dependence, Tobacco,Disorder, Nicotine Use,Disorder, Tobacco Use,Disorder, Tobacco-Use,Nicotine Addiction,nicotine addiction,nicotine addiction, susceptibility to,nicotine dependence,nicotine dependence, susceptibility to,NICOTINE USE DIS,Nicotine Use Disorder,Nicotine Use Disorders,smoking,smoking habit, susceptibility to,Smoking, Cigarette,Smoking, Tobacco,Smokings, Tobacco,susceptibility to tobacco addiction,tobacco addiction, susceptibility to,Tobacco Dependence,Tobacco Dependences,Tobacco Smoking,Tobacco Smokings,TOBACCO USE DIS,Tobacco Use Disorder,tobacco use disorder,Tobacco Use Disorders,Tobacco-Use Disorder,Use Disorder, Nicotine,smoking behavior
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HIV+ non-smokers
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HIV+ smokers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- People with HIV who currently smoke cigarettes
- Group 0 sample size Number of subjects in the control (unexposed) group
- 26
- Group 1 sample size Number of subjects in the case (exposed) group
- 23
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Figure 2E
Description: Differential bacterial abundance in oral samples from HIV+ individuals by smoking status
Abundance in Group 1: decreased abundance in HIV+ smokers
NCBI | Quality Control | Links |
---|---|---|
Alloprevotella | ||
Bergeyella | ||
Campylobacter | ||
Fusobacterium | ||
Johnsonella | ||
Neisseria | ||
Prevotella | ||
unclassified Neisseriaceae | ||
unclassified Pasteurellaceae |
Revision editor(s): Joyessa, Claregrieve1
Signature 2
Source: Figure 2E
Description: Differential bacterial abundance in oral samples from HIV+ individuals by smoking status
Abundance in Group 1: increased abundance in HIV+ smokers
NCBI | Quality Control | Links |
---|---|---|
Atopobium | ||
Bifidobacterium | ||
Lactobacillus | ||
Streptococcus | ||
Veillonella |
Revision editor(s): Joyessa, Claregrieve1
Experiment 3
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- lung functionlung function
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HIV+ patients with normal DLCO
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HIV+ patients with reduced DLCO
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- HIV+ patients with DLCO% predicted <80%
- Group 0 sample size Number of subjects in the control (unexposed) group
- 38
- Group 1 sample size Number of subjects in the case (exposed) group
- 37
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Figure 3 I
Description: Differential microbial abundance between reduced DLCO HIV+ patients and normal DLCO HIV+ patients
Abundance in Group 1: increased abundance in HIV+ patients with reduced DLCO
NCBI | Quality Control | Links |
---|---|---|
Lactobacillus | ||
Streptococcus | ||
Veillonella |
Revision editor(s): Joyessa, Claregrieve1
Signature 2
Source: Figure 3I
Description: Differential microbial abundance between reduced DLCO HIV+ patients and normal DLCO HIV+ patients
Abundance in Group 1: decreased abundance in HIV+ patients with reduced DLCO
Revision editor(s): Joyessa, Claregrieve1, Merit