Alterations in Oral Microbiota in HIV Are Related to Decreased Pulmonary Function/Experiment 2
From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/30
Curated date: 2021/12/15
Curator: Joyessa
Revision editor(s): WikiWorks, Claregrieve1, Joyessa, Victoria
Subjects
- Location of subjects
- United States of America
- 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
- 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,Nicotine dependence,Smoking behavior,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
- 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
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/30
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
Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/30
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
