Alterations in Oral Microbiota in HIV Are Related to Decreased Pulmonary Function/Experiment 3
From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/30
Curated date: 2021/12/16
Curator: Joyessa
Revision editor(s): WikiWorks, LGeistlinger, 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
- Abnormality on pulmonary function testing Abnormal pulmonary function test,Abnormal spirometry test,Abnormality on pulmonary function testing,abnormality on pulmonary function testing
- 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
- 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 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
Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/30
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
