Sputum bacterial load and bacterial composition correlate with lung function and are altered by long-term azithromycin treatment in children with HIV-associated chronic lung disease
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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
- 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
- Sputum Expectoration,Sputum
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- azithromycin (2R,3S,4R,5R,8R,10R,11R,12S,13S,14R)-2-ethyl-3,4,10-trihydroxy-3,5,6,8,10,12,14-heptamethyl-15-oxo-11-,10q24.1-q25.1,aritromicina,Azenil,Azifast,Azigram,Azimakrol,azithromycine,azithromycinum,Azitromin,AZM,Hemomycin,InChIKey=MQTOSJVFKKJCRP-BICOPXKEBK,Zithromax,Zmax,azithromycin
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- placebo
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- azithromycin(AZM)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants with HIV-associated Chronic Lung Disease (HCLD) who received azithromycin (AZM)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 174
- Group 1 sample size Number of subjects in the case (exposed) group
- 173
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).
- centered log-ratio
- Statistical test
- ANCOM
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Curated date: 2023/10/11
Curator: Chinelsy
Revision editor(s): Chinelsy, Peace Sandy, ChiomaBlessing
Source: Fig.5
Description: Analysis of composition of microbiomes (ANCOM2) differential abundance testing for samples at each visit and between trial arms Taxa identified as differentially abundant between trial arms at 48 weeks (A, left panel)
Abundance in Group 1: increased abundance in azithromycin(AZM)
NCBI | Quality Control | Links |
---|---|---|
Actinomyces | ||
Lautropia | ||
Peptococcus | ||
Rothia | ||
Streptobacillus | ||
Treponema | ||
Veillonella | ||
Clostridia | ||
Lachnospiraceae |
Revision editor(s): Chinelsy, Peace Sandy, ChiomaBlessing
Signature 2
Source: Fig.5
Description: Analysis of composition of microbiomes (ANCOM2) differential abundance testing for samples at each visit and between trial arms Taxa identified as differentially abundant between trial arms at 48 weeks (A, left panel)
Abundance in Group 1: decreased abundance in azithromycin(AZM)
NCBI | Quality Control | Links |
---|---|---|
Aggregatibacter | ||
Oribacterium | ||
Moraxella | ||
Haemophilus |
Revision editor(s): Chinelsy
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Participants on azithromycin at baseline (prior to treatment)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Participants on azithromycin at 48 weeks of treatment
- Group 0 sample size Number of subjects in the control (unexposed) group
- 164
- Group 1 sample size Number of subjects in the case (exposed) group
- 154
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Fig.5
Description: Analysis of composition of microbiomes (ANCOM2) differential abundance testing for samples at each visit and between trial arms. Taxa identified as differentially abundant between AZM arm at baseline and 48 weeks (A, middle panel).
Abundance in Group 1: increased abundance in Participants on azithromycin at 48 weeks of treatment
NCBI | Quality Control | Links |
---|---|---|
Lautropia | ||
Peptococcus | ||
Rothia | ||
Streptobacillus | ||
Treponema | ||
Veillonella | ||
Clostridia | ||
Lachnospiraceae | ||
Candidatus Absconditabacteria |
Revision editor(s): Chinelsy, Peace Sandy, Davvve
Signature 2
Source: Fig.5
Description: Analysis of composition of microbiomes (ANCOM2) differential abundance testing for samples at each visit and between trial arms. Taxa identified as differentially abundant between AZM arm at baseline and 48 weeks (A, middle panel).
Abundance in Group 1: decreased abundance in Participants on azithromycin at 48 weeks of treatment
NCBI | Quality Control | Links |
---|---|---|
Aggregatibacter | ||
Haemophilus | ||
Moraxella | ||
Oribacterium | ||
F0058 (Paludibacteria)F0058 (Paludibacteria) |
Revision editor(s): Chinelsy
Experiment 3
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Participants on azithromycin at 72 weeks (24 weeks post treatment)
- Group 1 sample size Number of subjects in the case (exposed) group
- 123
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Fig.5
Description: Analysis of composition of microbiomes (ANCOM2) differential abundance testing for samples at each visit and between trial arms. Taxa identified as differentially abundant between AZM arm at baseline and 72 weeks (A, right panel).
Abundance in Group 1: increased abundance in Participants on azithromycin at 72 weeks (24 weeks post treatment)
Revision editor(s): Chinelsy, Peace Sandy
Signature 2
Source: Fig.5
Description: Analysis of composition of microbiomes (ANCOM2) differential abundance testing for samples at each visit and between trial arms. Taxa identified as differentially abundant between AZM arm at baseline and 72 weeks (A, right panel).
Abundance in Group 1: decreased abundance in Participants on azithromycin at 72 weeks (24 weeks post treatment)
NCBI | Quality Control | Links |
---|---|---|
Aggregatibacter | ||
Haemophilus | ||
Moraxella | ||
Streptobacillus | ||
Veillonella | ||
Clostridia | ||
Lachnospiraceae |