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/Experiment 1

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-24

Curated date: 2023/10/11

Curator: Chinelsy

Revision editor(s): Chinelsy, Peace Sandy

Subjects

Location of subjects: Malawi; Zimbabwe

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,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,azithromycin

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Placebo at 48 Weeks

Group 1 name Corresponds to the case (exposed) group for case-control studies: Azithromycin(AZM) at 48 weeks

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: 150

Group 1 sample size Number of subjects in the case (exposed) group: 154

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): NIL

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: unchanged

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Reviewed Marked as Reviewed by Peace Sandy on 2024-2-24

Curated date: 2023/10/11

Curator: Chinelsy

Revision editor(s): Chinelsy, Peace Sandy, ChiomaBlessing

Source: Figure S 24

Description: Heatmap displaying the q values of the genera detected as differentially abundant between AZM and placebo arms at 48 weeks by 10 statistical methods. For ANCOM2, taxa with w 0.6, 0.7, 0.8 and 0.9 were assigned q value of 0.01, 0.001, 0.0001 and 0.00001 respectively. Five genera were detected as differentially abundant by all methods (Lautropia, Moraxella, Rothia, Treponema and Veilonella).

Abundance in Group 1: increased abundance in Azithromycin(AZM) at 48 weeks

NCBI	Quality Control	Links
Lautropia
Moraxella
Rothia
Treponema

Revision editor(s): Chinelsy, Peace Sandy, ChiomaBlessing