All code used to analyze data for the publication "Sputum microbiome and COPD status in a rural Ugandan cohort of well-controlled HIV" is deposited in this repository as R markdown scripts, as well as their repsective compiled versions in html format in the sub directory "compiled".

There is increased morbidity and mortality related to chronic obstructive pulmonary disease (COPD) in sub-Saharan Africa. COPD among people living with HIV (PLWH) has not been well studied in this region, where HIV/AIDS is endemic. Increasing evidence suggests that microbial composition plays a role in COPD severity. Therefore we aimed to investigate microbiome patterns and associations among PLWH with COPD in sub-Saharan Africa. We completed a cross-sectional study of 200 adults with equal numbers of participants by HIV and COPD status in rural Uganda, where participants underwent sputum induction as an easy-to-obtain proxy for the microbiota of the lower respiratory tract. To assess its composition, we performed 16S ribosomal RNA gene sequencing and analysis using a confounder-aware statistical tool, adjusting for age, sex and other collected metadata. To infer the functional profiles of the bacterial community PICCRUt (version 2.2.3) was used. Finally, we compared our results with a UK-based HIV cohort. Despite subtle compositional differences in sputum microbiota by COPD and HIV status in a suppressed HIV cohort, reduced bacterial richness and Campylobacter enrichment were significantly associated with HIV-COPD comorbidity. Furthermore, we observed bacterial clustering into three community types whose distribution was significantly impacted by HIV. Functional prediction with PICRUSt revealed an association between HIV status and bacterial pathway from the malate metabolism. Comparing our findings with the UK cohort revealed significant differences in the sputum microbiome composition irrespective of viral suppression.