Microbial ecological instability and non-linear host interactions shape airway inflammation in HIV-associated COPD
Abstract
Chronic obstructive pulmonary disease (COPD) is increasingly recognized among people living with HIV in sub-Saharan Africa, yet the mechanisms linking airway microbial ecology to chronic inflammation remain poorly understood. Here, we study 200 adults stratified by HIV and COPD status, including 160 participants with two-year longitudinal follow-up, using an integrated multi-omics framework combining sputum 16S rRNA profiling, bacterial outer membrane vesicle quantification, airway cytokine profiling, CyTOF immune phenotyping, bulk transcriptomics of induced sputum, bronchoalveolar lavage and peripheral blood, and bronchoalveolar lavage single-cell RNA sequencing-guided deconvolution. We find that sputum microbial communities are shaped predominantly by temporal ecological turnover rather than HIV or COPD status. Although microbial diversity, microbiome instability, outer membrane vesicle burden and inferred airway cellular composition remain largely preserved, HIV-associated COPD exhibits disease-specific microbial signatures together with inflammatory transcriptional remodeling concentrated in induced sputum. Integrated analyses identify selective host-microbe interaction networks linking discrete microbial taxa with inflammatory, immune and transcriptional programmes.
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BibTeX
@article{kayongo2026microbial,
title = {{Microbial ecological instability and non-linear host interactions shape airway inflammation in HIV-associated COPD}},
author = {Alex Kayongo and Theda Ulrike Patricia Bartolomaeus and Julia Hecker and Till Birkner and Eremire Vila and Moses Levi Ntayi and Lajos Markó and Ulrike Löber and Geoffrey Olweny and Edward Kyalo and Daisy Kyamulabi and Josephine Ndawula and Willy Ssengooba and Rose Nabatanzi and Samuel Kyobe and Faith Nassali and Edgar Kigozi and Robert Kalyesubula and Richard Munana and Jesca Namaganda and Caroline J. Musiime and Rogers Sekibira and Bernard S. Bagaya and David P. Kateete and Moses L. Joloba and Daudi Jjingo and John Lusiba and William Worodria and Harriet Mayanja-Kizza and Rejani Lalitha and Wasswa Ham and Ingvar Sanyu and Josephine Zawedde and Nicole M. Robertson and James Sande Obondo and Carl Weidinger and Desiree Kunkel and Bruce J. Kirenga and Trishul Siddharthan and John R. Hurst and William Checkley and William B. Cookson and Miriam F. Moffatt and Sofia K. Forslund-Startceva},
journal = {Nature Communications},
year = {2026},
month = oct,
doi = {10.1038/s41467-026-78400-4},
url = {https://www.nature.com/articles/s41467-026-78400-4},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Microbial ecological instability and non-linear host interactions shape airway inflammation in HIV-associated COPD
AU - Alex Kayongo
AU - Theda Ulrike Patricia Bartolomaeus
AU - Julia Hecker
AU - Till Birkner
AU - Eremire Vila
AU - Moses Levi Ntayi
AU - Lajos Markó
AU - Ulrike Löber
AU - Geoffrey Olweny
AU - Edward Kyalo
AU - Daisy Kyamulabi
AU - Josephine Ndawula
AU - Willy Ssengooba
AU - Rose Nabatanzi
AU - Samuel Kyobe
AU - Faith Nassali
AU - Edgar Kigozi
AU - Robert Kalyesubula
AU - Richard Munana
AU - Jesca Namaganda
AU - Caroline J. Musiime
AU - Rogers Sekibira
AU - Bernard S. Bagaya
AU - David P. Kateete
AU - Moses L. Joloba
AU - Daudi Jjingo
AU - John Lusiba
AU - William Worodria
AU - Harriet Mayanja-Kizza
AU - Rejani Lalitha
AU - Wasswa Ham
AU - Ingvar Sanyu
AU - Josephine Zawedde
AU - Nicole M. Robertson
AU - James Sande Obondo
AU - Carl Weidinger
AU - Desiree Kunkel
AU - Bruce J. Kirenga
AU - Trishul Siddharthan
AU - John R. Hurst
AU - William Checkley
AU - William B. Cookson
AU - Miriam F. Moffatt
AU - Sofia K. Forslund-Startceva
PY - 2026
DA - 2026/10/06
JO - Nature Communications
DO - 10.1038/s41467-026-78400-4
UR - https://www.nature.com/articles/s41467-026-78400-4
AB - Chronic obstructive pulmonary disease (COPD) is increasingly recognized among people living with HIV in sub-Saharan Africa, yet the mechanisms linking airway microbial ecology to chronic inflammation remain poorly understood. Here, we study 200 adults stratified by HIV and COPD status, including 160 participants with two-year longitudinal follow-up, using an integrated multi-omics framework combining sputum 16S rRNA profiling, bacterial outer membrane vesicle quantification, airway cytokine profiling, CyTOF immune phenotyping, bulk transcriptomics of induced sputum, bronchoalveolar lavage and peripheral blood, and bronchoalveolar lavage single-cell RNA sequencing-guided deconvolution. We find that sputum microbial communities are shaped predominantly by temporal ecological turnover rather than HIV or COPD status. Although microbial diversity, microbiome instability, outer membrane vesicle burden and inferred airway cellular composition remain largely preserved, HIV-associated COPD exhibits disease-specific microbial signatures together with inflammatory transcriptional remodeling concentrated in induced sputum. Integrated analyses identify selective host-microbe interaction networks linking discrete microbial taxa with inflammatory, immune and transcriptional programmes.
SN - 2041-1723
ER -