---
title: "Pulmonary tuberculosis linked to site-specific changes in respiratory and gut microbiomes in Uganda"
id: "biorxiv-0-pulmonary-tuberculosis-is-associated-with-body-site-specific-alterations-in-the"
canonical_url: "https://medichelpline.com/clinical-feed/biorxiv-0-pulmonary-tuberculosis-is-associated-with-body-site-specific-alterations-in-the"
content_type: "clinical_feed_article"
specialty: "Infectious Disease"
source_name: "bioRxiv (Biomedical Preprints)"
source_url: "https://www.biorxiv.org/content/10.64898/2026.10.14.759077v1?rss=1"
published_at: "2026-10-15T12:00:00.000Z"
evidence_level: "Verified Feed"
license: "CC-BY-NC-4.0 / Informational Use"
---
# Pulmonary tuberculosis linked to site-specific changes in respiratory and gut microbiomes in Uganda
## Provenance & Clinical Metadata
- **Canonical URL:** https://medichelpline.com/clinical-feed/biorxiv-0-pulmonary-tuberculosis-is-associated-with-body-site-specific-alterations-in-the
- **Specialty:** [Infectious Disease](https://medichelpline.com/clinical-feed/infectious-disease.md)
- **Primary Source:** bioRxiv (Biomedical Preprints)
- **Source URL:** [Original Journal Publication](https://www.biorxiv.org/content/10.64898/2026.10.14.759077v1?rss=1)
- **Published At:** 2026-10-15T12:00:00.000Z
- **Evidence Rating:** Verified Feed
## Executive GIST (TL;DR)
- Investigators conducted a cross-sectional microbiome study in Kampala, Uganda, profiling both **sputum** and **stool** using **16S rRNA** gene sequencing to compare adults with pulmonary tuberculosis (TB) and contacts without TB. - The cohort comprised 200 participants recruited at Mulago National Referral Hospital; the source reported 150 TB cases and 50 contacts, with 135 sputum and 151 stool samples retained after quality control. - In sputum, richness estimators (Chao1 and ACE) were lower in TB cases than controls; overall sputum community composition differences were not statistically significant after multiple-testing correction. - Stool samples showed multiple differences in richness and diversity measures between TB cases and controls, and beta-diversity tests detected compositional differences; however, TB cases had greater within-group dispersion. - The sequencing platform contributed substantially to variation in stool microbial profiles and, in multivariable models, was the only factor independently associated with stool community composition after multiple-testing correction. - Differential-abundance testing (ANCOM-BC2) identified body site–specific taxonomic associations: sputum differences involved Streptococcus, Parvimonas, and Actinobacillus; stool differences involved Dorea, Lachnoclostridium, and Turicibacter. - Investigators cautioned that dispersion and sequencing-platform effects complicated interpretation of community-level differences. They recommended longitudinal studies with standardized sequencing to determine temporal dynamics during treatment and assess diagnostic or clinical relevance.
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Monica Mbabazi 1 Makerere University CHS: Makerere University College of Health Sciences; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Monica%2BMbabazi%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Mbabazi%20M&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AMonica%2BMbabazi%2B) * [ORCID record for Monica Mbabazi](http://orcid.org/0000-0001-6621-0586 "Open in new tab") * For correspondence: mbabazimonica.mm@gmail.com Joanitah Nabwire 2 College of health Sciences, Makerere University; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Joanitah%2BNabwire%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Nabwire%20J&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AJoanitah%2BNabwire%2B) Naome Mutesi 3 College of Health Sciences, Makerere University; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Naome%2BMutesi%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Mutesi%20N&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3ANaome%2BMutesi%2B) Edgar Kigozi 1 Makerere University CHS: Makerere University College of Health Sciences; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Edgar%2BKigozi%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Kigozi%20E&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AEdgar%2BKigozi%2B) * [ORCID record for Edgar Kigozi](http://orcid.org/0009-0009-2579-2079 "Open in new tab") Sharon Namiiro 4 TB clinic, Mulago National Referral Hospital; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Sharon%2BNamiiro%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Namiiro%20S&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3ASharon%2BNamiiro%2B) * [ORCID record for Sharon Namiiro](http://orcid.org/0000-0001-6969-1098 "Open in new tab") Adrian Muwonge 5 University of Edinburgh; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Adrian%2BMuwonge%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Muwonge%20A&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AAdrian%2BMuwonge%2B) David Patrick Kateete 6 Makerere University * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=David%2B%2BPatrick%2BKateete%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Kateete%20D&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3ADavid%2B%2BPatrick%2BKateete%2B) * [ORCID record for David Patrick Kateete](http://orcid.org/0000-0001-8075-3069 "Open in new tab") * [Abstract](https://www.biorxiv.org/content/10.64898/2026.10.14.759077v1)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_art/node:5871020/1) * [Info/History](https://www.biorxiv.org/content/10.64898/2026.10.14.759077v1.article-info)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_info/node:5871020/1) * [Metrics](https://www.biorxiv.org/content/10.64898/2026.10.14.759077v1.article-metrics)[](https://www.biorxiv.org/panels_ajax_tab/article_tab_metrics/node:5871020/1) * [Supplementary material](https://www.biorxiv.org/content/10.64898/2026.10.14.759077v1.supplementary-material)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_data/node:5871020/1) * [ Preview PDF](https://www.biorxiv.org/content/10.64898/2026.10.14.759077v1.full.pdf+html)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_pdf/node:5871020/1) ![Loading](https://www.biorxiv.org/sites/all/modules/contrib/panels_ajax_tab/images/loading.gif) ## Abstract Abstract Background: Tuberculosis is a major infectious disease whose effects may extend beyond the lungs to influence microbial communities at other body sites. Although studies have reported alterations in the respiratory and gut microbiomes of people with TB, evidence from sub-Saharan Africa remains limited, and the extent to which these alterations differ between body sites is not fully understood. This study characterized sputum and stool microbiomes among Ugandan adults with pulmonary TB and those without TB. Methods: We conducted a cross-sectional study involving 200 participants, comprising 150 adults with pulmonary TB and 50 contacts, at Mulago National Referral Hospital in Kampala, Uganda. Sputum and stool samples were profiled using 16S rRNA gene sequencing. Following quality control and contaminant removal, within-sample diversity was assessed using multiple alpha diversity indices. Beta diversity was evaluated using distance-based methods, with group differences assessed by permutational multivariate analysis of variance (PERMANOVA) and homogeneity of dispersion tests. Differentially abundant taxa were identified using ANCOM-BC2. Results: After quality control, 135 sputum and 151 stool samples were retained for downstream analysis. In sputum, microbial richness estimators Chao1 and ACE were lower among TB cases than controls, whereas differences in overall community composition were not statistically significant after correction for multiple testing. In stool, several richness and diversity measures differed between groups, and beta-diversity analyses detected differences in community composition. However, TB cases exhibited greater within-group dispersion, and the sequencing platform contributed substantially to variation in stool microbial profiles. In multivariable analyses, the sequencing platform was the only factor independently associated with stool community composition after correction for multiple testing. Differential-abundance analyses identified body site-specific taxonomic associations with TB, including differences involving Streptococcus, Parvimonas, and Actinobacillus in sputum, and Dorea, Lachnoclostridium, and Turicibacter in stool. Conclusion: Pulmonary TB was associated with differences in microbial richness and the abundance of specific taxa in both sputum and stool, but evidence for overall community composition differences varied by body site and was influenced by dispersion and sequencing platform. These findings highlight the importance of examining both respiratory and gut microbial communities in TB research. Longitudinal studies using standardized sequencing methods are needed to clarify how these patterns change during treatment and whether they have diagnostic or clinical relevance. ### Competing Interest Statement The authors have declared no competing interest. Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a [CC-BY-NC 4.0 International license](http://creativecommons.org/licenses/by-nc/4.0/). bioRxiv and medRxiv thank the following for their generous financial support: > The Chan Zuckerberg Initiative, Cold Spring Harbor Laboratory, the Sergey Brin Family Foundation, California Institute of Technology, Centre National de la Recherche Scientifique, Fred Hutchinson Cancer Center, Imperial College London, Massachusetts Institute of Technology, Stanford University, The University of Edinburgh, University of Washington, and Vrije Universiteit Amsterdam. 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[ Download PDF](https://www.biorxiv.org/content/10.64898/2026.10.14.759077v1.full.pdf) Print/Save Options [Download PDF](https://www.biorxiv.org/content/biorxiv/early/2026/10/15/2026.10.14.759077.full.pdf)Full Text & In-line FiguresXML [More Info](https://www.biorxiv.org/about/FAQ#PrintOptions "More Information on Print/Save Options") [Supplementary Material ](https://www.biorxiv.org/content/10.64898/2026.10.14.759077v1.supplementary-material) [ Email](https://www.biorxiv.org/ "Email this Article") [ Share](https://www.biorxiv.org/) Pulmonary Tuberculosis Is Associated with Body Site-Specific Alterations in the Respiratory and Gut Microbiome in Uganda Monica Mbabazi, Joanitah Nabwire, Naome Mutesi, Edgar Kigozi, Sharon Namiiro, Adrian Muwonge, David Patrick Kateete bioRxiv 2026.10.14.759077; doi: https://doi.org/10.64898/2026.10.14.759077 This article is a preprint and has not been certified by peer review [[what does this mean?](https://www.biorxiv.org/about/FAQ#unrefereed)]. 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