ArticleBMC infectious diseases2026
Metatranscriptomic analysis of upper and lower respiratory tract microbiomes in patients with tuberculosis and community-acquired pneumonia.
Article in BMC infectious diseases, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
backgroundAlthough changes in the lung microbiome have been observed in many respiratory diseases, the lung microbiome of patients with tuberculosis (TB) remains largely undefined. The aim of this study was to determine and compare the composition of upper and lower respiratory microbial communities, changes in host gene expression, and functional pathway activation in patients with TB and community-acquired pneumonia using a Metatranscriptomic approach.
methodsFrom November 2020 to November 2021, 42 bronchoalveolar lavage fluid samples, 10 oropharyngeal swabs, and 10 nasopharyngeal swabs were collected from patients hospitalized with TB or community-acquired pneumonia for RNA-sequencing, within 72 h of admission. Data from 28 healthy controls were downloaded from the National Center for Biotechnology Information database.
resultsThe most common microorganisms in the samples from patients with TB were Prevotella, Escherichia, Mycobacterium, and Verrucoccus. Notable differences in microorganism diversity were observed between the TB and community-acquired pneumonia groups as well as between the upper and lower respiratory tracts compared to that in healthy controls. Altered microbial interactions were also observed. Rothia and Mycobacterium were identified as marker microorganisms in the TB group, which exhibited increased expression of SNAP25, MGAM2, CNTN4, MMP12, and GPR174, in parallel to IL36A, RHCG, and CYP2B6 downregulation relative to the community-acquired pneumonia group. The pathways enriched for differential genes were similar among all patient groups, particularly involving neuroactive ligand receptor interaction and Ca
conclusionsThe composition of microbial communities and host expression landscapes differs between TB and community-acquired pneumonia as well as between different respiratory tract sites. These changes in lung microbiota may impact lung disease development and prognosis.
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