Transcriptomics of the muco-microbiotic layer of the lower airways: a new frontier for translational research in pulmonology?| Rassegna di Patologia dell'Apparato Respiratorio

Abstract

he lower airways are traditionally described as comprising three layers: mucosa, fibro-musculo-cartilaginous layer, and adventitia. However, increasing interest in respiratory microbiota has led to the identification of a fourth, innermost component: the muco-microbiotic layer. This dynamic ecosystem consists of airway mucus, resident microbiota, and extracellular nanovesicles (originating from both host cells and microbes). Within this microenvironment, intricate molecular dialogues influence respiratory physiology and the pathogenesis of chronic or infectious diseases. Transcriptomics, the study of active RNA transcripts, emerges as a key tool to investigate this layer’s biological functions. Unlike metagenomics, which captures static genetic potential, transcriptomics reveals real-time gene expression in both microbial and host populations, offering insights into immune modulation, inflammation, and tissue regeneration. Metatranscriptomics enables functional profiling of the airway microbiota in diseases such as COPD, asthma, pulmonary fibrosis, and COVID-19, while extracellular vesicle-associated transcriptomics allows exploration of RNA-mediated cross-talk via exosomes and bacterial vesicles. This dual-transcriptomic approach facilitates the mapping of intercellular and interspecies signaling networks, potentially revealing early molecular alterations preceding clinical symptoms. It holds promise for non-invasive diagnostics, risk stratification, and personalized therapies – including inhaled probiotics, synthetic RNAs, and engineered vesicles. However, methodological challenges remain: standardization of sampling, nanovesicle isolation, RNA extraction, and complex data integration. Despite these hurdles, transcriptomics of the muco-microbiotic layer represents a transformative frontier in precision pulmonology, redefining respiratory pathophysiology from a static anatomical model to a dynamic, molecular, and ecological perspective.