Awad Nour, Larson Peter J, Sissoko Cheick A, Bond Laurel L, Dion Gregory R
Department of Otolaryngology - Head and Neck Surgery, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
College of Engineering and Applied Science, Department of Biomedical Engineering, University of Cincinnati, Cincinnati, OH, USA.
Sci Rep. 2025 Jul 22;15(1):26570. doi: 10.1038/s41598-025-11468-y.
The airway microbiome has been implicated in the pathogenesis of laryngotracheal stenosis (LTS), yet prior studies using 16 S rRNA sequencing have limited sub-genus level resolution. Metagenomic whole genome shotgun sequencing (mWGS) allows for strain-level taxonomic and functional genomic analysis, providing detailed insights into specific organisms and pathways. A pilot study was conducted to explore the advantages and challenges of mWGS in investigating the airway metagenome in LTS. mWGS was conducted on 12 intraoperative swab samples from 8 LTS patients, divided into tracheostomy-dependent (n = 3) and non-tracheostomy (n = 5) groups, and 4 controls. Patient comorbidities, antibiotic use, and medications were documented. Biobakery workflows were used for taxonomic and functional profiling. Species-specific reference databases were constructed for 6 abundant species for strain-level analyses. LTS samples had decreased taxonomic diversity and were dominated by species with previously described roles in other chronic inflammatory processes such as Staphylococcus aureus, Streptococcus parasanguinis, Streptococcus mitis, and Corynebacterium pseudogenitalium. LTS samples were enriched for pathways involved in fatty acid biosynthesis and formaldehyde metabolism. Our results identified tracheostomy as an important potential confounder in airway metagenomics but show mWGS techniques are promising in uncovering microbiota correlates in LTS that could reveal disease-specific biomarkers, comorbidity links, and therapeutic targets.
气道微生物群已被认为与喉气管狭窄（LTS）的发病机制有关，但先前使用16S rRNA测序的研究在亚属水平分辨率方面有限。宏基因组全基因组鸟枪法测序（mWGS）允许进行菌株水平的分类学和功能基因组分析，从而深入了解特定生物体和途径。开展了一项试点研究，以探索mWGS在研究LTS气道宏基因组中的优势和挑战。对来自8名LTS患者的12份术中拭子样本进行mWGS，分为依赖气管造口术组（n = 3）和非气管造口术组（n = 5），以及4名对照组。记录患者的合并症、抗生素使用情况和用药情况。使用Biobakery工作流程进行分类学和功能分析。为6种丰富物种构建了物种特异性参考数据库，用于菌株水平分析。LTS样本的分类学多样性降低，主要由在其他慢性炎症过程中具有先前描述作用的物种主导，如金黄色葡萄球菌、副血链球菌、缓症链球菌和假生殖器棒状杆菌。LTS样本富含参与脂肪酸生物合成和甲醛代谢的途径。我们的结果确定气管造口术是气道宏基因组学中一个重要的潜在混杂因素，但表明mWGS技术在揭示LTS中与微生物群相关的因素方面很有前景，这些因素可能揭示疾病特异性生物标志物、合并症联系和治疗靶点。
