BackgroundThe airway microbiome in severe asthma has not been characterised at species‐level by metagenomic sequencing, nor have the relationships between specific species and mucosal immune responses in ‘type‐2 low’, neutrophilic asthma been defined. We performed an integrated species‐level metagenomic data with inflammatory mediators to characterise prevalence of dominant potentially pathogenic organisms and host immune responses.MethodsSputum and nasal lavage samples were analysed using long‐read metagenomic sequencing with Nanopore and qPCR in two cross‐sectional adult severe asthma cohorts, Wessex (n = 66) and Oxford (n = 30). We integrated species‐level data with clinical parameters and 39 selected airway proteins measured by immunoassay and O‐link.ResultsThe sputum microbiome in health and mild asthma displayed comparable microbial diversity. By contrast, 23% (19/81) of severe asthma microbiomes were dominated by a single respiratory pathogen, namely H. influenzae (n = 10), M. catarrhalis (n = 4), S. pneumoniae (n = 4) and P. aeruginosa (n = 1). Neutrophilic asthma was associated with H. influenzae, M. catarrhalis, S. pneumoniae and T. whipplei with elevated type‐1 cytokines and proteases; eosinophilic asthma with higher M. catarrhalis, but lower H. influenzae, and S. pneumoniae abundance. H. influenzae load correlated with Eosinophil Cationic Protein, elastase and IL‐10. R. mucilaginosa associated positively with IL‐6 and negatively with FGF. Bayesian network analysis also revealed close and distinct relationships of H. influenzae and M. catarrhalis with type‐1 airway inflammation. The microbiomes and cytokine milieu were distinct between upper and lower airways.ConclusionsThis species‐level integrated analysis reveals central, but distinct associations between potentially pathogenic bacteria and airways inflammation in severe asthma.

中文翻译：

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严重哮喘中微生物-免疫相互作用的物种水平、宏基因组学和蛋白质组学分析


背景严重哮喘的气道微生物组尚未通过宏基因组测序在物种水平上进行表征，也未定义“2 型低”中性粒细胞性哮喘中特定物种与粘膜免疫反应之间的关系。我们使用炎症介质进行了物种水平的宏基因组数据，以表征主要潜在病原微生物的患病率和宿主免疫反应。方法使用纳米孔和 qPCR 的长读长宏基因组测序分析两个横断面成人严重哮喘队列 Wessex （n = 66） 和 Oxford （n = 30） 的痰液和洗鼻液样本。我们将物种水平数据与临床参数和通过免疫测定和 O-link 测量的 39 种选定的气道蛋白相结合。结果健康和轻度哮喘中的痰液微生物组表现出相当的微生物多样性。相比之下，23% （19/81） 的严重哮喘微生物组由单一呼吸道病原体主导，即流感嗜血杆菌 （n = 10）、卡他支原体 （n = 4）、肺炎链球菌 （n = 4） 和铜绿假单胞菌 （n = 1）。中性粒细胞性哮喘与流感嗜血杆菌、卡他莫拉菌、肺炎链球菌和惠普尔毛滴虫有关 1 型细胞因子和蛋白酶升高;嗜酸性粒细胞性哮喘，伴有较高的卡他莫拉菌，但较低的流感嗜血杆菌和肺炎链球菌。H. influenzae 负荷与嗜酸性粒细胞阳离子蛋白、弹性蛋白酶和 IL-10 相关。R. mucilaginosa 与 IL-6 呈正相关，与 FGF 呈负相关。贝叶斯网络分析还揭示了流感嗜血杆菌和卡他分枝杆菌与 1 型气道炎症的密切而明显的关系。微生物组和细胞因子环境在上下气道之间是不同的。结论这种物种水平的综合分析揭示了严重哮喘中潜在病原菌与气道炎症之间的核心但不同的关联。