Culture-independent microbial sequencing techniques have revealed that the respiratory tract harbours a complex microbiome not detectable by conventional culturing methods. The contribution of the microbiome to chronic obstructive pulmonary disease (COPD) pathobiology and the potential for microbiome-based clinical biomarkers in COPD are still in the early phases of investigation. Sputum is an easily obtainable sample and has provided a wealth of information on COPD pathobiology, and thus has been a preferred sample type for microbiome studies. Although the sputum microbiome likely reflects the respiratory microbiome only in part, there is increasing evidence that microbial community structure and diversity are associated with disease severity and clinical outcomes, both in stable COPD and during the exacerbations. Current evidence has been limited to mainly cross-sectional studies using 16S rRNA gene sequencing, attempting to answer the question ‘who is there?’ Longitudinal studies using standardised protocols are needed to answer outstanding questions including differences between sputum sampling techniques. Further, with advancing technologies, microbiome studies are shifting beyond the examination of the 16S rRNA gene, to include whole metagenome and metatranscriptome sequencing, as well as metabolome characterisation. Despite being technically more challenging, whole-genome profiling and metabolomics can address the questions ‘what can they do?’ and ‘what are they doing?’ This review provides an overview of the basic principles of high-throughput microbiome sequencing techniques, current literature on sputum microbiome profiling in COPD, and a discussion of the associated limitations and future perspectives.

中文翻译：

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COPD 中的痰微生物组分析：超越单一病原体检测


不依赖于培养物的微生物测序技术表明，呼吸道含有传统培养方法无法检测到的复杂微生物组。微生物组对慢性阻塞性肺疾病 (COPD) 病理学的贡献以及基于微生物组的 COPD 临床生物标志物的潜力仍处于研究的早期阶段。痰是一种容易获得的样本，提供了有关慢性阻塞性肺病病理学的丰富信息，因此一直是微生物组研究的首选样本类型。尽管痰微生物组可能仅部分反映呼吸道微生物组，但越来越多的证据表明，无论是在稳定期还是急性加重期，微生物群落结构和多样性与疾病严重程度和临床结果相关。目前的证据主要限于使用 16S rRNA 基因测序的横断面研究，试图回答“谁在那里？”的问题。需要使用标准化方案进行纵向研究来回答悬而未决的问题，包括痰液采样技术之间的差异。此外，随着技术的进步，微生物组研究正在超越 16S rRNA 基因的检查，包括整个宏基因组和宏转录组测序以及代谢组表征。尽管在技术上更具挑战性，全基因组分析和代谢组学可以解决“它们能做什么？”的问题。以及“他们在做什么？”本综述概述了高通量微生物组测序技术的基本原理、COPD 痰微生物组分析的最新文献，并讨论了相关局限性和未来前景。