The advent of next generation sequencing has rapidly challenged the paediatric respiratory physician’s understanding of lung microbiology and the role of the lung microbiome in host health and disease. In particular, the role of “microbial key players” in paediatric respiratory disease is yet to be fully explained. Accurate profiling of the lung microbiome in children is challenging since the ability to obtain lower airway samples coupled with processing “low-biomass specimens” are both technically difficult. Many studies provide conflicting results. Early microbiota-host relationships may be predictive of the development of chronic respiratory disease but attempts to correlate lower airway microbiota in premature infants and risk of developing bronchopulmonary dysplasia (BPD) have produced mixed results. There are differences in lung microbiota in asthma and cystic fibrosis (CF). The increased abundance of oral taxa in the lungs may (or may not) promote disease processes in asthma and CF. In CF, correlation between microbiota diversity and respiratory decline is commonly observed. When one considers other pathogens beyond the bacterial kingdom, the contribution and interplay of fungi and viruses within the lung microbiome further increase complexity. Similarly, the interaction between microbial communities in different body sites, such as the gut-lung axis, and the influence of environmental factors, including diet, make the co-existence of host and microbes ever more complicated. Future, multi-omics approaches may help uncover novel microbiome-based biomarkers and therapeutic targets in respiratory disease and explain how we can live in harmony with our microbial companions.

中文翻译：

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下呼吸道微生物组在儿科健康和慢性病中的作用

下一代测序的出现迅速挑战了儿科呼吸科医生对肺部微生物学以及肺部微生物组在宿主健康和疾病中的作用的理解。特别是，“微生物关键参与者”在儿科呼吸道疾病中的作用尚未得到充分解释。准确分析儿童肺部微生物组具有挑战性，因为获取下呼吸道样本以及处理“低生物量样本”在技术上都很困难。许多研究提供了相互矛盾的结果。早期微生物群与宿主的关系可能可以预测慢性呼吸道疾病的发生，但将早产儿下呼吸道微生物群与支气管肺发育不良 (BPD) 发生风险联系起来的尝试却产生了不同的结果。哮喘和囊性纤维化 (CF) 患者的肺部微生物群存在差异。肺部口腔类群丰富度的增加可能（或可能不会）促进哮喘和囊性纤维化的疾病进程。在CF中，微生物群多样性与呼吸衰退之间的相关性是常见的。当人们考虑细菌界以外的其他病原体时，肺部微生物组内真菌和病毒的贡献和相互作用进一步增加了复杂性。同样，不同身体部位（例如肠肺轴）的微生物群落之间的相互作用，以及饮食等环境因素的影响，使得宿主和微生物的共存变得更加复杂。未来，多组学方法可能有助于发现新的基于微生物组的生物标志物和呼吸系统疾病的治疗靶点，并解释我们如何与微生物伙伴和谐相处。