Culture-independent studies of the cystic fibrosis (CF) airway microbiome typically rely on expectorated sputum to assess the microbial makeup of lower airways. These studies have revealed rich bacterial communities. There is often considerable overlap between taxa observed in sputum and those observed in saliva, raising questions about the reliability of expectorated sputum as a sample representing lower airway microbiota. These concerns prompted us to compare pairs of sputum and saliva samples from 10 persons with CF. Using 16S rRNA gene sequencing and droplet digital PCR (ddPCR), we analyzed 37 pairs of sputum and saliva samples, each collected from the same person on the same day. We developed an in silico postsequencing decontamination procedure to remove from sputum the fraction of DNA reads estimated to have been contributed by saliva during expectoration. We demonstrate that while there was often sizeable overlap in community membership between sample types, expectorated sputum typically contains a higher bacterial load and a less diverse community compared to saliva. The differences in diversity between sputum and saliva were more pronounced in advanced disease stage, owing to increased relative abundance of the dominant taxa in sputum. Our effort to model saliva contamination of sputum in silico revealed generally minor effects on community structure after removal of contaminating reads. Despite considerable overlap in taxa observed between expectorated sputum and saliva samples, the impact of saliva contamination on measures of lower airway bacterial community composition in CF using expectorated sputum appears to be minimal.

中文翻译：

---

囊性纤维化痰和唾液的并行分析揭示了重叠的社区和样品净化的机会。

囊性纤维化（CF）气道微生物组的独立于培养的研究通常依靠痰液痰评估下气道的微生物组成。这些研究揭示了丰富的细菌群落。在痰液中观察到的分类单元与唾液中观察到的分类单元之间通常存在相当大的重叠，这引发了关于痰痰作为代表下呼吸道微生物群的样本的可靠性的疑问。这些担忧促使我们比较了10名CF患者的痰和唾液样本对。使用16S rRNA基因测序和液滴数字PCR（ddPCR），我们分析了37对痰和唾液样本，每个样本都是在同一天从同一个人收集的。我们开发了计算机测序后的去污程序可从痰液中去除估计由痰液中唾液贡献的DNA读数片段。我们证明，虽然样本类型之间的社区成员经常有相当大的重叠，但与唾液相比，痰液痰通常包含较高的细菌载量和较少多样性的社区。在疾病晚期，由于痰中优势类群的相对丰度增加，痰与唾液之间的多样性差异更加明显。我们对模拟唾液唾液污染进行计算机模拟的工作揭示了去除污染读物后对群落结构的影响一般较小。尽管在痰液痰和唾液样品之间观察到的分类单元有相当大的重叠，但是唾液污染对使用痰液痰对CF中较低气道细菌群落组成的测量的影响似乎很小。