Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, 1161 21st Avenue South, Medical Center North, Suite A2200, Nashville, TN, 37232, USA.
Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA.
Sci Rep. 2020 Nov 26;10(1):20618. doi: 10.1038/s41598-020-77289-3.
Despite being commonly used to collect upper airway epithelial lining fluid, nasal washes are poorly reproducible, not suitable for serial sampling, and limited by a dilution effect. In contrast, nasal filters lack these limitations and are an attractive alternative. To examine whether nasal filters are superior to nasal washes as a sampling method for the characterization of the upper airway microbiome and immune response, we collected paired nasal filters and washes from a group of 40 healthy children and adults. To characterize the upper airway microbiome, we used 16S ribosomal RNA and shotgun metagenomic sequencing. To characterize the immune response, we measured total protein using a BCA assay and 53 immune mediators using multiplex magnetic bead-based assays. We conducted statistical analyses to compare common microbial ecology indices and immune-mediator median fluorescence intensities (MFIs) between sample types. In general, nasal filters were more likely to pass quality control in both children and adults. There were no significant differences in microbiome community richness, α-diversity, or structure between pediatric samples types; however, these were all highly dissimilar between adult sample types. In addition, there were significant differences in the abundance of amplicon sequence variants between sample types in children and adults. In adults, total proteins were significantly higher in nasal filters than nasal washes; consequently, the immune-mediator MFIs were not well detected in nasal washes. Based on better quality control sequencing metrics and higher immunoassay sensitivity, our results suggest that nasal filters are a superior sampling method to characterize the upper airway microbiome and immune response in both children and adults.
尽管鼻腔冲洗常用于收集上呼吸道上皮衬里液，但它的重复性较差，不适合连续采样，并且受到稀释效应的限制。相比之下，鼻腔过滤器没有这些限制，是一种有吸引力的替代品。为了研究鼻腔过滤器作为上呼吸道微生物组和免疫反应特征的采样方法是否优于鼻腔冲洗，我们从一组 40 名健康儿童和成年人中收集了配对的鼻腔过滤器和冲洗液。为了描述上呼吸道微生物组，我们使用了 16S 核糖体 RNA 和 shotgun 宏基因组测序。为了描述免疫反应，我们使用 BCA 测定法测量总蛋白，并使用多重磁珠基测定法测量 53 种免疫介质。我们进行了统计分析，以比较两种样本类型之间常见的微生物生态学指标和免疫介质中荧光强度（MFI）中位数。总体而言，鼻腔过滤器在儿童和成人中更有可能通过质量控制。儿科样本类型之间的微生物群落丰富度、α多样性或结构没有显著差异；然而，成人样本类型之间的这些差异非常大。此外，儿童和成人样本类型之间的扩增子序列变体丰度存在显著差异。在成年人中，鼻腔过滤器中的总蛋白明显高于鼻腔冲洗液；因此，鼻腔冲洗液中免疫介质的 MFI 无法很好地检测到。基于更好的质量控制测序指标和更高的免疫测定灵敏度，我们的结果表明，鼻腔过滤器是一种更好的采样方法，可用于描述儿童和成年人的上呼吸道微生物组和免疫反应。
