Nasopharyngeal Microbiome Diversity Changes over Time in Children with Asthma.
Nasopharyngeal Microbiome Diversity Changes over Time in Children with Asthma.
复制标题
哮喘儿童的鼻咽微生物组多样性随着时间的流逝而变化。
DOI：
10.1371/journal.pone.0170543
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发表时间：
2017
期刊：
影响因子：
3.7
通讯作者：
Freishtat RJ
中科院分区：
文献类型：
--
作者：
Pérez-Losada M;Alamri L;Crandall KA;Freishtat RJ
鼻咽是与呼吸道疾病（如哮喘）相关的病原体的储存库。下一代测序（NGS）已被用于表征婴儿和成人在健康和疾病期间的鼻咽微生物组;然而，关于其组成和时间动态（即，纵向变化）的微生物从儿童和青少年。在这里，我们使用NGS技术来表征哮喘儿童和青少年（6至18岁）的鼻咽微生物组，并确定其随时间的稳定性。从居住在华盛顿地区的40名患有哮喘的儿童和青少年中采集了两次相隔5.5至6.5个月的鼻咽冲洗液。使用MiSeq平台从样品中收集来自16 S-V4 rRNA基因区（约250 bp）的序列数据。在mothur（SILVA 123参考数据库）中处理原始数据，并估计基于操作分类单位（OTU）的α-和β-多样性度量。使用PCoA排序和Procrustes分析评估样本之间的相关性。微生物多样性和类群平均相对比例的差异进行了评估，采用线性混合效应模型。还进行了核心微生物组分析，以鉴定鼻咽部稳定和一致的微生物。总共产生了2，096，584个干净的16 S序列，对应于每个样品平均167个OTU。莫拉氏菌属 *、葡萄球菌属 *、柔丝菌属、棒状杆菌属、普雷沃氏菌属、链球菌属 *、嗜血杆菌属 *、梭杆菌属 * 和奈瑟氏菌科属的代表占总读数的86%。这九个属以前曾在婴儿和成人的鼻咽中发现过，但比例不同。来自上述突出显示的五个属（*）的OTU将鼻咽核心微生物组定义为95%水平。没有显着差异，α-和β-多样性，观察季节之间，但细菌的平均相对比例嗜血杆菌，莫拉氏菌，葡萄球菌和棒状杆菌夏秋季和年龄组之间的变化显着（患者间的变化）。此外，在所分析的40名患者中，35名患者的OTU在时间点之间在患者内显著变化。未来的横断面研究应注意鼻咽微生物群的时间动态。
The nasopharynx is a reservoir for pathogens associated with respiratory illnesses such as asthma. Next-generation sequencing (NGS) has been used to characterize the nasopharyngeal microbiome of infants and adults during health and disease; less is known, however, about the composition and temporal dynamics (i.e., longitudinal variation) of microbiotas from children and adolescents. Here we use NGS technology to characterize the nasopharyngeal microbiomes of asthmatic children and adolescents (6 to 18 years) and determine their stability over time. Two nasopharyngeal washes collected 5.5 to 6.5 months apart were taken from 40 children and adolescents with asthma living in the Washington D.C. area. Sequence data from the 16S-V4 rRNA gene region (~250 bp) were collected from the samples using the MiSeq platform. Raw data were processed in mothur (SILVA123 reference database) and Operational Taxonomic Units (OTU)-based alpha- and beta-diversity metrics were estimated. Relatedness among samples was assessed using PCoA ordination and Procrustes analyses. Differences in microbial diversity and taxon mean relative proportions were assessed using linear mixed effects models. Core microbiome analyses were also performed to identify stable and consistent microbes of the nasopharynx. A total of 2,096,584 clean 16S sequences corresponding to an average of 167 OTUs per sample were generated. Representatives of Moraxella*, Staphylococcus*, Dolosigranulum, Corynebacterium, Prevotella, Streptococcus*, Haemophilus*, Fusobacterium* and a Neisseriaceae genus accounted for 86% of the total reads. These nine genera have been previously found in the nasopharynxes of both infants and adults, but in different proportions. OTUs from the five genera highlighted (*) above defined the nasopharyngeal core microbiome at the 95% level. No significant differences in alpha- and beta-diversity were observed between seasons, but bacterial mean relative proportions of Haemophilus, Moraxella, Staphylococcus and Corynebacterium varied significantly between summer-fall and age groups (inter-patient variation). Additionally, OTUs varied significantly within patients between time points in 35 of the 40 patients analyzed. Future cross-sectional studies should be mindful of the temporal dynamics of the nasopharyngeal microbiota.