Targeted metagenomics and IS-Pro method are two of the many methods that have been used to study the microbiome. The two methods target different regions of the 16 S rRNA gene. The aim of this study was to compare targeted metagenomics and IS-Pro methods for the ability to discern the microbial composition of the lung microbiome of COPD patients. Spontaneously expectorated sputum specimens were collected from COPD patients. Bacterial DNA was extracted and used for targeted metagenomics and IS-Pro method. The analysis was performed using QIIME2 (targeted metagenomics) and IS-Pro software (IS-Pro method). Additionally, a laboratory cost per isolate and time analysis was performed for each method. Statistically significant differences were observed in alpha diversity when targeted metagenomics and IS-Pro methods’ data were compared using the Shannon diversity measure (p-value = 0.0006) but not with the Simpson diversity measure (p-value = 0.84). Distinct clusters with no overlap between the two technologies were observed for beta diversity. Targeted metagenomics had a lower relative abundance of phyla, such as the Proteobacteria, and higher relative abundance of phyla, such as Firmicutes when compared to the IS-Pro method. Haemophilus, Prevotella and Streptococcus were most prevalent genera across both methods. Targeted metagenomics classified 23 % (144/631) of OTUs to a species level, whereas IS-Pro method classified 86 % (55/64) of OTUs to a species level. However, unclassified OTUs accounted for a higher relative abundance when using the IS-Pro method (35 %) compared to targeted metagenomics (5 %). The two methods performed comparably in terms of cost and time; however, the IS-Pro method was more user-friendly. It is essential to understand the value of different methods for characterisation of the microbiome. Targeted metagenomics and IS-Pro methods showed differences in ability in identifying and characterising OTUs, diversity and microbial composition of the lung microbiome. The IS-Pro method might miss relevant species and could inflate the abundance of Proteobacteria. However, the IS-Pro kit identified most of the important lung pathogens, such as Burkholderia and Pseudomonas and may work in a more diagnostics-orientated setting. Both methods were comparable in terms of cost and time; however, the IS-Pro method was easier to use.

中文翻译：

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用于分析肺微生物组的靶向宏基因组学和 IS-Pro 方法的比较

靶向宏基因组学和 IS-Pro 方法是用于研究微生物组的众多方法中的两种。这两种方法针对 16 S rRNA 基因的不同区域。本研究的目的是比较靶向宏基因组学和 IS-Pro 方法识别 COPD 患者肺微生物组微生物组成的能力。从COPD患者中收集自发咳出的痰标本。提取细菌 DNA 并用于靶向宏基因组学和 IS-Pro 方法。使用 QIIME2（靶向宏基因组学）和 IS-Pro 软件（IS-Pro 方法）进行分析。此外，对每种方法进行了每个分离物的实验室成本和时间分析。当使用香农多样性测量（p 值 = 0.0006）而不是辛普森多样性测量（p 值 = 0.84）比较靶向宏基因组学和 IS-Pro 方法的数据时，在 alpha 多样性中观察到了统计学上的显着差异。观察到两种技术之间没有重叠的不同集群的β多样性。与 IS-Pro 方法相比，靶向宏基因组学的门的相对丰度较低，例如变形菌门，而门的相对丰度较高，例如厚壁菌门。嗜血杆菌属、普氏菌属和链球菌属是两种方法中最普遍的属。靶向宏基因组学将 23% (144/631) 的 OTU 分类为物种水平，而 IS-Pro 方法将 86% (55/64) 的 OTU 分类为物种水平。然而，与靶向宏基因组学 (5%) 相比，使用 IS-Pro 方法 (35%) 时未分类的 OTU 的相对丰度更高。这两种方法在成本和时间方面表现相当；但是，IS-Pro 方法对用户更友好。了解不同方法对微生物组表征的价值至关重要。靶向宏基因组学和 IS-Pro 方法在识别和表征肺微生物组的 OTU、多样性和微生物组成方面的能力存在差异。IS-Pro 方法可能会遗漏相关物种，并可能增加变形菌的丰度。然而，IS-Pro 试剂盒识别出大多数重要的肺部病原体，如伯克霍尔德菌属和假单胞菌属，并且可能在更以诊断为导向的环境中发挥作用。两种方法在成本和时间方面具有可比性；然而，