我们能降到多低?低细菌负荷在呼吸道微生物群研究中的意义。

IF 8.5 Q1 RESPIRATORY SYSTEM
Pneumonia Pub Date : 2018-07-05 eCollection Date: 2018-01-01 DOI:10.1186/s41479-018-0051-8
Robyn L Marsh, Maria T Nelson, Chris E Pope, Amanda J Leach, Lucas R Hoffman, Anne B Chang, Heidi C Smith-Vaughan
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引用次数: 39

摘要

背景:与培养无关的测序方法越来越多地用于研究与人类粘膜表面相关的微生物群,包括健康个体中细菌负荷低的部位(例如肺)。当细菌负荷较低时,为分析高细菌负荷标本(如粪便)而开发的标准微生物群方法可能需要修改,因为当细菌很少时,无菌实验室试剂和试剂盒产生的本底污染可能会主导序列数据。主体:呼吸道标本中的细菌负荷可能因标本类型、标本体积、解剖部位和临床参数而异。这篇综述讨论了分析低细菌负荷标本所固有的方法学问题,并推荐了成功进行呼吸微生物群研究的策略。目前用于处理低细菌负荷标本DNA的方法范围,以及用于识别和排除背景污染的策略也进行了讨论。结论:包括低细菌负荷标本在内的微生物群研究需要额外的测试,以确保背景污染不会使结果或解释产生偏差。目前有几种方法用于分析低细菌负荷呼吸道标本中的微生物群;然而,比较不同方法的有效性和偏差的文献很少。需要进一步研究确定低细菌负荷标本中微生物群分析的最佳方法。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
How low can we go? The implications of low bacterial load in respiratory microbiota studies.

Background: Culture-independent sequencing methods are increasingly used to investigate the microbiota associated with human mucosal surfaces, including sites that have low bacterial load in healthy individuals (e.g. the lungs). Standard microbiota methods developed for analysis of high bacterial load specimens (e.g. stool) may require modification when bacterial load is low, as background contamination derived from sterile laboratory reagents and kits can dominate sequence data when few bacteria are present.

Main body: Bacterial load in respiratory specimens may vary depending on the specimen type, specimen volume, the anatomic site sampled and clinical parameters. This review discusses methodological issues inherent to analysis of low bacterial load specimens and recommends strategies for successful respiratory microbiota studies. The range of methods currently used to process DNA from low bacterial load specimens, and the strategies used to identify and exclude background contamination are also discussed.

Conclusion: Microbiota studies that include low bacterial load specimens require additional tests to ensure that background contamination does not bias the results or interpretation. Several methods are currently used to analyse the microbiota in low bacterial load respiratory specimens; however, there is scant literature comparing the effectiveness and biases of different methods. Further research is needed to define optimal methods for analysing the microbiota in low bacterial load specimens.

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来源期刊
Pneumonia
Pneumonia RESPIRATORY SYSTEM-
自引率
1.50%
发文量
7
审稿时长
11 weeks
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