Inherent bacterial DNA contamination of extraction and sequencing reagents may affect interpretation of microbiota in low bacterial biomass samples.
Inherent bacterial DNA contamination of extraction and sequencing reagents may affect interpretation of microbiota in low bacterial biomass samples.
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DOI：
10.1186/s13099-016-0103-7
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发表时间：
2016
期刊：
影响因子：
4.2
通讯作者：
Chiodini RJ
中科院分区：
文献类型：
--
作者：
Glassing A;Dowd SE;Galandiuk S;Davis B;Chiodini RJ
用于探索环境和组织样本中的微生物群和微生物组的高灵敏度分子生物学技术的出现和使用已经检测到试剂中存在污染微生物 DNA。这些微生物 DNA 污染物可能会扭曲微生物数据集中的分类分布和相对频率，并导致错误的解释和识别。我们在此报告了常用 DNA 提取试剂盒和 PCR 试剂中细菌 DNA 污染的发生情况以及这些污染物对数据解释的影响。与之前的报告相比，我们额外确定了 88 个细菌属作为分子生物学级试剂的潜在污染物，使已知污染微生物的总数达到 181 个属。检测到的许多污染物被认为是人类胃肠道和环境中的正常居民，并且通常与样品中真正存在的污染物无法区分。研究细菌群体的实验室需要确定 DNA 处理中使用的所有提取试剂盒和试剂中存在的污染物。任何不寻常和/或意外的发现都需要被视为可能的污染，而不是独特的发现。本文的在线版本 (doi:10.1186/s13099-016-0103-7) 包含补充材料，可供授权用户使用。
The advent and use of highly sensitive molecular biology techniques to explore the microbiota and microbiome in environmental and tissue samples have detected the presence of contaminating microbial DNA within reagents. These microbial DNA contaminants may distort taxonomic distributions and relative frequencies in microbial datasets, as well as contribute to erroneous interpretations and identifications. We herein report on the occurrence of bacterial DNA contamination within commonly used DNA extraction kits and PCR reagents and the effect of these contaminates on data interpretation. When compared to previous reports, we identified an additional 88 bacterial genera as potential contaminants of molecular biology grade reagents, bringing the total number of known contaminating microbes to 181 genera. Many of the contaminants detected are considered normal inhabitants of the human gastrointestinal tract and the environment and are often indistinguishable from those genuinely present in the sample. Laboratories working on bacterial populations need to define contaminants present in all extraction kits and reagents used in the processing of DNA. Any unusual and/or unexpected findings need to be viewed as possible contamination as opposed to unique findings. The online version of this article (doi:10.1186/s13099-016-0103-7) contains supplementary material, which is available to authorized users.