Evaluation of the Effect of Storage Methods on Fecal, Saliva, and Skin Microbiome Composition.
Evaluation of the Effect of Storage Methods on Fecal, Saliva, and Skin Microbiome Composition.
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储存方法对粪便、唾液和皮肤微生物组组成影响的评价。
DOI：
10.1128/msystems.01329-20
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发表时间：
2021-04-27
期刊：
影响因子：
6.4
通讯作者：
Knight R
中科院分区：
文献类型：
--
作者：
Marotz C;Cavagnero KJ;Song SJ;McDonald D;Wandro S;Humphrey G;Bryant M;Ackermann G;Diaz E;Knight R
扩大我们对不同环境中微生物群落的了解包括在远离实验室的地方收集样本。确定具有成本效益的防腐剂，使微生物群落能够在室温下储存以进行测序分析，对于实现不同人群的微生物组分析至关重要。随着人类微生物组研究数量的增加，确定具有成本效益的实用防腐剂以实现室温样品储存变得越来越重要。在这里，我们重新分析了2016年发表的一项大样本储存研究的16S rRNA基因扩增子测序数据，并对该实验的残留DNA进行了鸟枪宏基因组测序。这两个结果都支持了最初的发现，即95%乙醇，一种无毒，成本效益高的防腐剂，在室温下保存样品数周是有效的。我们通过收集一组新的粪便、唾液和皮肤样本来扩大这种分析，以确定95%乙醇与样本的最佳比例。我们确定了粪便样本（将粪便拭子储存在95%乙醇中）和唾液样本（将未刺激的唾液以1：2的比例储存在95%乙醇中）的最佳收集方案。将皮肤拭子储存在95%乙醇中会减少微生物生物量并破坏群落组成，突出了低生物量样品保存的困难。这项研究的结果为粪便和口腔微生物群落的大规模分析确定了实用的解决方案。重要性扩大我们对不同环境中微生物群落的了解包括在远离实验室的地方收集样本。确定具有成本效益的防腐剂，使微生物群落能够在室温下储存以进行测序分析，对于实现不同人群的微生物组分析至关重要。在这里，我们验证了95%乙醇在室温下有效保存微生物成分数周的发现。我们还确定了95%乙醇与粪便和唾液样品的最佳比例，以保持微生物负荷和组成。这些结果为一种可获得的，无毒的，具有成本效益的解决方案提供了理论基础，该解决方案将使众包微生物组研究成为可能，例如Microsetta倡议，并降低收集不同样本的障碍。
Expanding our knowledge of microbial communities across diverse environments includes collecting samples in places far from the laboratory. Identifying cost-effective preservatives that will enable room temperature storage of microbial communities for sequencing analysis is crucial to enabling microbiome analyses across diverse populations. As the number of human microbiome studies expand, it is increasingly important to identify cost-effective, practical preservatives that allow for room temperature sample storage. Here, we reanalyzed 16S rRNA gene amplicon sequencing data from a large sample storage study published in 2016 and performed shotgun metagenomic sequencing on remnant DNA from this experiment. Both results support the initial findings that 95% ethanol, a nontoxic, cost-effective preservative, is effective at preserving samples at room temperature for weeks. We expanded on this analysis by collecting a new set of fecal, saliva, and skin samples to determine the optimal ratio of 95% ethanol to sample. We identified optimal collection protocols for fecal samples (storing a fecal swab in 95% ethanol) and saliva samples (storing unstimulated saliva in 95% ethanol at a ratio of 1:2). Storing skin swabs in 95% ethanol reduced microbial biomass and disrupted community composition, highlighting the difficulties of low biomass sample preservation. The results from this study identify practical solutions for large-scale analyses of fecal and oral microbial communities. IMPORTANCE Expanding our knowledge of microbial communities across diverse environments includes collecting samples in places far from the laboratory. Identifying cost-effective preservatives that will enable room temperature storage of microbial communities for sequencing analysis is crucial to enabling microbiome analyses across diverse populations. Here, we validate findings that 95% ethanol efficiently preserves microbial composition at room temperature for weeks. We also identified the optimal ratio of 95% ethanol to sample for stool and saliva to preserve both microbial load and composition. These results provide rationale for an accessible, nontoxic, cost-effective solution that will enable crowdsourcing microbiome studies, such as The Microsetta Initiative, and lower the barrier for collecting diverse samples.