Bolt Botnen Amanda, Bjørnsen Mads Bjørn, Alberdi Antton, Gilbert M Thomas P, Aizpurua Ostaizka
Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Denmark.
University Museum, NTNU, Trondheim, Norway.
Heliyon. 2023 Jan 7;9(1):e12861. doi: 10.1016/j.heliyon.2023.e12861. eCollection 2023 Jan.
As metagenomic studies continue to increase in size and complexity, they are often required to incorporate data from geographically isolated locations or longitudinal time samples. This represents a technical challenge, given that many of the commonly used methods used for sample collection, storage, and DNA extraction are sensitive to differences related to the time, storage and chemistry involved. FTA cards have been previously proposed as a simple, reliable and cost-efficient method for the preservation of animal faecal microbiomes. In this study, we report a simplified extraction methodology for recovering microbiome DNA from faeces stored on FTA cards and compare its performance to a common alternative means of characterising such microbiomes; namely, immediate freezing of the faeces followed by DNA extraction using the Qiagen PowerSoil DNA isolation kit. Our results show that overall the application of our simplified DNA extraction methodology yields microbial community results that have higher diversity and an expanded core microbiome than that found using the PowerSoil methodology. This suggests that the FTA card extraction method presented here is a viable alternative for metagenomic studies using faecal material when traditional freeze-based storage methods are not feasible.
随着宏基因组学研究的规模和复杂性不断增加，它们常常需要纳入来自地理上孤立地点或纵向时间样本的数据。鉴于许多常用的样本采集、储存和DNA提取方法对与时间、储存和化学相关的差异敏感，这带来了一项技术挑战。FTA卡此前已被提议作为一种保存动物粪便微生物群的简单、可靠且经济高效的方法。在本研究中，我们报告了一种从存储在FTA卡上的粪便中回收微生物组DNA的简化提取方法，并将其性能与表征此类微生物组的一种常见替代方法进行比较；即立即冷冻粪便，然后使用Qiagen PowerSoil DNA提取试剂盒进行DNA提取。我们的结果表明，总体而言，我们简化的DNA提取方法的应用产生的微生物群落结果比使用PowerSoil方法具有更高的多样性和更广泛的核心微生物组。这表明，当传统的基于冷冻的储存方法不可行时，这里介绍的FTA卡提取方法是使用粪便材料进行宏基因组学研究的一种可行替代方法。
