First insights on the human gut microbiome have been gained from medium-sized, cross-sectional studies. However, given the modest portion of explained variance of currently identified covariates and the small effect size of gut microbiota modulation strategies, upscaling seems essential for further discovery and characterisation of the multiple influencing factors and their relative contribution. In order to guide future research projects and standardisation efforts, we here review currently applied collection and preservation methods for gut microbiome research. We discuss aspects such as sample quality, applicable omics techniques, user experience and time and cost efficiency. In addition, we evaluate the protocols of a large-scale microbiome cohort initiative, the Flemish Gut Flora Project, to give an idea of perspectives, and pitfalls of large-scale faecal sampling studies. Although cryopreservation can be regarded as the gold standard, freezing protocols generally require more resources due to cold chain management. However, here we show that much can be gained from an optimised transport chain and sample aliquoting before freezing. Other protocols can be useful as long as they preserve the microbial signature of a sample such that relevant conclusions can be drawn regarding the research question, and the obtained data are stable and reproducible over time.

中文翻译：

---

大规模肠道微生物组研究的实际考虑。


关于人类肠道微生物组的初步见解是从中等规模的横断面研究中获得的。然而，考虑到目前确定的协变量的解释方差的比例不大，并且肠道微生物群调节策略的影响较小，扩大规模对于进一步发现和表征多个影响因素及其相对贡献似乎至关重要。为了指导未来的研究项目和标准化工作，我们在此回顾目前应用于肠道微生物组研究的收集和保存方法。我们讨论样本质量、适用的组学技术、用户体验以及时间和成本效率等方面。此外，我们还评估了大规模微生物群计划“佛兰德肠道菌群项目”的方案，以给出大规模粪便采样研究的观点和陷阱。尽管冷冻保存可以被视为黄金标准，但由于冷链管理，冷冻方案通常需要更多资源。然而，我们在这里表明，优化的运输链和冷冻前的样品等分可以带来很多好处。其他协议也可能有用，只要它们保留样本的微生物特征，以便可以得出有关研究问题的相关结论，并且获得的数据随着时间的推移保持稳定和可重复。