Practical considerations for large-scale gut microbiome studies.
Practical considerations for large-scale gut microbiome studies.
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DOI：
10.1093/femsre/fux027
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发表时间：
2017-08-01
影响因子：
11.3
通讯作者：
Raes J
中科院分区：
文献类型：
--
作者：
Vandeputte D;Tito RY;Vanleeuwen R;Falony G;Raes J
对人类肠道微生物群的首次洞察是从中型横断面研究中获得的。然而，考虑到目前已确定的协变量的适度解释方差和肠道微生物区系调制策略的小效应规模，上调似乎对于进一步发现和表征多种影响因素及其相对贡献是必不可少的。为了指导未来的研究项目和标准化工作，我们在这里回顾了目前应用于肠道微生物组研究的收集和保存方法。我们讨论了样本质量、适用的组学技术、用户体验以及时间和成本效率等方面的问题。此外，我们评估了大规模微生物群组倡议的协议，佛兰德肠道菌群项目，以提供一个大规模粪便采样研究的前景和陷阱的想法。虽然冷冻保存可以被视为黄金标准，但由于冷链管理，冷冻协议通常需要更多的资源。然而，我们在这里表明，在冷冻之前，通过优化传送链和样品等分可以获得很大好处。其他方案只要保留样本的微生物特征，以便能够就研究问题得出相关结论，并且所获得的数据随着时间的推移是稳定和可重现的，就可以是有用的。作者综述了目前肠道微生物组研究中应用的收集和保存方法，讨论了样本质量、适用的组学技术、用户体验和时间和成本效益等方面的问题，并对比利时大规模肠道微生物组采样工作佛兰德肠道菌群计划的方案进行了评估，以期对实施粪便采样进行肠道微生物组研究的全人群研究的前景和陷阱有所了解。
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. The authors review currently applied collection and preservation methods for gut microbiome research, discussing aspects such as sample quality, applicable omics techniques, user experience and time and cost-efficiency, and evaluate the protocols of the Flemish Gut Flora Project, a large-scale gut microbiome sampling effort in Belgium, to give an idea of perspectives, and pitfalls of population-wide studies implementing faecal sampling for gut microbiome research.
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DOI：
10.1038/nrmicro3552
发表时间：
2016-01
期刊：
Nature reviews. Microbiology
影响因子：
--
作者：
Donaldson GP;Lee SM;Mazmanian SK
通讯作者：
Mazmanian SK
影响因子：
4.6
作者：
Anderson EL;Li W;Klitgord N;Highlander SK;Dayrit M;Seguritan V;Yooseph S;Biggs W;Venter JC;Nelson KE;Jones MB
通讯作者：
Jones MB
影响因子：
3.7
作者：
Bai G;Gajer P;Nandy M;Ma B;Yang H;Sakamoto J;Blanchard MH;Ravel J;Brotman RM
通讯作者：
Brotman RM
影响因子：
4.6
作者：
Choo JM;Leong LE;Rogers GB
通讯作者：
Rogers GB
影响因子：
12.3
作者：
Debelius J;Song SJ;Vazquez-Baeza Y;Xu ZZ;Gonzalez A;Knight R
通讯作者：
Knight R