Wissenbach Dirk K, Oliphant Kaitlyn, Rolle-Kampczyk Ulrike, Yen Sandi, Höke Henrike, Baumann Sven, Haange Sven B, Verdu Elena F, Allen-Vercoe Emma, von Bergen Martin
Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research-UFZ, Permoserstrasse 15, D-04318 Leipzig, Germany.
Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.
Int J Med Microbiol. 2016 Aug;306(5):280-289. doi: 10.1016/j.ijmm.2016.03.007. Epub 2016 Mar 16.
The metabolic functionality of a microbial community is a key to the understanding of its inherent ecological processes and the interaction with the host. However, the study of the human gut microbiota is hindered by the complexity of this ecosystem. One way to resolve this issue is to derive defined communities that may be cultured ex vivo in bioreactor systems and used to approximate the native ecosystem. Doing so has the advantage of experimental reproducibility and ease of sampling, and furthermore, in-depth analysis of metabolic processes becomes highly accessible. Here, we review the use of bioreactor systems for ex vivo modelling of the human gut microbiota with respect to analysis of the metabolic output of the microbial ecosystem, and discuss the possibility of mechanistic insights using these combined techniques. We summarize the different platforms currently used for metabolomics and suitable for analysis of gut microbiota samples from a bioreactor system. With the help of representative datasets obtained from a series of bioreactor runs, we compare the outputs of both NMR and mass spectrometry based approaches in terms of their coverage, sensitivity and quantification. We also discuss the use of untargeted and targeted analyses in mass spectroscopy and how these techniques can be combined for optimal biological interpretation. Potential solutions for linking metabolomic and phylogenetic datasets with regards to active, key species within the ecosystem will be presented.
微生物群落的代谢功能是理解其内在生态过程以及与宿主相互作用的关键。然而，人类肠道微生物群的研究受到该生态系统复杂性的阻碍。解决这一问题的一种方法是构建特定的群落，这些群落可在生物反应器系统中进行体外培养，并用于模拟天然生态系统。这样做具有实验可重复性和采样便捷性的优点，此外，对代谢过程的深入分析也变得非常容易实现。在此，我们综述了生物反应器系统在体外模拟人类肠道微生物群以分析微生物生态系统代谢输出方面的应用，并讨论了使用这些联合技术获得机理见解的可能性。我们总结了目前用于代谢组学且适用于分析来自生物反应器系统的肠道微生物群样本的不同平台。借助从一系列生物反应器运行中获得的代表性数据集，我们从覆盖范围、灵敏度和定量方面比较了基于核磁共振（NMR）和质谱的方法的输出结果。我们还讨论了质谱中无靶向和靶向分析的使用，以及如何将这些技术结合起来以实现最佳的生物学解释。我们将提出关于将代谢组学和系统发育数据集与生态系统内活跃的关键物种相联系的潜在解决方案。
