4.4 Review

Optimization of metabolomics of defined in vitro gut microbial ecosystems

Journal

INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY
Volume 306, Issue 5, Pages 280-289

Publisher

ELSEVIER GMBH
DOI: 10.1016/j.ijmm.2016.03.007

Keywords

Human gut microbiota; Bioreactor; Metabolic profiling; Metabolomics; LC-MS/MS; H-1 NMR

Funding

  1. Crohn's and Colitis Canada
  2. DFG [SPP1656]

Ask authors/readers for more resources

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. (C) 2016 Elsevier GmbH. All rights reserved.

Authors

I am an author on this paper
Click your name to claim this paper and add it to your profile.

Reviews

Primary Rating

4.4
Not enough ratings

Secondary Ratings

Novelty
-
Significance
-
Scientific rigor
-
Rate this paper

Recommended

No Data Available
No Data Available