TY - JOUR
T1 - Optimization of metabolomics of defined in vitro gut microbial ecosystems
AU - Wissenbach, Dirk K
AU - Oliphant, Kaitlyn
AU - Rolle-Kampczyk, Ulrike
AU - Yen, Sandi
AU - Hoeke, Henrike
AU - Baumann, Sven
AU - Haange, Sven-Bastiaan
AU - Verdu, Elena F.
AU - Allen-Vercoe, Emma
AU - von Bergen, Martin
PY - 2016
Y1 - 2016
N2 - 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.
AB - 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.
KW - H NMR
KW - Bioreactor
KW - Human gut microbiota
KW - LC–MS/MS
KW - Metabolic profiling
KW - Metabolomics
UR - http://www.scopus.com/inward/record.url?scp=84961774618&partnerID=8YFLogxK
U2 - 10.1016/j.ijmm.2016.03.007
DO - 10.1016/j.ijmm.2016.03.007
M3 - Review article
C2 - 27020116
AN - SCOPUS:84961774618
SN - 1438-4221
VL - 306
SP - 280
EP - 289
JO - International Journal of Medical Microbiology
JF - International Journal of Medical Microbiology
IS - 5
ER -