title: Optimization of metabolomics of defined in vitro gut microbial ecosystems.
abstract: 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.
authors.affiliation: Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research-UFZ, Permoserstrasse 15, D-04318 Leipzig, Germany.
authors.forename: Dirk K
authors.initials: DK
authors.lastname: Wissenbach
authors.affiliation: Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.
authors.forename: Kaitlyn
authors.initials: K
authors.lastname: Oliphant
authors.affiliation: Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research-UFZ, Permoserstrasse 15, D-04318 Leipzig, Germany.
authors.forename: Ulrike
authors.initials: U
authors.lastname: Rolle-Kampczyk
authors.affiliation: Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.
authors.forename: Sandi
authors.initials: S
authors.lastname: Yen
authors.affiliation: Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research-UFZ, Permoserstrasse 15, D-04318 Leipzig, Germany; Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, University of Leipzig, Leipzig, Germany.
authors.forename: Henrike
authors.initials: H
authors.lastname: Höke
authors.affiliation: Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research-UFZ, Permoserstrasse 15, D-04318 Leipzig, Germany.
authors.forename: Sven
authors.initials: S
authors.lastname: Baumann
authors.affiliation: Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research-UFZ, Permoserstrasse 15, D-04318 Leipzig, Germany.
authors.forename: Sven B
authors.initials: SB
authors.lastname: Haange
authors.affiliation: Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada.
authors.forename: Elena F
authors.initials: EF
authors.lastname: Verdu
authors.affiliation: Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada. Electronic address: eav@uoguelph.ca.
authors.forename: Emma
authors.initials: E
authors.lastname: Allen-Vercoe
authors.affiliation: Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research-UFZ, Permoserstrasse 15, D-04318 Leipzig, Germany; Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, Germany; Aalborg University, Department of Chemistry and Biosciences, Aalborg University, 9000 Aalborg, Denmark. Electronic address: martin.vonbergen@ufz.de.
authors.forename: Martin
authors.initials: M
authors.lastname: von Bergen
mesh_terms: D019149:Bioreactors / Q000382:microbiology*; D017753:Ecosystem; D000069196:Gastrointestinal Microbiome; D041981:Gastrointestinal Tract / Q000382:microbiology*; D006801:Humans; D055432:Metabolomics / Q000379:methods*; D064307:Microbiota; D008962:Models, Theoretical
keywords: (1)H NMR; Bioreactor; Human gut microbiota; LC–MS/MS; Metabolic profiling; Metabolomics