title: Challenges of metabolomics in human gut microbiota research.
abstract: The review highlights the role of metabolomics in studying human gut microbial metabolism. Microbial communities in our gut exert a multitude of functions with huge impact on human health and disease. Within the meta-omics discipline, gut microbiome is studied by (meta)genomics, (meta)transcriptomics, (meta)proteomics and metabolomics. The goal of metabolomics research applied to fecal samples is to perform their metabolic profiling, to quantify compounds and classes of interest, to characterize small molecules produced by gut microbes. Nuclear magnetic resonance spectroscopy and mass spectrometry are main technologies that are applied in fecal metabolomics. Metabolomics studies have been increasingly used in gut microbiota related research regarding health and disease with main focus on understanding inflammatory bowel diseases. The elucidated metabolites in this field are summarized in this review. We also addressed the main challenges of metabolomics in current and future gut microbiota research. The first challenge reflects the need of adequate analytical tools and pipelines, including sample handling, selection of appropriate equipment, and statistical evaluation to enable meaningful biological interpretation. The second challenge is related to the choice of the right animal model for studies on gut microbiota. We exemplified this using NMR spectroscopy for the investigation of cross-species comparison of fecal metabolite profiles. Finally, we present the problem of variability of human gut microbiota and metabolome that has important consequences on the concepts of personalized nutrition and medicine.
authors.affiliation: Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany.
authors.forename: Kirill S
authors.initials: KS
authors.lastname: Smirnov
authors.affiliation: Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany.
authors.forename: Tanja V
authors.initials: TV
authors.lastname: Maier
authors.affiliation: Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany.
authors.forename: Alesia
authors.initials: A
authors.lastname: Walker
authors.affiliation: Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany.
authors.forename: Silke S
authors.initials: SS
authors.lastname: Heinzmann
authors.affiliation: Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany.
authors.forename: Sara
authors.initials: S
authors.lastname: Forcisi
authors.affiliation: Department of Agriculture, Food and Nutritional Science, University of Alberta, T6G 2E1 Edmonton, AB, Canada.
authors.forename: Inés
authors.initials: I
authors.lastname: Martinez
authors.affiliation: Department of Agriculture, Food and Nutritional Science, University of Alberta, T6G 2E1 Edmonton, AB, Canada.
authors.forename: Jens
authors.initials: J
authors.lastname: Walter
authors.affiliation: Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany; Chair of Analytical Food Chemistry, Technische Universität München, Alte Akademie 10, 85354 Freising, Germany; ZIEL, Institute for Food & Health, Weihenstephaner Berg 1, 85354 Freising, Germany. Electronic address: Schmitt-Kopplin@helmholtz-muenchen.de.
authors.forename: Philippe
authors.initials: P
authors.lastname: Schmitt-Kopplin
mesh_terms: D000818:Animals; D004195:Disease Models, Animal; D005243:Feces / Q000737:chemistry* / Q000382:microbiology*; D000069196:Gastrointestinal Microbiome; D006801:Humans; D009682:Magnetic Resonance Spectroscopy; D013058:Mass Spectrometry; D055432:Metabolomics / Q000379:methods*; D064307:Microbiota; D015203:Reproducibility of Results
keywords: Gut microbiota; IBD; Mass spectrometry; Metabolomics; NMR