title: Enhancing metaproteomics--The value of models and defined environmental microbial systems.
abstract: Metaproteomics--the large-scale characterization of the entire protein complement of environmental microbiota at a given point in time--has provided new features to study complex microbial communities in order to unravel these "black boxes." New technical challenges arose that were not an issue for classical proteome analytics before that could be tackled by the application of different model systems. Here, we review different current and future model systems for metaproteome analysis. Following a short introduction to microbial communities and metaproteomics, we introduce model systems for clinical and biotechnological research questions including acid mine drainage, anaerobic digesters, and activated sludge. Model systems are useful to evaluate the challenges encountered within (but not limited to) metaproteomics, including species complexity and coverage, biomass availability, or reliable protein extraction. The implementation of model systems can be considered as a step forward to better understand microbial community responses and ecological functions of single member organisms. In the future, improvements are necessary to fully explore complex environmental systems by metaproteomics.
authors.affiliation: Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark.
authors.forename: Florian-Alexander
authors.initials: FA
authors.lastname: Herbst
authors.affiliation: Department of Proteomics, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.|Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.
authors.forename: Vanessa
authors.initials: V
authors.lastname: Lünsmann
authors.affiliation: Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark.
authors.forename: Henrik
authors.initials: H
authors.lastname: Kjeldal
authors.affiliation: Department of Proteomics, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.
authors.forename: Nico
authors.initials: N
authors.lastname: Jehmlich
authors.affiliation: Systematic Proteome Research and Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Tholey
authors.affiliation: Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark.|Department of Proteomics, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: von Bergen
authors.affiliation: Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark.
authors.forename: Jeppe Lund
authors.initials: JL
authors.lastname: Nielsen
authors.affiliation: Chemical Sciences Division, Oak Ridge National Lab, Oak Ridge, TN, USA.
authors.forename: Robert L
authors.initials: RL
authors.lastname: Hettich
authors.affiliation: Institute of Animal Science, University of Hohenheim, Stuttgart, Germany.
authors.forename: Jana
authors.initials: J
authors.lastname: Seifert
authors.affiliation: Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark.
authors.forename: Per Halkjaer
authors.initials: PH
authors.lastname: Nielsen
mesh_terms: D000818:Animals; D001419:Bacteria / Q000235:genetics*; D017173:Caenorhabditis elegans / Q000235:genetics; D017753:Ecosystem; D000069196:Gastrointestinal Microbiome / Q000235:genetics*; D041981:Gastrointestinal Tract / Q000382:microbiology; D006801:Humans; D056186:Metagenomics / Q000379:methods*; D020543:Proteome / Q000032:analysis*; D040901:Proteomics / Q000379:methods*; D012722:Sewage / Q000382:microbiology*
chemical_list: D020543:Proteome; D012722:Sewage
keywords: Community proteomics; Metaproteomics; Microbiology; Microbiota; Model systems