title: Proteomic profiling of an undefined microbial consortium cultured in fermented dairy manure: Methods development.
abstract: The production of polyhydroxyalkanoates (PHA; bioplastics) from waste or surplus feedstocks using mixed microbial consortia (MMC) and aerobic dynamic feeding (ADF) is a growing field within mixed culture biotechnology. This study aimed to optimize a 2DE workflow to investigate the proteome dynamics of an MMC synthesizing PHA from fermented dairy manure. To mitigate the challenges posed to effective 2DE by this complex sample matrix, the bacterial biomass was purified using Accudenz gradient centrifugation (AGC) before protein extraction. The optimized 2DE method yielded high-quality gels suitable for quantitative comparative analysis and subsequent protein identification by LC-MS/MS. The optimized 2DE method could be adapted to other proteomic investigations involving MMC in complex organic or environmental matrices.
authors.affiliation: Microbiology, Molecular Biology, and Biochemistry Graduate Program, Department of Biological Sciences, University of Idaho, Moscow, ID, USA.
authors.forename: Andrea J
authors.initials: AJ
authors.lastname: Hanson
authors.affiliation: University of Idaho and Washington State University School of Food Science, Food Research Center, Moscow, ID, USA.
authors.forename: Andrzej J
authors.initials: AJ
authors.lastname: Paszczynski
authors.affiliation: Department of Civil Engineering, University of Idaho, Moscow, ID, USA.
authors.forename: Erik R
authors.initials: ER
authors.lastname: Coats
mesh_terms: D001426:Bacterial Proteins / Q000032:analysis* / Q000737:chemistry; D015180:Electrophoresis, Gel, Two-Dimensional / Q000379:methods; D008372:Manure / Q000382:microbiology*; D059013:Microbial Consortia / Q000502:physiology*; D020543:Proteome / Q000032:analysis* / Q000737:chemistry; D040901:Proteomics / Q000379:methods*; D053719:Tandem Mass Spectrometry / Q000379:methods
chemical_list: D001426:Bacterial Proteins; D008372:Manure; D020543:Proteome
keywords: 2DE; Accudenz gradient centrifugation; Mixed culture biotechnology; Mixed microbial consortia