title: Experimental reproducibility in flow-chamber biofilms.
abstract: The structural organization of microbial communities is influenced by many factors, e.g. nutrient composition, shear stress and temperature. This paper presents a general method for quantitative comparison of biofilm structures and assessment of experimental reproducibility between independent biofilm experiments. By using a novel computer program, COMSTAT, biofilm structures of Pseudomonas aeruginosa and an isogenic rpoS mutant were quantified. The strains were tagged with the green fluorescent protein (GFP) and grown in flow chambers with a defined minimal medium as substrate. Three independent rounds of biofilm experiments were performed and in each round, each of the two variants was grown in two separate channels. Nine image stacks were acquired in each channel 146 h after inoculation. An analysis of variance model incorporating the factors experiment round, bacterial strain, channel number and image stack number was used to analyse the data calculated by COMSTAT. Experimental reproducibility was verified by estimating the magnitude of the variance of the effects round (sigma(2)R) and the interaction between bacterial strain and round (sigma(2)BR). Mean thickness of the wild-type and rpoS mutant biofilms was estimated at 6.31 microm (SE 0.81 microm) and 16.85 microm (SE 0.87 microm), respectively.
authors.affiliation: Molecular Microbial Ecology Group, Department of Microbiology, The Technical University of Denmark block 301,DK-2800 Lyngby, Denmark1.
authors.forename: Arne
authors.initials: A
authors.lastname: Heydorn
authors.affiliation: Department of Mathematical Modelling, The Technical University of Denmark, DK-2800 Lyngby, Denmark2.
authors.forename: Bjarne Kjær
authors.initials: BK
authors.lastname: Ersbøll
authors.affiliation: Molecular Microbial Ecology Group, Department of Microbiology, The Technical University of Denmark block 301,DK-2800 Lyngby, Denmark1.
authors.forename: Morten
authors.initials: M
authors.lastname: Hentzer
authors.affiliation: Environmental Engineering Group, Department of Civil Engineering, NorthWestern University, Evanston, Illinois, USA3.
authors.forename: Matthew R
authors.initials: MR
authors.lastname: Parsek
authors.affiliation: Molecular Microbial Ecology Group, Department of Microbiology, The Technical University of Denmark block 301,DK-2800 Lyngby, Denmark1.
authors.forename: Michael
authors.initials: M
authors.lastname: Givskov
authors.affiliation: Molecular Microbial Ecology Group, Department of Microbiology, The Technical University of Denmark block 301,DK-2800 Lyngby, Denmark1.
authors.forename: Søren
authors.initials: S
authors.lastname: Molin
mesh_terms: D000704:Analysis of Variance; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D018441:Biofilms / Q000254:growth & development; D003470:Culture Media; D049452:Green Fluorescent Proteins; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D008164:Luminescent Proteins / Q000235:genetics / Q000378:metabolism; D011550:Pseudomonas aeruginosa / Q000235:genetics / Q000254:growth & development*; D015203:Reproducibility of Results; D012808:Sigma Factor / Q000235:genetics / Q000378:metabolism; D012984:Software
chemical_list: D001426:Bacterial Proteins; D003470:Culture Media; D008164:Luminescent Proteins; D012808:Sigma Factor; C069567:sigma factor KatF protein, Bacteria; D049452:Green Fluorescent Proteins