title: A methodology for a quantitative interpretation of DGGE with the help of mathematical modelling: application in biohydrogen production.
abstract: Molecular biology techniques provide valuable insights in the investigation of microbial dynamics and evolution. Denaturing gradient gel electrophoresis (DGGE) analysis is one of the most popular methods which have been used in bioprocess assessment. Most of the anaerobic digestion models consider several microbial populations as state variables. However, the difficulty of measuring individual species concentrations may cause inaccurate model predictions. The integration of microbial data and ecosystem modelling is currently a challenging issue for improved system control. A novel procedure that combines common experimental measurements, DGGE, and image analysis is presented in this study in order to provide a preliminary estimation of the actual concentration of the dominant bacterial ribotypes in a bioreactor, for further use as a variable in mathematical modelling of the bioprocess. This approach was applied during the start-up of a continuous anaerobic bioreactor for hydrogen production. The experimental concentration data were used for determining the kinetic parameters of each species, by using a multi-species chemostat-model. The model was able to reproduce the global trend of substrate and biomass concentrations during the reactor start-up, and predicted in an acceptable way the evolution of each ribotype concentration, depicting properly specific ribotype selection and extinction.
authors.affiliation: Escuela de Ingeniería Bioquímica, Facultad de Ingeniería, Pontiﬁcia Universidad Católica de Valparaíso. General Cruz 34, Valparaíso, Chile E-mail: gonzalo.ruiz@ucv.cl.
authors.forename: Estela
authors.initials: E
authors.lastname: Tapia
authors.affiliation: Escuela de Ingeniería Bioquímica, Facultad de Ingeniería, Pontiﬁcia Universidad Católica de Valparaíso. General Cruz 34, Valparaíso, Chile E-mail: gonzalo.ruiz@ucv.cl; INRIA-Chile. Chilean Informatics Research and Innovation Centre (CIRIC), Rosario Norte 555 of. 703, Las Condes, Santiago, Chile.
authors.forename: Andres
authors.initials: A
authors.lastname: Donoso-Bravo
authors.affiliation: Escuela de Ingeniería Bioquímica, Facultad de Ingeniería, Pontiﬁcia Universidad Católica de Valparaíso. General Cruz 34, Valparaíso, Chile E-mail: gonzalo.ruiz@ucv.cl.
authors.forename: Léa
authors.initials: L
authors.lastname: Cabrol
authors.affiliation: Centre of Biological Engineering, Institute for Biotechnology and Bioengineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
authors.forename: Madalena
authors.initials: M
authors.lastname: Alves
authors.affiliation: Centre of Biological Engineering, Institute for Biotechnology and Bioengineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
authors.forename: Alcina
authors.initials: A
authors.lastname: Pereira
authors.affiliation: UMR, INRA-SupAgro 'MISTEA', 2 place Viala, 34090 Montpellier, France and EPI 'MODEMIC', INRIA 06902 Sophia-Antipolis, France.
authors.forename: Alain
authors.initials: A
authors.lastname: Rapaport
authors.affiliation: Escuela de Ingeniería Bioquímica, Facultad de Ingeniería, Pontiﬁcia Universidad Católica de Valparaíso. General Cruz 34, Valparaíso, Chile E-mail: gonzalo.ruiz@ucv.cl.
authors.forename: Gonzalo
authors.initials: G
authors.lastname: Ruiz-Filippi
mesh_terms: D019149:Bioreactors / Q000382:microbiology*; D058645:Denaturing Gradient Gel Electrophoresis; D006859:Hydrogen / Q000378:metabolism; D059013:Microbial Consortia; D008954:Models, Biological; D021521:Ribotyping
chemical_list: D006859:Hydrogen