title: Critical review on biofilm methods.
abstract: Biofilms are widespread in nature and constitute an important strategy implemented by microorganisms to survive in sometimes harsh environmental conditions. They can be beneficial or have a negative impact particularly when formed in industrial settings or on medical devices. As such, research into the formation and elimination of biofilms is important for many disciplines. Several new methodologies have been recently developed for, or adapted to, biofilm studies that have contributed to deeper knowledge on biofilm physiology, structure and composition. In this review, traditional and cutting-edge methods to study biofilm biomass, viability, structure, composition and physiology are addressed. Moreover, as there is a lack of consensus among the diversity of techniques used to grow and study biofilms. This review intends to remedy this, by giving a critical perspective, highlighting the advantages and limitations of several methods. Accordingly, this review aims at helping scientists in finding the most appropriate and up-to-date methods to study their biofilms.
authors.affiliation: a CEB ? Centre of Biological Engineering, LIBRO, Laboratórios de Biofilmes Rosário Oliveira, University of Minho Campus de Gualtar , Braga , Portugal.
authors.forename: Joana
authors.initials: J
authors.lastname: Azeredo
authors.affiliation: b LEPABE, Department of Chemical Engineering, Faculty of Engineering , University of Porto , Porto , Portugal.
authors.forename: Nuno F
authors.initials: NF
authors.lastname: Azevedo
authors.affiliation: c Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay , Jouy-en-Josas , France.
authors.forename: Romain
authors.initials: R
authors.lastname: Briandet
authors.affiliation: a CEB ? Centre of Biological Engineering, LIBRO, Laboratórios de Biofilmes Rosário Oliveira, University of Minho Campus de Gualtar , Braga , Portugal.
authors.forename: Nuno
authors.initials: N
authors.lastname: Cerca
authors.affiliation: d Laboratory of Pharmaceutical Microbiology , Ghent University , Ghent , Belgium.
authors.forename: Tom
authors.initials: T
authors.lastname: Coenye
authors.affiliation: a CEB ? Centre of Biological Engineering, LIBRO, Laboratórios de Biofilmes Rosário Oliveira, University of Minho Campus de Gualtar , Braga , Portugal.
authors.forename: Ana Rita
authors.initials: AR
authors.lastname: Costa
authors.affiliation: e INRA Centre Auvergne-Rhône-Alpes , UR454 Microbiologie , Saint-Genès Champanelle , France.
authors.forename: Mickaël
authors.initials: M
authors.lastname: Desvaux
authors.affiliation: f Department of Medical, Oral, and Biotechnological Sciences, and Center of Excellence on Aging and Translational Medicine (CeSI-MeT) , "G. d'Annunzio" University of Chieti-Pescara , Chieti , Italy.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Di Bonaventura
authors.affiliation: e INRA Centre Auvergne-Rhône-Alpes , UR454 Microbiologie , Saint-Genès Champanelle , France.
authors.forename: Michel
authors.initials: M
authors.lastname: Hébraud
authors.affiliation: g Department of Food and Feed Safety, Laboratory of Food Bacteriology , Veterinary Research Institute , Brno , Czech Republic.
authors.forename: Zoran
authors.initials: Z
authors.lastname: Jaglic
authors.affiliation: h Department of Microbiology, Faculty of Biotechnology and Food Sciences , Slovak University of Agriculture in Nitra , Nitra , Slovakia.
authors.forename: Miroslava
authors.initials: M
authors.lastname: Kačániová
authors.affiliation: i Department of Food Science (FOOD) , University of Copenhagen , Frederiksberg C , Denmark.
authors.forename: Susanne
authors.initials: S
authors.lastname: Knøchel
authors.affiliation: j Department of Computer Science , University of Vigo , Ourense , Spain.
authors.forename: Anália
authors.initials: A
authors.lastname: Lourenço
authors.affiliation: b LEPABE, Department of Chemical Engineering, Faculty of Engineering , University of Porto , Porto , Portugal.
authors.forename: Filipe
authors.initials: F
authors.lastname: Mergulhão
authors.affiliation: k Aarhus University, Interdisciplinary Nanoscience Center (iNANO) , Aarhus , Denmark.
authors.forename: Rikke Louise
authors.initials: RL
authors.lastname: Meyer
authors.affiliation: l Agricultural University of Athens, Lab of Microbiology and Biotechnology of Foods , Athens , Greece.
authors.forename: George
authors.initials: G
authors.lastname: Nychas
authors.affiliation: b LEPABE, Department of Chemical Engineering, Faculty of Engineering , University of Porto , Porto , Portugal.
authors.forename: Manuel
authors.initials: M
authors.lastname: Simões
authors.affiliation: m LUNAM Université, Oniris, SECALIM UMR1024 INRA , Université de Nantes , Nantes , France.
authors.forename: Odile
authors.initials: O
authors.lastname: Tresse
authors.affiliation: n Department of Biotechnology and Biomedicine , Technical University of Denmark , Lyngby, Denmark.
authors.forename: Claus
authors.initials: C
authors.lastname: Sternberg
mesh_terms: D001422:Bacterial Adhesion; D018441:Biofilms / Q000254:growth & development; D016208:Databases, Factual; D004867:Equipment Design; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D017404:In Situ Hybridization, Fluorescence; D056656:Lab-On-A-Chip Devices; D008828:Microbiological Techniques / Q000295:instrumentation* / Q000379:methods; D008853:Microscopy / Q000379:methods*; D008967:Molecular Biology / Q000379:methods*; D012984:Software
keywords: Biofilm formation; biofilm data analysis; biofilm formation devices; biofilm measurement; biofilm omics