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.

b LEPABE Department of Chemical Engineering Faculty of Engineering University of Porto Porto Portugal

c Micalis Institute INRA AgroParisTech Université Paris Saclay Jouy en Josas France

CEB ? Centre of Biological Engineering LIBRO Laboratórios de Biofilmes Rosário Oliveira University of Minho Campus de Gualtar Braga Portugal

Department of Biotechnology and Biomedicine Technical University of Denmark Lyngby Denmark

e INRA Centre Auvergne Rhône Alpes UR454 Microbiologie Saint Genès Champanelle France

f Department of Medical Oral and Biotechnological Sciences and Center of Excellence on Aging and Translational Medicine G d'Annunzio University of Chieti Pescara Chieti Italy

g Department of Food and Feed Safety Laboratory of Food Bacteriology Veterinary Research Institute Brno Czech Republic

h Department of Microbiology Faculty of Biotechnology and Food Sciences Slovak University of Agriculture in Nitra Nitra Slovakia

i Department of Food Science University of Copenhagen Frederiksberg C Denmark

j Department of Computer Science University of Vigo Ourense Spain

k Aarhus University Interdisciplinary Nanoscience Center Aarhus Denmark

l Agricultural University of Athens Lab of Microbiology and Biotechnology of Foods Athens Greece

Laboratory of Pharmaceutical Microbiology Ghent University Ghent Belgium

m LUNAM Université Oniris SECALIM UMR1024 INRA Université de Nantes Nantes France

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