REVIEW PAPER Methodologies for the characterization of microbes in industrial environments: a review Received: 1 November 2002 / Accepted: 2 April 2003 / Published online: 23 May 2003 Ó Society for Industrial Microbiology 2003 Abstract There is growing interest in research and development to develop novel tools to study, detect, and characterize microbes and their communities in indus- trial environments. However, knowledge about their validity in practical industrial use is still scarce. This review describes the advantages and limitations of tra- ditional and molecular methods used for biofilm and/or planktonic cell studies, especially those performed with Listeria monocytogenes, Bacillus cereus, and/or Clos- tridium perfringens. In addition, the review addresses the importance of isolating the microorganisms from the industrial environment and the possibilities and future prospects for exploiting the described methods in the industrial environment. Keywords Biofilm Culture Molecular techniques Fingerprinting Introduction Microorganisms inhabiting the food and processing industries are mostly benign, but some can be harmful to the processing and safety of the product. Therefore, the control of harmful microorganisms is essential. Indus- trial processes that deal with any biological material provide nutrients and conditions for microorganisms to grow, either in the shelter of sessile biofilms on surfaces or as planktonic cells in the circulating process waters. Moreover, in most natural and industrial systems where the supply of nutrients is sufficient, microorganisms grow as spatially organized, matrix-enclosed, multispe- cies communities in biofilms. Besides a solid surface, the microbes need only water to initiate biofilm formation [72, 73, 270]. Microbial biofilms and biofouling of sur- faces and interfaces within the industrial environment are major problems. In industry, the first step is identi- fying the problem of biofilms and biofouling in a par- ticular process or site. Subsequently, it is important to determine the best possible methods for detection of biofilms in situ, so that they can be characterized and possibly further studied in the laboratory. Finally, this information can be used to define strategies for con- trolling biofilm formation in that specific environment [208]. Microorganisms in food and in industrial environ- ments are distributed unevenly; and there is a great variation in the cell density and composition of micro- bial population over space and time. Typically, the microbial cells are located in the surfaces of the food matrix and process equipment; and the cell density and species distribution may vary in different parts of a food product [77, 156, 158]. Changes in the ecosystem cause continuous qualitative and quantitative variation in the composition of the microbial community over time [152]. Both intrinsic (e.g. chemical composition, natural microbiota) and extrinsic factors (e.g. processing, stor- age conditions) affect microbial growth [272] and consequently the composition of the microbial commu- nity. All these factors affect the actual sampling of the industrial environment, making it a demanding task to perform. Published data on microbial detection and charac- terization from industrial environments is abundant and therefore the following review is restricted to the most relevant and widely applied techniques and to just a few specific bacterial species important in the food and process industrial environments, namely Listeria mono- cytogenes, Bacillus cereus, and Clostridium perfringens. Both traditional and molecular identification and char- acterization methods for bacteria and their communities are discussed, in addition to typing methods for bacterial isolates obtained from the industrial environment and/ or foodstuff. Future prospects for the exploitation of the J Ind Microbiol Biotechnol (2003) 30: 327–356 DOI 10.1007/s10295-003-0056-y Johanna Maukonen Jaana Ma¨tto¨ Gun Wirtanen Laura Raaska Tiina Mattila-Sandholm Maria Saarela J. Maukonen J. Ma¨tto¨ G. Wirtanen L. Raaska T. Mattila-Sandholm M. Saarela (&) VTT Biotechnology, P.O. Box 1500, 02044 VTT, Finland E-mail: maria.saarela@vtt.fi Tel.: +358-9-4564466 Fax: +358-9-4552103