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According to Louis Pasteur, “The microorganism will have the last word”. Industrial microorganism primes itself in the commercial exploitation of microorganisms for the benefit of man, plants, animals and the environment. And microbial products over the years have had phenomenal direct and indirect impact on man and the environment especially through the several economic products that are derived from them. The microorganisms of industrial importance include bacteria, yeasts, moulds, actinomycetes, algae and viruses in some cases. The isolation of industrially-important microorganisms including bacteria and fungi from their natural habitats is usually the first step in producing or developing producer strains of microbes for industrial fermentation processes. Microorganisms are ubiquitous and thus can be found in various environments including air, soil, water, and in or on the body surfaces of animals, plants and animals. However, the soil seems to be the most important source of industrially important microbes – since most products of microbial origin have been sourced from microbes that dwell in the soil.

Microorganisms have made tremendous contribution to the sustenance of man and his environment especially in the areas of health and food production. Over the years, microorganisms have contributed to the health and wellbeing of man and animals especially in producing several metabolites that are of economic importance. Microbes produce primary metabolites such as amino acids, nucleotides and vitamins; and the organisms in turn use these primary metabolites (vital to the growth and development of microbes) to synthesize secondary metabolites that are of commercial importance in several sectors including agriculture, medicine, pharmaceutical industry, and the food industry. Microbes have also been used to produce alternative fuel (e.g. biofuels), better starter cultures for the food industry, enzyme inhibitors, and pharmaceutically active substances such as hormones. Microbes are important sources of antibiotics, useful chemicals, enzymes, alcohol/ethanol, pesticide degrading agents and food (e.g. probiotics); and they have been extensively used since time immemorial to provide a variety of products and services.  Microbes are easy to cultivate and they grow or utilize cheap substrates or raw materials for growth. They have rapid growth and they produce diverse biological products or metabolites.

Microbes have genetic makeup that can be genetically manipulated for improved product yields; and this has contributed significantly in the production of various products through industrial fermentation processes. Thus, the isolation, characterization and preservation of microorganisms of industrial importance are an important aspect of industrial microbiology – because these organisms drive most of the fermentation processes that are the core of industrial microbiology. As aforementioned, the microorganisms of industrial importance are mainly sourced naturally from their natural habitats. But alternatively, these microbes can also be obtained as pure cultures from culture collection and preservation organizations – whose main responsibility is to maintain culture collections of different microbes for the purpose of commercialization. The American Type Culture Collection (ATCC) located in Rockville, Maryland, U.S.A; the National Culture Collection (NCC) in the UK; Commonwealth Mycological Institute (CMI) located in Kew, Surrey, England; the Fermentation Research Institute (FERM) located in Tokyo, Japan; and the Research Institute for Antibiotics (RIA) located in Moscow, Russia are some examples of culture collection organizations found around the world. These organizations are constant suppliers of pure cultures of microbes required for various industrial, medical and commercial purposes; and they serve as repositories of important microbes at their pure forms.  

The ecological habitat from which a desired microorganism is more likely to be isolated will depend on the characteristics of the product desired from the microbe, and of the particular industrial process it is to be applied (Table 1).

Table 1. Microorganisms and their natural habitat

YeastsWine yards and fruit juices  
AcidophilesPine growing sites and fruits  
ThermophilesHot springs and compost sites  
AlkalophilesHigh salinity soils  
OsmophilesSeas and oceans  
Protease enzyme producersMeat processing units and diary industries
Enzymes (cellulases, xylanase, pectinase)Paper and pulp industry, waste disposal sites of plants and fruits, agricultural soil  
Hydrocarbon-degrading microbesOil-contaminated sites, oil fields and oil vessels  
Biogas producers (e.g. methanogens)Effluent collection sites and refuse dump sites

For example, if the task is to isolate an organism that produces enzymes that can withstand high temperatures, the obvious place to look for such an organism will be in environments where the temperature is high (e.g. hot water springs) – since the enzymes might be applied in processes that deal with high temperature processes. Once an organism is initially selected from their natural habitat or purchased/collected from a culture collection center, the strain is usually modified through strain improvement techniques in order to improve cell biomass buildup and product yield. The screening of microbes from their natural habitats or samples is a major aspect of discovering novel products that are of economic importance as aforementioned. And once a particular product is isolated, the product is tested for toxicity and effectiveness before it can be used for commercial productions. The goal of screening microbes from their natural habitat is to detect and identify novel substances or microbial metabolites of economic interest to man, plants, animals and the environment. Secondly, the screening techniques used are expected to separate the isolated substances of interest in the fastest possible way from the numerous easily detected substances that are of no commercial interest.

Screening methods for the isolation of microbes from their natural habitat is usually based on the newest screening techniques and proper knowledge of the literature involved in such procedures. To be successful in screening microbes for certain industrial process, several disciplines including microbiology, biochemistry, chemistry and engineering are usually involved. The microbiologist is tasked with the isolation, identification, strain improvement and preservation and testing of the isolated microbes for possible biological and/or fermentative activity. While the chemist sees to the synthesis of substrates and inhibitory substances by the isolated organism, the biochemist provides the analytical procedures and approaches required for the purification of the desired molecules of interest. The chemical and mechanical engineers are saddled with the task of developing a suitable fermentation vessel for a successful fermentation process.

Further reading

Bushell M.E (1998). Application   of   the   principles   of   industrial   microbiology   to   biotechnology (ed. Wiseman, A.) Chapman and Hall, New York.

Byong H. Lee (2015). Fundamentals of Food Biotechnology. Second edition. Wiley-Blackwell, New Jersey, United States.

Frazier W.C, Westhoff D.C and Vanitha N.M (2014). Food Microbiology. Fifth edition. McGraw-Hill Education (India) Private Limited, New Delhi, India.

Jay J.M (2005). Modern Food Microbiology. Fourth edition. Chapman and Hall Inc, New York, USA.

Bushell M.E (1998). Application   of   the   principles   of   industrial   microbiology   to   biotechnology (ed. Wiseman, A.) Chapman and Hall, New York.

Farida A.A (2012). Dairy Microbiology. First edition. Random Publications. New Delhi, India.

Nduka Okafor (2007). Modern industrial microbiology and biotechnology. First edition. Science Publishers, New Hampshire, USA.

Roberts D and Greenwood M (2003). Practical Food Microbiology. Third edition. Blackwell publishing Inc, USA.

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