Food Microbiology: Application of Microorganisms in Food Industry

Abstract

Industrial microbiology is one branch of applied microbiology where microbes are used to produce important products such as metabolic manufacture, biotransformation, manufacture of energy (bio-fuels), management of organic and industrial wastes, manufacture of microbial biomass (microbial protein) for food and feed, manufacture of bio-control agents (antibiotics) and fermentation of food products. Microbial food processing is used to transform simple food into a value-added form with the assistance of microbes. In addition, it involves converting low-value, often inedible, perishable natural resources into high-value, safe food products. Since antiquity, mankind have used microbes to produce a variety of food products such as dairy products, bread, vinegar, wine and beer, as well as fermented seafood, meat and vegetables. There are many useful applications of microbes in the food processing industry, which have a strong influence on the quality and quantity of food. Recently, microbial approaches of food processing have garnered global attention as a workable method to food conservation and a good source of vital nutrients. Microbial contamination of food commodities typically occurs between the field and the processing plant or during processing, storage, transportation and distribution or prior to consumption. Consequently, microbes are being considered as very significant elements in food manufacturing, food quality maintenance and food safety. In this chapter, we focus on the beneficial roles of microorganisms, the applications of microorganisms in the food industry and the risks of microbial contamination.

1. Introduction

Microorganisms are microscopic organisms that cannot be seen with the eye and are less than one millimeter in length [1]. Despite their simple structure, these microorganisms are capable of basic physiological activities [2]. Microbes are ubiquitous, that is, they exist everywhere such as air, water, soil, human body, on plants and animals. The general assumption is that microbes are harmful to humans; however, there are various organisms that are valuable in many ways to humankind. Microbes are responsible, on the one hand, for the spoilage of food and disease and, on the other hand, they are used for the production of valuable materials (Figure 1). Louis Pasteur first showed the role of microorganisms in food spoilage and fermentation [3]. In 1845, Berkeley proved that the Irish potato blight is a type of fungus that causes great damage to the economy of Ireland [4]. In 1836, Bassi asserted that fungi are the causative agents of disease in animals, and the following year, Schonlein proved that fungi are the cause of some skin diseases in humans [5]. Microbes that live in association with humans (live on different surfaces of the human body) protect them against infections and other diseases. For instance, the presence of Bifidobacterium and Lactobacilli in the human body limits the growth of pathogenic microbes, they are used to treat wastewater and support reduce atmospheric nitrogen and turn it into useful ammonia. Once this fact was established, scientists tried to isolate microorganisms that were more efficient in producing better products or improving processes [6]. Many kinds of microorganisms from yeasts, bacteria and fungi are useful to humanity and have a major contribution in the food industry. Yeast is the most widely absorbed microbes in the food- and feed-processing industry, followed by bacteria. Microbes confer the favorable physico-chemical and biological properties and improve the taste, aroma and shelf life of products at very low cost. All processes which are carried out using microorganisms are called fermentation processes. Microorganisms also contribute to cost savings and revenue manufacture within the food industry. They can be genetically manipulated to create the product with the necessary properties on a large scale. Apart from the manufacture of the desired products, microbes also aid to warrant the quality and safety of the products. In the past, microorganisms were used to prepare food products such as bread, yogurt or curd, beverages, cheese, etc. for a long time, without even being aware of their role in fermentation [7]. Due to the increasing demand for the production of food products with desirable sensory quality, long shelf life and containing natural ingredients, fermented products have been given attention in order to meet the needs of consumers [8]. With the increase in people’s awareness, the demand for foods containing natural preservatives instead of artificial preservatives has increased [9]. One of the most important bacteria in fermented foods is lactic acid bacteria [10]. Conservation cultures have been used as one of the oldest methods of biological food preservation [10]. Lactic acid is obtained from carbohydrate fermentation and by acidifying the environment, it prevents the growth of harmful microorganisms [10]. Some strains of these microorganisms produce bacteriocin and are considered as an additional barrier against pathogens in addition to acid [11]. Also, the metabolites produced by these bacteria during fermentation have a favorable effect on the sensory and texture characteristics [10]. Other microorganisms, such as bread yeast, can ferment the hydrocarbons in the dough and create carbon dioxide gas in the dough tissue, causing the dough to rise and the bread to become crispy [12].

Figure 1.

Microorganisms range from the essential and useful, to the pathogenic and harmful.

2. Useful application of microorganisms in food industry

Microbes produce different food products through a process recognized as fermentation. Fermentation method is the biochemical change of simple sugars into favorable products such as alcohol, acid, carbon dioxide via a variety of metabolic pathways. Today, the use of microbes to produce food or increase the quality of food is very common, and biotechnologists are trying to produce special food products with the help of microbes. There is a multitude of valuable applications of microbes in the food processing industry that highly impact the quality and quantity of the food (Figure 1). Recently, microbial food processing approaches have increased global attention as a feasible method for food preservation and a good source of vital nutrients. For example, Lactobacillus spp. and Streptococcus spp. ferment lactose to lactic acid during the manufacture of dairy. Yeast (Saccharomyces spp.) decomposes sugar to ethanol and carbon dioxide during low alcoholic beverages (bear, cider, rum) and other alcoholic manufacture process. Table 1 shows different commercial products/applications of microorganisms in food industry [13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79]. In the following, we examine the types of applications of microorganisms in the food industry.

2.1 Application of microorganisms in dairy industry

From time immemorial, dairy products have been part of the human nutrition. They provide an excellent source of calcium, vitamin D, protein and other important and essential nutrients [80]. They also supply phosphorus, potassium, magnesium and a variety of vitamins such as vitamin A (retinol), vitamin B12 (cyanocobalamine) and riboflavin [81]. A variety of fermented dairy products are prepared with various microbial strains (Table 1). The main genera that belong to the lactic acid bacteria group are: Lactobacillus, Leuconostoc, Lactococcus, Pediococcusand, Streptococcus [82]. Microorganisms ferment the carbohydrates found in milk, which is mostly lactose with lactic acid and some other products [83]. Acid precipitates protein in milk, which is why fermented products tend to be thicker than milk. Strong acidity and low pH limit the growth of other microbes, including pathogens [84]. Fermentation of the milk provided a simple method to increase its life expectancy and improve its safety. Consumers now have access to a large variety of fermented dairy products. While a small proportion of these products are manufactured at home, the majority are manufactured industrially. Produce of fermented products is of economic significance in numerous countries. While the need for fermented products is increasing every day, dairy industries are contributing to economic growth in many countries. The first instance of fermented milk was probably manufactured accidentally by nomads. It became acidic and clotted under the influence of certain microbes [85]. By chance, the bacteria they used were harmless, acidic and non-toxic. Many types of fermented milks and related products have been made worldwide. Their nature is largely dependent on the type of milk used, the pre-treatment of the milk, the temperature (climate), the fermentation conditions and subsequent technological treatments. The most commonly used and popular dairy products include curd, yogurt, cheese and kefir [84].

2.2 Application of microorganisms in alcoholic beverages industries

All over the world, different raw materials are used for the production of alcoholic beverages traditionally [86]. The forms of alcoholic beverage consumed in different regions of the world vary substantially in accordance to location and ingredients. Beverages like wine, beer, whisky, brandy, rum are manufactured from malted cereals and fruit juices. Microbes can be grown in fermenters to make beverages at industrial scale (Table 1) [87]. Low-alcoholic content beverages can be prepared by the fermentation of starch products, while high-alcoholic content beverages can be manufactured by the distillation of fermented malted barley, molasses etc. [88] Wine and beer manufactured without distillation. While whisky, brandy, rum manufactured after distillation. Yeast is the main fermenter and alcohol producer in the manufacture of wine, beer and other alcoholic drinks [89]. Depending on the substrate used for fermentation and the type of processing, different alcoholic drinks can be prepared [90]. Saccharomyces cerevisiae is commonly known as “brewer’s yeast” as it produces alcohol by fermentation of different malted cereals and fruit juices [88]. Vinegar is a food product made by acetic acid bacteria that can ferment the alcohol in alcoholic liquids to acetic acid [91].

2.3 Application of microorganisms in cereal industries

Probiotic cereal-based food products and drinks containing human-made friendly microorganisms (Bifidobacterium, Saccharomyces, Streptococcus, Enterococcus, Escherichia and Bacillus species), as well as prebiotic food products and drinks formulations containing ingredients that cannot be digested by the human host in the upper gastrointestinal tract (stomach and intestines) but can selectively stimulate the growth of one or a limited number of colon bacteria, have recently entered the market [92]. The objective of these food products and drinks is to positively affect the composition and intestinal microbial activities. The many beneficial effects of cereals can be exploited in several ways, leading to the development of new cereal feeds or cereal ingredients that can target specific populations [92]. Cereals can provide a fermentable substrate for probiotic microorganism growth [92]. The composition and processing of the cereal grains for the food and beverage, the substrate (medium) formulation, the starter culture growth capability and productivity, the stability of the probiotic strain during storage, the organoleptic properties (the sensory characteristics including taste, sight, smell and touch) and the nutritional value of the final product are the main factors to consider [93]. Moreover, Cereals are the dominant source of non-digestible carbohydrates that besides promoting several useful physiological effects can also selectively stimulate the growth of friendly microorganisms present in the colon and act as prebiotics [92]. Cereals have highest water-soluble fiber (like arabinoxylan and β-glucan), oligosaccharides (like fructo-oligosaccharides and galacto-oligosaccharides) and resistant starch, which have been recommended to fulfill the prebiotic concept [93]. Isolation of specific soluble or insoluble fiber fractions from different cereal types or grain by-products can be achieved by processing techniques such as milling, sieving, decalcining or pearling, depending on knowledge of fiber distribution in grains [92]. Finally, grain ingredients (for example starch) can be used as encapsulating tools and materials for probiotics to increase stability during storage and improve survival as they pass through the harsh circumstance of the gastrointestinal tract [92]. Although it can be concluded that functional grain-based foods are a challenging prospect, the development of novel grain processing technologies that improve the health potential and acceptability of foods is paramount [92]. Today, consumers demand healthy food, and the food industry has developed innovative nutraceutical and functional food products. Foods fermented from grains are known to have health benefits. Cereals and grain-based food products contain sufficient amounts of nutrients such as carbohydrates/starch, trans-fats, proteins, oligosaccharides, fiber, wide range of vitamins (such as vitamin B and E) and minerals (such as iron, zinc, magnesium and phosphorus). Surprisingly, fermentation using various probiotic and lactic acid bacteria improves the nutrients in cereal-based products [94]. The genera Lactobacillus, Bifidobacterium, Saccharomyces, Enterococcus, Leuconostoc, Streptococcus, Pediococcus, Propionibacterium and Enterococcus are important strains of probiotic bacteria used in non-dairy probiotic products [95]. Probiotics can release bioactive molecules therefore they have a positive effect on host health by inhibiting the growth or interfere of pathogenic bacteria. These probiotic microorganisms workout their health benefits by utilizing bio-therapeutic practices such as pH reduction in the intestine, increase of antimicrobials, growth of enzymes, and vitamins, reduction of serum cholesterol, control and regulation of the immune system, recovery and balancing of the intestinal micro-flora after diarrhea, reduction of food allergens, anti-oxidative activity and decrease of lactose malabsorption symptoms. Grain-based probiotic products that are likely to progress quality of life have scientifically proven health claims (Table 1) [95].

2.4 Application of microorganisms in chocolate production technology

Chocolates are complex, multi-phase systems of particulate matter (sugar, cocoa, defined milk components) and continuous phases (cocoa butter, milk fat and emulsifiers). Cocoa solids are derived from beans obtained from the fruit of Theobroma cocoa. West Africa now produces over 70% of world cocoa [96]. Chocolate is a regular food, has an individually attractive taste and it is beneficial for health [97]. Chocolate’s popularity is for its good taste and desirable sensory properties [97]. Based on studies, chocolate is a food that can be easily digested and it could be useful for the nervous system [97]. The production of finished bars of chocolate takes the input of many people and, something you may not realize microorganisms. The unique flavors of chocolate come from the growth conditions and fermentation of the cocoa bean. Useful microbes can improve the taste of chocolate (Table 1), but harmful microbes can pose quality and safety issues if left uncontrolled [98]. The production of chocolate begins with the hand-picking of ripe cocoa pods and fruits. The chosen pods are opened and the cocoa beans are removed. After husking, the cocoa fermentation occurs naturally by friendly microorganisms found on fresh fruits, knives and also other surfaces with which the beans come into contact. To support the growth of beneficial microbes on these surfaces, proper conditions must be maintained. Successive microbial populations carry out the fermentation process. Initially, yeasts dominate, after that the genus Lactobacillus (lactic acid bacteria) and finally, acetobacters (acetic acid bacteria) dominate the population. If left to ferment for an extended period of time, spore-forming bacteria, like Bacillus, and molds can take over. Spore growth results in the production of off flavors in chocolate. Mold can have a negative impact on flavor and safety. Some mold strains can produce mycotoxins, which are dangerous compounds. Mold growth can be prevented by storing items at or below 8% humidity. Removing the husk from the bean in the manufacturing process can also reduce the amount of toxin in the sample. The degree of fermentation is determined by the color of the beans. Once fermented, the beans are dried, which reduces bitterness, astringency and acidity. Additionally, it brings down the moisture content to ranges that are secure for both storage and transportation. Products may become contaminated or spoiled by harmful microorganisms if the moisture level is too high. After that, the beans are turned into chocolate. Chocolate must have three characteristics in order to be microbially safe: low water activity, a large portion of fats and sugars and a pH of around 5.5. Bacteria are not completely eradicated by these circumstances, but their growth is restricted. Salmonella are the pathogenic organisms that should be taken into consideration, but there is little chance that eating chocolate will cause salmonellosis. Workers handling the beans could introduce Salmonella into the product. Salmonella cannot grow due to the low pH and low water activity, but it can survive in chocolate. In order to produce chocolate safely, the roasting stage is essential because it is the only process that can completely remove the pathogen from the product. Chocolate production is a complex process that requires several steps to bring out the distinctive flavors. Although microorganisms play a significant role in flavor production, they must be managed for the product to remain tasty and secure. Improper nutrition and its impact on the occurrence of cardiovascular diseases, obesity and diabetes among people in the society have caused the food industry to look for new and less harmful formulations in the production of snacks and eat between meals. Since chocolate has a special place among people in society, especially children, to reduce the effectiveness of harmful compounds in chocolate, bioactive compounds such as probiotics and prebiotics can be used in its formulation. Research has shown that chocolate is a suitable carrier for probiotics due to its protective fats. The source of fatty acid in chocolates containing milk includes milk fat, cocoa butter and emulsifier, and these three substances in chocolate, because they have a stable phase, remain stable in combination with probiotics and are safely transported and absorbed by the body. Important probiotic species include Lactobacillus acidophilus, Lactobacillus johnsonii, Bifidobacterium longum and Bifidobacterium bifidum [98]. The effectiveness of probiotics in diseases depends on factors such as microbial diversity and genetics. Lactobacillus is part of the family of lactic bacteria, whose use has a long history; Therefore, their safety has been proven. In general, lactobacilli constitute the majority of probiotic starter cultures and are widely used in the production of probiotic food products. L. acidophilus is the most important and widely used species of Lactobacillus, and along with Bifidobacterium, it is considered the most important probiotic microorganism. Among lactobacilli, L. acidophilus and Lactobacillus casei have found the most commercial use. When chocolate containing probiotic microorganisms is consumed, it moves actively and alive from the beginning of the digestive tract, which is the mouth, and goes to the stomach. These probiotics in the stomach must be resistant to stomach acid, and then they go to the small intestine, attach to the intestinal epithelium and produce harmful antibacterial compounds such as lactic acid and bacteriocin. In the part of the colon wall, probiotic bacteria grow and multiply and produce acids such as butyric, propionic and acetic, which by lowering the pH destroy the pathogenic bacteria in this part and increase the health of the digestive system. In plain chocolate, the source of fatty acid is cocoa butter and emulsifier [99]. It is better to protect probiotics in chocolate making and to maintain the viability of Bifidobacterium berry bacteria in adverse conditions of the production process and digestive system, the method of microencapsulation of Bifidobacterium probiotic bacteria with calcium alginate and resistant corn starch should be used by emulsion method and capsule technology. Microcoating of probiotics with sodium alginate gum preserves the survival of probiotics from the body’s digestive tract. Also, due to the presence of flavonoids and polyphenols, chocolate has a high antioxidant activity and is a suitable probiotic carrier, and the cocoa butter part protects well from Bifidobacterium. In addition to flavonoids, stearic acid present in cocoa also improves the antioxidant status. In general, the survival of probiotics in the food sample depends on the pH, storage temperature, oxygen content, warm storage temperature, refrigerator storage temperature and time, the presence of competitive and inhibitory microorganisms [100]. Prebiotics are cheaper sources than probiotics. Prebiotics are food compounds that work selectively and improve the composition of microflora residing in the intestinal environment and are indigestible or minimally digestible dietary fibers that can be digested by the digestive system and its enzymes along with probiotics. Probiotics need prebiotic cofactors for their vital activity and play a vital role in the body. Research has shown that by adding dietary fiber inulin to chocolate, which is a prebiotic, when it reaches the intestine, it increases the growth and activity of probiotics, and also increases the absorption of magnesium and calcium minerals [101].

2.5 The use of microorganisms in the meat industry and related products

Fermented meat products are a suitable environment for the growth of probiotic bacteria, but for the production of these products, limitations must be met, such as; the natural microflora of meat, nitrite and salt, low water activity and the absence of sugar compounds prevailed [102]. Microbial flora in meat and meat products is affected by environmental conditions that cause the growth of primary microorganisms in raw meat or the growth of microorganisms caused by secondary contamination. Preservation of food using microorganisms or their antimicrobial metabolites is called biological preservation or biological protection [103]. Lactic acid bacteria have a high ability to be used for biological preservation because they do not cause problems for the consumer and prevent the growth of most microorganisms during storage [103]. These bacteria are known as safe and their use has a long history. Also, the antimicrobial peptides obtained from the lactic acid of bacteria can be broken by the body’s proteases and do not cause problems for the intestinal microbial flora. The growth of lactic acid bacteria in meat is considered a secret fermentation because due to the low amount of carbohydrates and the buffering capacity of meat, these bacteria cannot cause extensive changes in the taste characteristics of meat. Lactic acid bacteria play a protective or preventive role against other microorganisms by competing for food or producing bacteriocin or other antimicrobial substances such as organic acids, hydrogen peroxide and enzymes. The difference between starter culture and maintenance culture is that in starter culture, metabolic activity (acid production, hydrolysis of proteins) is the goal, but in maintenance culture, antimicrobial activity is desired. Moreover, recently edible mushrooms as a novel trend in the development of healthier meat products. Mycoprotein is a meat replacement product that’s available in a variety of forms such as cutlets, burgers, patties and strips. It’s marketed under the brand name Quorn, and is sold in many countries. Mycoprotein is a protein manufactured from the naturally occurring fungal Fusarium venenatum. To create mycoprotein, manufacturers ferment fungal spores along with glucose and other nutrients. The fermentation process is similar to what’s used to create beer. It results in a doughy mixture with a meat-like texture that’s high in protein and fiber [104]. Table 1 shows some applications of microorganisms in meat industry.

2.6 The use of microorganisms in the production of food additives (color and flavor)

The most important microbial colors that are produced are carotenoid pigments. Carotenoids are yellow and orange-red pigments that exist in nature and their chemical structure has 40-carbon atoms. Some microorganisms produce microbial dyes [105]. The importance of this issue is because today research shows that synthetic colors have pathogenic effects such as cancer and so on in the body, and for this reason, attention has been directed toward the production of colors from natural sources and one of these natural sources are microorganisms [106]. Different microorganisms around the world are capable of producing dyes, and researchers are trying to find the best ones. Bacteria, fungi and green algae are able to produce color, and among these microorganisms, a number of species such as Dunaleilla, Heamatococcus, Penicillium, Monascus have reached industrial production and their pigments are used in various cases. Artificial colors are widely used in various industries such as food, textile, cosmetic and medicine. However, the toxicity problems of synthetic dyes have led to a lot of research in the field of natural dyes. Among the sources of natural colors, pigments produced by microorganisms have attracted a lot of attention and have been considered as emerging sources of pigments. In addition to increasing the marketability of products, these pigments improve their biological properties such as antioxidant, antimicrobial and anticancer properties. Microorganisms are added to food as additives and supplements in many products of microbial fermentation. These substances include antioxidants, flavoring substances, colors, preservatives, amino acids, etc. [107] Microorganisms play an important role in the production of flavor compounds in foods. Foods such as vinegar, beer, fermented vegetables, milk, soybeans and meat are flavored due to the presence of microorganisms. Synthetic food additives that are produced through chemical processes are less desirable than natural compounds, as a result, there is a great desire to expand and use natural food additives that are obtained from microorganisms [105]. Various microorganisms are promising candidates for production food additives (Table 1).

2.7 The use of microorganisms to produce microbial emulsifiers

Emulsifiers are a large class of compounds that are considered surface active agents. An emulsifier works by slowing down chemical reactions and increasing its stability. Surface-active compounds produced by microorganisms attract considerable attention due to their potential advantages over synthetic ones and also because they can replace some chemicals in many environmental and industrial applications. Bioemulsifiers are known as active biomolecules due to their unique characteristics compared to chemical types, such as non-toxicity, biodegradability, biocompatibility, efficiency at low concentrations, resistance to pH, temperature and concentration of different salts. Bioemulsifiers are synthesized in various biological sources such as bacteria, fungi and yeast. Because of their functional abilities and environmentally friendly properties, emulsions and biosurfactants are considered as multifunctional biomolecules of the recent century, especially in the food industry [108]. Several microorganisms are promising candidates for production emulsifiers (Table 1).

2.8 The use of microorganisms to produce microbial enzymes

Enzymes of microbial origin have various effects and are extremely active. Enzymes are widely used in industry and are gradually replacing materials produced by plants and animals [71]. Amylase of bread mold is used in the beer industry and the production of industrial alcohol, as well as in baking bread [109]. During bread manufacture, enzymes are mixed with cereal flour to convert complex starch molecules into simpler molecules and support produce the desired product. Enzyme supplementation during bread production improves the flavor, increases the volume and gives the necessary texture to the bread. Microbial enzymes such as hydrolases, transferases, oxidative enzymes and isomers are found in most bacteria and play an important role in sugar metabolism [110]. Like the tryptophanase enzyme produced by some microbes and causing indole gas [111]. Various methods are used to improve the technological quality of meat. Among these methods is the use of microorganisms and proteolytic enzymes and recently bacteria with collagenase to make the meat crispy and as a result dissolve its proteins [110]. Due to their ability to digest native collagen, bacterial collagenases are metalloproteinases involved in the destruction of the extracellular matrix of animal cells. These enzymes are important pathogenic factors in all types of pathogenic bacteria. Clostridium collagenases are the first identified and characterized reference enzymes to compare newly discovered collagenolytic enzymes. Bacterial collagenases are largely unknown and understudied [112]. However, their application is very diverse and useful in many fields. Molds and bacteria produce large amounts of amylases [71]. Hydrolytic enzymes from Rhizopus dalremocorzoxii molds and Bacillus subtilis bacteria are the main producers of amylases [109]. Fungal amylases are used in the separation of starch from fruits [71]. In general, enzymes are used to increase the solubility of insoluble starch in the brewing industry, to prepare fruit juice, to improve the consistency of dough, to improve starch for fermentation and to accelerate the performance of reactions and to reduce side products. Microbial cells with a short fermentation time and relatively cheap growth media are suitable agents for enzyme production. In recent times, microbial enzymes have been greatly welcomed by industry practitioners. In this regard, Bacillus and Aspergillus amylases have been used in the brewing and bakery industries instead of yogurt, barley and wheat amylases [71, 109]. Different microorganisms are promising candidates for production important enzymes (Table 1).

2.9 The use of microorganisms to remove mycotoxins produced in food

Mycotoxins are toxic and carcinogenic secondary metabolites produced by some fungi such as Aspergillus flavus and Aspergillus parasiticus [113]. Some of them have proven to have a carcinogenic (aflatoxin-B₁, ochratoxin A), mutagenic (aflatoxins, ochratoxin A), teratogenic (patulin, aflatoxin B₁, ochratoxin A), estrogenic (zearalenone), nephrotoxic and hepatotoxic (aflatoxins, patulin) effect. Food contamination with mycotoxins is a serious problem for human and animal health. Consumption of food contaminated with mycotoxins has been assessed as one of the causes of liver and kidney cancers in humans and animals [113]. The most common mycotoxin is aflatoxin, which is one of the causes of congenital abnormalities and carcinogenesis [113]. Since the contamination of food with mycotoxins threatens the quality of food, the detoxification of mycotoxins in order to reduce contamination can be of significant importance to increase the safety level and control the quality of food. The use of microorganisms to remove mycotoxins in food is considered a relatively new method for detoxification, this method not only does not have a harmful effect on food value, but is an efficient and environmentally friendly method [114]. Various microorganisms such as Lactobacillus plantarum, L. acidophilus and B. subtilis have shown good detoxification capabilities in mycotoxin-contaminated food (Table 2). Therefore, microbial detoxification has shown high potential for detoxifying food on a large scale and cost-effectively [115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149].

Group	Genera/species	Product/application(s)	References
Bacteria	Acetobacter aceti	Vinegar fermentation	[13]
	Acetobacter pasteurianus	Vinegar fermentation, cocoa fermentation	[14, 15]
	Bacillus coagulans	Cocoa, glucose isomerase (food additive),fermented soybeans	[16]
	Bacillus licheniformis	Protease (food additive)	[17]
	Bacillus subtilis	Fermented soybeans, protease, glycolipids, riboflavin-B2 (food additive)	[18]
	Bacillus paranthrasis	Food waste biodegradation	[19]
	Bacillus siamenis
	Bacillus tequilensis
	Bacillus cereus
	Bacillus velezensis
	Bifidobacterium animalis	Fermented milks with probiotic properties	[20]
	Bifidobacterium breve	Common in European fermented milks	[21]
	Brachybacterium alimentarium	Gruyere and beaufort cheese	[22]
	Brevibacterium flavum	Amino acid producer, malic acid, glutamic acid, lysine, monosodium glutamate (food additives)	[23]
	Corynebacterium ammoniagenes	Cheese ripening	[24]
	Enterobacter aerogenes	Bread fermentation	[25]
	Enterococcus durans	Cheese and sourdough fermentation	[26]
	Enterococcus faecium	Soybean, dairy, meat, vegetables	[26, 27]
	Exiguobacterium acetylicum	Food waste biodegradation
	Burkholderia contaminans
	Klebsiella pneumonia	Tempeh fermentation, production of vitamin B12	[28]
	Lactobacillus acetotolerans	Vinegar fermentation	[29]
	Lactobacillus acidophilus	Fermented milks, probiotics, vegetables	[30]
	Lactobacillus brevis	Bread fermentation, wine, dairy	[31]
	Lactobacillus buchneri	Malolactic fermentation in wine, sourdough	[32, 33]
	Lactobacillus casei	Dairy starter, cheese ripening, green table olives	[34]
	Lactobacillus delbrueckii	Yogurt and other fermented milks, mozarella	[35]
	Lactobacillus fermentum	Fermented milks, sourdough, urease (food additive)	[36]
	Lactobacillus ghanensis	Cocoa	[37]
	Lactobacillus helveticus	Starter for cheese, cheese ripening, vegetables	[38]
	Lactobacillus hilgardii	Wine malolactic fermentation	[39]
	Lactobacillus kefiri	Fermented milk (kefir), reduction of bitter taste in citrus juice	[40, 41]
	Lactobacillus kimchii	Kimchi fermentation	[42]
	Lactobacillus oeni	Malolactic fermentation of wine	[43]
	Lactobacillus paracasei	Cheese fermentation, probiotic cheese, probiotics, wine, meat	[44]
	Lactobacillus plantarum	Fermentation of vegetables, malolactic fermentation, green table olives, dairy, meat	[45]
	Lactobacillus sakei	Fermentation of cheese and meat products, beverages	[46]
	Lactobacillus salivarius	Cheese fermentation	[47]
	Lactobacillus sanfranciscensis	Sourdough fermentation	[48]
	Lactobacillus versmoldensis	Raw fermented sausage	[49]
	Lactococcus lactis	Dairy starter, nisin (protective culture)	[50]
	Pediococcus acidilactici	Meat fermentation and biopreservation of meat, cheese starter	[51]
	Pediococcus pentosaceus	Meat fermentation and biopreservation of meat	[51]
	Propionibacterium acidipropionic	Meat fermentation and biopreservation of meat	[52]
	Propionibacterium freudenreichii	Cheese fermentation (emmental cheese starter), probiotics	[53]
	Streptococcus natalensis	Natamycin (food additive)	[54]
	Weissella genus	Cocoa fermentation, Fermented sausage, Croatian cheese fermented from raw milk, Chinese yogurt,	[55]
	Zymomonas mobilis	Beverages fermentation	[56]
Yeast	Debaryomyces hansenii (Candida famata)	Fermentation of blue veined cheese, Fermentation white brined cheeses, ripening of smear cheeses, and sausages and dry-meat products	[57, 58]
	Candida guilliermondii	Citric acid fermentation (fodd additive)	[59]
	Geotrichum candidum	Fermented dairy products (ripening of many soft and semi-hard cheeses and make a positive contribution to the development of taste and aroma or fermented milks), bioformation of flavour on glucose, peptone, maize oil and meat extract	[60, 61]
	Kluyveromyces marxianus	Cheese ripening, lactase (food additive)	[62]
	Kluyveromyces lactis	Cheese ripening, lactase (food additive)	[62]
	Saccharomyces bayanus	Kefir fermentation, juice and wine fermentation	[63]
	Saccharomyces cerevisiae	Probiotic culture, bioethanol, cocoa fermentation, Sake fermentation, cheese-ripening, beer fermentation, bread, invertase (food additive)	[62, 64, 65, 66]
	Saccharomyces pastorianus	Beer fermentation, removes and transforms Fusarium trichothecene mycotoxins during fermentation of brewer's wort	[67]
	Saccharomyces unisporus	Fermented milk products such as kefir and koumiss	[68]
	Schizosaccharomyces pombe	Wine fermentation	[69]
	Zygosaccharomyces rouxii	Soy sauce	[70]
Filamentous moulds	Aspergillus flavus	Laccase, lipases, pectinase, protease, α-amylases (food additive)	[71]
	Aspergillus fumigatus	Amylases, cellulases, chitosanases	[71]
	Aspergillus awamori	Amylases	[71]
	Aspergillus sydowii	Amylases	[71]
	Aspergillus nidulans	Invertases, laccases	[71]
	Aspergillus niger	Beverages, industrial production of citric acid, α-amylases, cellulases, chitosanases, galactosidases, invertases, lipases, naringinases, phytases, tannases, amyloglucosidases, pectinase, celluloses, glucose oxidase, protease (food additives)	[71, 72]
	Aspergillus terreus	Amylases, celluloses, phytases	[71]
	Aspergillus tamarii	Amylases	[71]
	Aspergillus oryzae	Soy sauce, beverages, α-amylases, chitosanases, amyloglucosidase, naringinases, proteases, lipases (food additives)	[71, 73]
	Aspergillus sojae	Soy sauce, beverages, α-amylases, amyloglucosidase, lipase (food additives)	[71, 74]
	Penicillium camemberti	White mold cheeses (maturation of soft cheeses, such as camembert and brie)	[75]
	Penicillium notatum	Glucose oxidase (food additive)	[76]
	Penicillium roqueforti	Blue mold cheeses
	penicillium candidum	Bioformation of flavour on glucose, peptone, maize oil and meat extract	[61]
	penicillium nalgiovense	Bioformation of flavour on glucose, peptone, maize oil and meat extract	[61]
	Rhizopus oligosporus	Tempe-type fermentation	[77]
	Rhizopus oryzae	Tempeh fermentation, Soy sauce, koji	[78]
	Fusarium venenatum	Mycoprotein (meat-like)	[79]

Table 1.

Various commercial products/applications of microorganisms in foods industry.

Group	Genera/species	Mycotoxin decontamination	Mechanism of inhibition	References
Bacteria	Alcaligenes faecalis	Ochratoxin	Biodegradation to ochratoxin-α due to carboxypeptidase activity	[115]
	Bacillus licheniformis	Zearalenone	Biocontrol due to cell-wall adsorption	[116, 117]
	Bacillus megaterium	Ochratoxin	Biocontrol due to cell-wall adsorption	[118]
	Bacillus pumilus	Ochratoxin	Biocontrol due to cell-wall adsorption	[119]
		Zearalenone	Biotransformation due to esterase activity	[120]
	Bacillus subtilis	Aflatoxin-B1	Biotransformation into less toxic products due to laccase activity	[121]
		Ochratoxin	Biocontrol due to cell-wall adsorption	[122]
		Zearalenone	Biotransformation into Zearalenone-14-phosphate	[123]
	Bacillus velezensis	Aflatoxin-B1	Biotransformation into less cytotoxic products	[124]
	Bifidobacterium animalis	Patulin	Biocontrol due to cell-wall adsorption	[125]
	Devosia insulae	Deoxynivalenol	Biotransformation into 3-keto- deoxynivalenol	[126]
	Escherichia coli	Aflatoxin-B1	Biotransformation into less toxic products	[127]
		Zearalenone	Biocontrol due to cell-wall adsorption	[128]
	Gluconobacter oxydans	Aflatoxin-B1	biotransformation of mycotoxins (Physical binding to bacterial cell wall proteins and polysaccharides)	[129]
		Ochratoxin
		Citrinin
		Patulin
	Lactiplantibacillus plantarum	Aflatoxin-B1	Production of antimicrobial peptides/ involves non-covalent bonds between the cell wall components and the mycotoxin dissolved in the liquid medium	[130]
		Ochratoxin
		Zearalenone
	Levilactobacillus brevis	Ochratoxin	Biocontrol due to cell-wall adsorption	[131]
		Aflatoxin-B1
	Lactiplantibacillus pentosus	Ochratoxin
		Aflatoxin-B1
	Lacticaseibacillus paracasei	Ochratoxin
		Aflatoxin-B1
	Lacticaseibacillus casei	Ochratoxin	Biodegradation and/or adsorption	[132]
Yeast	Candida guilliermondii	Patulin	Biotransformation into E-ascladiol with short-chain dehydrogenase	[133]
	Candida parapsilosis	Zearalenone	Glucosyltransferase activities toward main derivatives of Zearalenone	[134]
	Candida utilis	Zearalenone	Biodegradation by the combination of probiotics with fungal cell-free extracts	[135]
		Ochratoxin	Biocontrol due to cell-wall adsorption	[136]
	Kodameae ohmeri	Patulin	Biotransformation into hydroascladiol	[137]
	Komagataella phaffi	Fumonisin B1	Biotransformation due to fumonisin esterase	[138]
	Pichia caribbica	Patulin	Enzymatic biodegradation	[137]
	Rhodosporidium spp.	Patulin	Biotransformation into desoxypatulinic acid	[137]
	Rhodotorula mucilaginosa	Patulin	Enzymatic biotransformation/ Cell-wall adsorption	[139]
	Rhodotorula glutinis	Patulin	Biocontrol agent	[140]
	Saccharomyces cerevisiae	Patulin	Adsorption to proteins and polysaccharides in the cell-walls	[137]
		Ochratoxin	Biological degradation due to dechlorination, hydrolysis, hydroxylation, and conjugation	[141]
		Aflatoxin M1	Biological Biodegradation and/or adsorption	[142]
	Saccharomyces pastorianus	Deoxynivalenol;	Biodegradation and/or adsorption	[143]
		Zearalenone
Filamentous molds	Aspergillus niger	Ochratoxin	Biodegradation into ochratoxin-α by extracellular ochratoxinase/Biotransformation pathway	[144, 145]
	Byssochlamys nivea	Patulin	Biodegradation	[146]
	Clonostachys rosea	Zearalenone	Detoxify Zearalenone through the enzyme zearalenone lactonohydrolase	[147]
	Rhizopus oryzae	Aflatoxin	Enzymatic biodegradation	[148]
	Trichoderma reesei
	Cladosporium uredinicola	Aflatoxin-B1	Biotransformation and detoxification	[149]

Table 2.

Microorganisms have shown good detoxification capabilities in mycotoxin-contaminated food.

2.10 The use of microorganisms in order to reduce food industry waste

The development of industries and the rapid growth of the population due to the increase in consumables as a result of the increase in liquid and solid wastes are issues that have recently caused huge crises in human societies [150]. The severity of pollution resulting from these materials in cities and centers of industrial concentration is such that it has drawn the attention of scientific and executive resources of the world to the correct disposal or basic recycling of these materials. In between, high amounts of food industry wastes and effluents are seen, and today the use of these two is considered as one of the topics of interest among researchers. Using different microorganisms, cellulose nanocrystals can be produced using waste and sewage [151, 152]. Cellulose is one of the richest natural polymers in the world, which is usually extracted from plant tissues, but it can be produced by some microorganisms, such as a variety of bacteria, such as Stobacter, Agrobacterium, Cloconosteobacter, Rhizobium and Sarcina. The characteristic of the cellulose produced by these organisms is that the size of its fibers is about 100 times smaller than plant cellulose and consists of cellulose fibers with nano dimensions, the various characteristics of these materials are such as: high water retention capacity (more than 200 times dry weight) and high elasticity, interesting mechanical properties in dry and wet state and high biodegradability and biocompatibility are of interest [153]. Microorganisms are promising candidates for the biodegradation of food waste (Table 1).

3. Conclusion

Microbes have been used for food purposes since antiquity. The significance of microbes has improved as a result of the growth of food making and processing industries. Manufacturing of food and related products through microbial processes is cheaper and easier because large-scale production and genetic modification for higher quality products are easier. A treasure of opportunity exists for the use of microbes or their derivatives in household, village level and large-scale processing applications in developing countries. However, a number of these microbial processes require further exploration and exploitation in light of the potential benefits of their use. Today, it is very common to use microorganisms to produce food or increase the quality of food, and biotechnologists try to produce special food products with the help of microorganisms. Food processing with microorganisms can save time and energy and provide a more reproducible processing system on a commercial scale. In the current busy life, most people are required to take processed foods; consequently, the request for processed foods has risen. This requires the large-scale manufacture of low-cost, long-term food products. Technological developments make it easier to discover useful microorganisms; as a result, studies should focus on the detection of novel natural sources of microbial manufacture, existing process progresses, finding novel approaches for large-scale manufacture of foods with nutritional and health benefits. In a summary of the most important applications of microorganisms in the food industry, the use of microorganisms, especially probiotics, in the dairy, grain, meat and related products industries, the use of microorganisms to remove mycotoxins produced in food, the use of metabolites it mentioned the products of microorganisms such as enzymes, flavorings, dyes, emulsifiers, etc., in order to maintain the quality and increase the shelf life of food products, and finally, the use of microorganisms to reduce food industry waste.

Acknowledgments

Research reported in this publication was supported by Elite Researcher Grant Committee under award numbers [958634 and 963646] from the National Institute for Medical Research Development (NIMAD), Tehran, Iran to MRA.

Conflict of interest

Authors declare no conflict of interest.