Food microbiology is the study of the microorganisms which inhabit, create or contaminate food. Of major importance is the study of microorganisms causing food spoilage.[1] However "good" bacteria such as probiotics are becoming increasingly important in food science.[2] In addition, microorganisms are essential for the production of foods such as cheese, yogurt, other fermented foods, bread, beer and wine
Food safety
Food safety is a major focus of food microbiology. Pathogenic bacteria, viruses and toxins produced by microorganisms are all possible contaminants of food. However, microorganisms and their products can also be used to combat these pathogenic microbes. Probiotic bacteria, including those which produce bacteriocins can kill and inhibit pathogens. Alternatively, purified bacteriocins such as nisin can be added directly to food products. Finally, bacteriophage, viruses which only infect bacteria, can be used to kill bacterial pathogens. Thorough preparation of food, including proper cooking will eliminate most bacteria and viruses. However, toxins produced by contaminants may not be heat-labile, and some will not be eliminated by cooking.
[edit] Fermentation
Fermentation is one way microorganisms can change a food. Yeast, especially S. cerevisiae, is used to leaven bread, brew beer and make wine. Certain bacteria, including lactic acid bacteria, are used to make yogurt, cheese, hot sauce, pickles and dishes such as kimchi. A common effect of these fermentations is that the food product is less hospitable to other microorganisms, including pathogens and spoilage-causing microorganisms, thus extending the food's shelf-life.
Some cheese varieties also require mold microorganisms to ripen and develop their characteristic flavors.
[edit] Foodborne pathogens
Foodborne pathogens are the leading causes of illness and death in less developed countries killing approximately 1.8 million people annually. In developed countries foodborne pathogens are responsible for millions of cases of infectious gastrointestinal diseases each year, costing billions of dollars in medical care and lost productivity. New foodborne pathogens and foodborne diseases are likely to emerge driven by factors such as pathogen evolution, changes in agricultural and food manufacturing practices, and changes to the human host status. There are growing concerns that terrorists could use pathogens to contaminate food and water supplies in attempts to incapacitate thousands of people and disrupt economic growth.[1]
[edit] Enteric Viruses
Food and waterborne viruses contribute to a substantial number of illnesses throughout the world. Among those most commonly known are hepatitis A virus, rotavirus, astrovirus, enteric adenovirus, hepatitis E virus, and the human caliciviruses consisting of the noroviruses and the Sapporo viruses. This diverse group are transmitted by the fecal-oral route, often by ingestion of contaminated food and water.[3]
[edit] Protozoan Parasites
Protozoan parasites associated with food and water can cause illness in humans. Although parasites are more commonly found in developing countries, developed countries have also experienced several foodborne outbreaks. Contaminants may be inadvertently introduced to the foods by inadequate handling practices, either on the farm or during processing of foods. Protozoan parasites can be found worldwide, either infecting wild animals or in water and contaminating crops grown for human consumption. The disease can be much more severe and prolonged in immunocompromissed individuals.[4]
[edit] Mycotoxins
Molds produce mycotoxins, which are secondary metabolites that can cause acute or chronic diseases in humans when ingested from contaminated foods. Potential diseases include cancers and tumors in different organs (heart, liver, kidney, nerves), gastrointestinal disturbances, alteration of the immune system, and reproductive problems. Species of Aspergillus, Fusarium, Penicillium, and Claviceps grow in agricultural commodities or foods and produce the mycotoxins such as aflatoxins, deoxynivalenol, ochratoxin A, fumonisins, ergot alkaloids, T-2 toxin, and zearalenone and other minor mycotoxins such as cyclopiazonic acid and patulin. Mycotoxins occur mainly in cereal grains (barley, maize, rye, wheat), coffee, dairy products, fruits, nuts and spices. Control of mycotoxins in foods has focused on minimizing mycotoxin production in the field, during storage or destruction once produced. Monitoring foods for mycotoxins is important to manage strategies such as regulations and guidelines, which are used by 77 countries, and for developing exposure assessments essential for accurate risk characterization.[5]
[edit] Yersinia enterocolitica
Yersinia enterocolitica includes pathogens and environmental strains that are ubiquitous in terrestrial and fresh water ecosystems. Evidence from large outbreaks of yersiniosis and from epidemiological studies of sporadic cases has shown that Y. enterocolitica is a foodborne pathogen. Pork is often implicated as the source of infection. The pig is the only animal consumed by man that regularly harbours pathogenic Y. enterocolitica. An important property of the bacterium is its ability to multiply at temperatures near to 0°C, and therefore in many chilled foods. The pathogenic serovars (mainly O:3, O:5,27, O:8 and O:9) show different geographical distribution. However, the appearance of strains of serovars O:3 and O:9 in Europe, Japan in the 1970s, and in North America by the end of the 1980s, is an example of a global pandemic. There is a possible risk of reactive arthritis following infection with Y. enterocolitica.[6]
[edit] Vibrio
Vibrio species are prevalent in estuarine and marine environments and seven species can cause foodborne infections associated with seafood. Vibrio cholerae O1 and O139 serovtypes produce cholera toxin and are agents of cholera. However, fecal-oral route infections in the terrestrial environment are responsible for epidemic cholera. V. cholerae non-O1/O139 strains may cause gastroenteritis through production of known toxins or unknown mechanism. Vibrio parahaemolytitucs strains capable of producing thermostable direct hemolysin (TDH) and/or TDH-related hemolysin are most important cause of gastroenteritis associated with seafood consumption. Vibrio vulnificus is responsible for seafoodborne primary septicemia and its infectivity depends primarily on the risk factors of the host. V. vulnificus infection has the highest case fatality rate (50%) of any foodborne pathogen. Four other species (Vibrio mimicus, Vibrio hollisae, Vibrio fluvialis, and Vibrio furnissii) can cause gastroenteritis. Some strains of these species produce known toxins but the pathogenic mechanism is largely not understood. The ecology of and detection and control methods for all seafoodborne Vibrio pathogens are essentially similar.[7]
[edit] Staphylococcus aureus
Staphylococcus aureus is a common cause of bacterial foodborne disease worldwide. Symptoms include vomiting and diarrhea that occur shortly after ingestion of S. aureus-contaminated food. The symptoms arise from ingestion of preformed enterotoxin, which accounts for the short incubation time. Staphylococcal enterotoxins are superantigens and, as such, have adverse effects on the immune system. The enterotoxin genes are accessory genetic elements in S. aureus, meaning that not all strains of this organism are enterotoxin-producing. The enterotoxin genes are found on prophage, plasmids, and pathogenicity islands in different strains of S. aureus. Expression of the enterotoxin genes is often under the control of global virulence gene regulatory systems.[8]
[edit] Campylobacter
Campylobacter spp., primarily C. jejuni subsp. jejuni is one of the major causes of bacterial gastroenteritis in the U.S. and worldwide. Campylobacter infection is primarily a foodborne illness, usually without complications; however, serious sequelae such as Guillain-Barre Syndrome occur in a small subset of infected patients. Detection of C. jejuni in clinical samples is readily accomplished by culture and non-culture methods.[9]
[edit] Listeria monocytogenes
Listeria monocytogenes is Gram-positive foodborne bacterial pathogen and the causative agent of human listeriosis. Listeriae are acquired primarily through the consumption of contaminated foods including soft cheese, raw milk, deli salads, and ready-to-eat foods such as luncheon meats and frankfurters. Although L. monocytogenes infection is usually limited to individuals that are immunocompromised, the high mortality rate associated with human listeriosis makes L. monocytogenes the leading cause of death amongst foodborne bacterial pathogens. As a result, tremendous effort has been made at developing methods for the isolation, detection and control of L. monocytogenes in foods.[10]
[edit] Salmonella
Salmonella serotypes continue to be a prominent threat to food safety worldwide. Infections are commonly acquired by animal to human transmission though consumption of undercooked food products derived from livestock or domestic fowl. The second half of the 20th century saw the emergence of Salmonella serotypes that became associated with new food sources (i.e. chicken eggs) and the emergence of Salmonella serotypes with resistance against multiple antibiotics.[11]
[edit] Shigella
Shigella species are members of the family Enterobacteriacae and are Gram negative, non-motile rods. Four subgroups exist based on O-antigen structure and biochemical properties; S. dysenteriae (subgroup A), S. flexneri (subgroup B), S. boydii (subgroup C) and S. sonnei (subgroup D). Symptoms include mild to severe diarrhea with or without blood, fever, tenesmus, and abdominal pain. Further complications of the disease may be seizures, toxic megacolon, reactive arthritis and hemolytic uremic syndrome. Transmission of the pathogen is by the fecal-oral route, commonly through food and water. The infectious dose ranges from 10-100 organisms. Shigella spp. have a sophisticated pathogenic mechanism to invade colonic epithelial cells of the host, man and higher primates, and the ability to multiply intracellularly and spread from cell to adjacent cell via actin polymerization. Shigellae are one of the leading causes of bacterial foodborne illnesses and can spread quickly within a population.[12]
[edit] Escherichia coli
More information is available concerning Escherichia coli than any other organism, thus making E. coli the most thoroughly studied species in the microbial world. For many years, E. coli was considered a commensal of human and animal intestinal tracts with low virulence potential. It is now known that many strains of E. coli act as pathogens inducing serious gastrointestinal diseases and even death in humans. There are six major categories of E. coli strains that cause enteric diseases in humans including the (1) enterohemorrhagic E. coli, which cause hemorrhagic colitis and hemolytic uremic syndrome, (2) enterotoxigenic E. coli, which induce traveler's diarrhea, (3) enteropathogenic E. coli, which cause a persistent diarrhea in children living in developing countries, (4) enteroaggregative E. coli, which provoke diarrhea in children, (5) enteroinvasive E. coli that are biochemically and genetically related to Shigella species and can induce diarrhea, and (6) diffusely adherent E. coli, which cause diarrhea and are distinguished by a characteristic type of adherence to mammalian cells.[13]
[edit] Clostridium botulinum and Clostridium perfringens
Clostridium botulinum produces extremely potent neurotoxins that result in the severe neuroparalytic disease, botulism. The enterotoxin produced by C. perfringens during sporulation of vegetative cells in the host intestine results in debilitating acute diarrhea and abdominal pain. Sales of refrigerated, processed foods of extended durability including sous-vide foods, chilled ready-to-eat meals, and cook-chill foods have increased over recent years. Anaerobic spore-formers have been identified as the primary microbiological concerns in these foods. Heightened awareness over intentional food source tampering with botulinum neurotoxin has arisen with respect to genes encoding the toxins that are capable of transfer to nontoxigenic clostridia.[14]
[edit] Bacillus cereus
The Bacillus cereus group comprises six members: B. anthracis, B. cereus, B. mycoides, B. pseudomycoides, B. thuringiensis and B. weihenstephanensis. These species are closely related and should be placed within one species, except for B. anthracis that possesses specific large virulence plasmids. B. cereus is a normal soil inhabitant and is frequently isolated from a variety of foods, including vegetables, dairy products and meat. It causes a vomiting or diarrhoea illness that is becoming increasingly important in the industrialized world. Some patients may experience both types of illness simultaneously. The diarrhoeal type of illness is most prevalent in the western hemisphere, whereas the emetic type is most prevalent in Japan. Desserts, meat dishes, and dairy products are the foods most frequently associated with diarrhoeal illness, whereas rice and pasta are the most common vehicles of emetic illness. The emetic toxin (cereulide) has been isolated and characterized; it is a small ring peptide synthesised non-ribosomally by a peptide synthetase. Three types of B. cereus enterotoxins involved in foodborne outbreaks have been identified. Two of these enterotoxins are three-component proteins and are related, while the last is a one-component protein (CytK). Deaths have been recorded both by strains that produce the emetic toxin and by a strain producing only CytK. Some strains of the B. cereus group are able to grow at refrigeration temperatures. These variants raise concern about the safety of cooked, refrigerated foods with an extended shelf life. B. cereus spores adhere to many surfaces and survive normal washing and disinfection (except for hypochlorite and UVC) procedures. B. cereus foodborne illness is likely underreported because of its relatively mild symptoms, which are of short duration.[15]
Environmental microbiology
Environmental microbiology is the study of the composition and physiology of microbial communities in the environment. The environment in this case means the soil, water, air and sediments covering the planet and can also include the animals and plants that inhabit these areas. Environmental microbiology also includes the study of microorganisms that exist in artificial environments such as bioreactors.
Microbial life is amazingly diverse and microorganisms literally cover the planet. It is estimated that we know fewer than 1% of the microbial species on Earth. Microorganisms can survive in some of the most extreme environments on the planet and some, for example the Archaea, can survive high temperatures, often above 100°C, as found in geysers, black smokers, and oil wells. Some are found in very cold habitats and others in highly saline, acidic, or alkaline water.[1]
An average gram of soil contains approximately one billion (1,000,000,000) microbes representing probably several thousand species. Microorganisms have special impact on the whole biosphere. They are the backbone of ecosystems of the zones where light cannot approach. In such zones, chemosynthetic bacteria are present which provide energy and carbon to the other organisms there. Some microbes are decomposers which have ability to recycle the nutrients. Microbes have a special role in biogeochemical cycles. Microbes, especially bacteria, are of great importance because their symbiotic relationship (either positive or negative) have special effects on the ecosystem.
Microorganisms are used for in-situ microbial biodegradation or bioremediation of domestic, agricultural and industrial wastes and subsurface pollution in soils, sediments and marine environments. The ability of each microorganism to degrade toxic waste depends on the nature of each contaminant. Since most sites typically have multiple pollutant types, the most effective approach to microbial biodegradation is to use a mixture of bacterial species and strains, each specific to the biodegradation of one or more types of contaminants. It is vital to monitor the composition of the indigenous and added bacteria in order to evaluate the activity level and to permit modifications of the nutrients and other conditions for optimizing the bioremediation process.[2]
Oil biodegradation
Petroleum oil is toxic, and pollution of the environment by oil causes major ecological concern. Oil spills of coastal regions and the open sea are poorly containable and mitigation is difficult; much of the oil can, however, be eliminated by the hydrocarbon-degrading activities of microbial communities, in particular the hydrocarbonoclastic bacteria (HCB). These organisms can help remedy the ecological damage caused by oil pollution of marine habitats. HCB also have potential biotechnological applications in the areas of bioplastics and biocatalysis.[3]
[edit] Degradation of aromatic compounds by Acinetobacter
Acinetobacter strains isolated from the environment are capable of the biodegradation of a wide range of aromatic compounds. The predominant route for the final stages of assimilation to central metabolites is through catechol or protocatechuate (3,4-dihydroxybenzoate) and the beta-ketoadipate pathway and the diversity within the genus lies in the channelling of growth substrates, most of which are natural products of plant origin, into this pathway.[4]
[edit] Analysis of waste biotreatment
Biotreatment, the processing of wastes using living organisms, is an environmentally friendly alternative to other options for treating waste material. Bioreactors] have been designed to overcome the various limiting factors of biotreatment processes in highly controlled systems. This versatility in the design of bioreactors allows the treatment of a wide range of wastes under optimized conditions. It is vital to consider various microorganisms and a great number of analyses are often required.[5]
[edit] Environmental genomics of Cyanobacteria
The application of molecular biology and genomics to environmental microbiology has led to the discovery of a huge complexity in natural communities of microbes. Diversity surveying, community fingerprinting and functional interrogation of natural populations have become common, enabled by a range of molecular and bioinformatics techniques. Recent studies on the ecology of Cyanobacteria have covered many habitats and have demonstrated that cyanobacterial communities tend to be habitat-specific and that much genetic diversity is concealed among morphologically simple types. Molecular, bioinformatics, physiological and geochemical techniques have combined in the study of natural communities of these bacteria.[6]
[edit] Corynebacteria
Corynebacteria are a diverse group Gram-positive bacteria found in a range of different ecological niches such as soil, vegetables, sewage, skin, and cheese smear. Some, such as Corynebacterium diphtheriae, are important pathogens while others, such as Corynebacterium glutamicum, are of immense industrial importance. C. glutamicum is one of the biotechnologically most important bacterial species with an annual production of more than two million tons of amino acids, mainly L-glutamate and L-lysine.[7]
[edit] Legionella
Legionella is common in many environments, with at least 50 species and 70 serogroups identified. Legionella is commonly found in aquatic habitats where its ability to survive and to multiply within different protozoa equips the bacterium to be transmissible and pathogenic to humans.[8]
[edit] Archaea
Originally, Archaea were once thought of as extremophiles existing only in hostile environments but have since been found in all habitats and may contribute up to 20% of total biomass. Archaea are particularly common in the oceans, and the archaea in plankton may be one of the most abundant groups of organisms on the planet. Archaea are subdivided into four phyla of which two, the Crenarchaeota and the Euryarchaeota, are most intensively studied.[1]
[edit] Winogradsky
In the late 1800s and early 1900s, Sergei Winogradsky, Russian microbiologist, pioneered the investigation of microbial auto trophy, and initiated the field of Environmental Microbiology. He was a strong supporter of examining freshly-isolated organisms rather than 'domesticated' laboratory strains.One of the methods he developed for the study of microbial nutrient cycling in the environment is what is now known as the "Windogradsky column". These can be set up in an amazing variety of ways to study sulfur, nitrogen, carbon, phosphorus, or other nutrients, most often cycling between the upper aerobic zone and the lower anaerobic zone. [9][10]
Industrial microbiology
Industrial microbiology or microbial biotechnology encompasses the use of microorganisms in the manufacture of food or industrial products. The use of microorganisms for the production of food, either human or animal, is often considered a branch of food microbiology. The microorganisms used in industrial processes may be natural isolates, laboratory selected mutants or genetically engineered organisms.
Food microbiology
Yogurt, cheese, chocolate, butter, pickles, sauerkraut, soya sauce, vitamins, amino acids, food thickeners (microbial polysaccharides), alcohol, sausages, and silage (animal food) are all produced by industrial microbiology processes. "Good" bacteria such as probiotics are becoming increasingly important in the food industry.[1]
[edit] Biopolymers
A huge variety of biopolymers, such as polysaccharides, polyesters, and polyamides, are produced by microorganisms. These products range from viscous solutions to plastics. The genetic manipulation of microorganisms has permitted the biotechnological production of biopolymers with tailored material properties suitable for high-value medical application such as tissue engineering and drug delivery. Industrial microbiology can be used for the biosynthesis of xanthan, alginate, cellulose, cyanophycin, poly(gamma-glutamic acid), levan, hyaluronic acid, organic acids, oligosaccharides and polysaccharides, and polyhydroxyalkanoates.[2]
[edit] Bioremediation
Microbial biodegradation of pollutants can be used to cleanup contaminated environments. These bioremediation and biotransformation methods harness naturally occurring microbes to degrade, transform or accumulate a huge range of compounds including hydrocarbons (e.g. oil), polychlorinated biphenyls (PCBs), polyaromatic hydrocarbons (PAHs), pharmaceutical substances, radionuclides and metals.[3]
[edit] Waste biotreatment
Microorganisms are used to treat the vast quantities of wastes generated by modern societies. Biotreatment, the processing of wastes using living organisms, is an environmentally friendly, relatively simple and cost-effective alternative to physico-chemical clean-up options. Confined environments, such as bioreactors] can be employed in biotreatment processes. [4]saka zvinhu zvenyu zvakadhakwa nhai?
[edit] Health-care and medicine
Microorganisms are used to produce human or animal biologicals such as insulin, growth hormone, and antibodies. Diagnostic assays that use monoclonal antibody, DNA probe technology or real-time PCR are used as rapid tests for pathogenic organisms in the clinical laborarory.[5]
[edit] Archaea
Examination of microbes living in unusual environments (e.g. high temperatures, salt, low pH or temperature, high radiation) an lead to discovery of microbes with new abilities that can be harnessed for industrial purposes.[6]
[edit] Corynebacteria
Corynebacteria are a diverse group Gram-positive bacteria found in a range of different ecological niches such as soil, vegetables, sewage, skin, and cheese smear. Corynebacterium glutamicum is of immense industrial importance and is one of the biotechnologically most important bacterial species with an annual production of more than two million tons of amino acids, mainly L-glutamate and L-lysine. The genome sequence of C. glutamicum has been published.[7]
