Application of Microbiology and the Role of Favorable Microorganisms

Microbiology develops along with the needs and problems that exist in nature. The problems in question include the problems of food, the environment, and also diseases that eventually produce new techniques to manipulate existing microorganisms to meet the interests of human life, and are known as biotechnology. 

Biotechnology comes from the Latin terms namely bio (life), teknos (technology = application), and logos (science), literally meaning science that applies the principles of biology. A more complete definition of biotechnology is the use of principles and engineering of organisms, systems, or biological processes to produce or enhance the potential of organisms and to produce products and services for the benefit of human life. 

In terms of products, for example, microorganisms produce various kinds of substances such as vitamins, organic acids, help humans make various kinds of drinks such as alcohol, wine, various foods such as soy sauce, tauco, oncom, tempeh, shrimp paste, boiled, and so on. In terms of services, microorganisms can help humans to analyze the content of a particular material (bioassay), help humans in mining certain metals (biomining). 

Finally in genetic engineering, the services of microorganisms such as viruses are needed to move DNA fragments from one cell to another. 

Microorganisms can also be human enemies, because of the losses they cause. The intended losses such as the emergence of diseases in humans, livestock, and crops. Diseases in humans from minor diseases such as tinea versicolor, dandruff, to severe diseases such as tuberculosis, wet lungs, and AIDS. These diseases are caused by microorganisms. Microorganisms can also cause damage to food and cause poisoning. Many microorganisms that produce toxins are harmful to humans.

The existence of microorganisms in nature, some are beneficial but some are detrimental to human life. The following are given several examples of applied microbiology that are beneficial in human life.


Microorganisms have the ability to change the nutritional value of food or drinks. The fermentation process is an anaerobic enzymatic change of the substrate, from organic compounds to simpler organic products. 

The activities of microorganisms in fermentation include being able to turn tofu or soybean pulp into oncom, being able to turn soybeans into tempeh or soy sauce, turning grapes into wine, and turning black or white sticky rice into black or white wine. In the fermentation process, microorganisms cause changes in complex compounds in food or drink into simpler compounds and can improve the taste and aroma of food or drink. 

This change is caused by the influence of microorganisms such as Neurospores with the enzymes they contain. Neurospores secrete amylase, lipase, and protease enzymes that are active during the fermentation process. In addition, it also describes the ingredients of cell walls of soybean pulp, cassava, or coconut. Fermentation in the manufacture of oncom causes the formation of a little alcohol and a variety of delicious-smelling esters.

Examples of other fermentation processes occur in the following processes.

  • Soybean is changed to tempeh. Tempe has a higher value than soy because it is easier to digest, and can be manipulated into many types of food compared to soy.
  • Rotting fish and shrimp, after fermenting into shrimp paste by microorganisms, can be reused for food.
  • Glucose through synergistic fermentation can produce a variety of products using the services of microorganisms. Synergistic occurs in the process of changing flour into glucose, then glucose is converted into alcohol, vinegar, and then into methane. The latter gas is known as biogas.
In the process mentioned above involved several microorganisms such as Aspergillus (fungus / mold), Saccharomyces (fungus / yeast), Acetobacter (bacteria), and Methanobacterium (bacteria). Another example of the utilization of these microorganism services is in the process of starch hydrolysis using the microorganism Bacillus subtilis which has the amylase enzyme and Aspergillus niger which has the enzyme amiloglucosidase, milk fermentation and its derivatives using the services of Streptococcus and Lactobacillus.

Some examples of fermentation products, raw materials, and offending microorganisms are shown in the following table.

Table: List of Fermented Foods

 Food / drink name Raw material Acting Microbes
 Cheese Milk Lactobacillus
 Yogurt Milk Streptoccoccus / Lactobacillus
 Pickles Cucumber Pediococcus
 Sake Paddy Aspergillus oryzae
Saccharomyces sake
 Beer Wheat Saccharomyces sp.
 Soy Sauce Soybean seeds Aspergillus
 Vinegar Wine ethanol Acetobacter
 WineGrapes  Saccharomyces
 Bread Wheat flour Saccharomyces
 Tempe Soy Rhizopus oligosporus
 Bongkrek tempeh Coconut + soy pulp R. oligosporus
 Oncom Peanut pulp R. stolonifer
 Soy sauce Black Soybean Neurospora crassa
 Tauco Soy A. wendtii
 Makassar Pindang Sea food R. oligosporus
 Shrimp paste Fish + flour Lactobacillus
 Pindang Garut Freshwater fish Lactobacillus
 Petis Fish / shrimp Lactobacillus
 Asinan Vegetables / fruit

Another example of fermentation is the manufacture of kefir. Kefir is a dairy product that tastes acidic, alcoholic, and carbonic. In Russia, kefir is a popular beverage that is produced and traded in large quantities. The seeds of kefir seeds needed to make kefir milk are sold in food stores. 

Housewives usually make kefir for their families. Kefir can also be produced in Western Europe and the United States. Making kefir is an inexpensive way to preserve milk. The method of making it is quite simple so it can be done on a household scale. Kefir is made from milk and seeds of kefir seeds. Milk can be taken from goat, sheep or cow milk. Kefir seeds can be purchased or obtained from the "rest" of the previous kefir. If properly stored, kefir seedlings can be reused for an unlimited number of times.

Milk kefir is first pasteurized (heated at 85°C for 30 minutes) and cooled in glass containers to room temperature (18-25 °C). Then 5-6% of kefir seedlings are added (50-60 g of kefir seeds for 1 liter of milk). The mixture of milk and kefir seeds is incubated by settling at room temperature for 24-48 hours, until complete clumping occurs. Next, the kefir is filtered to separate the kefir grains which can be used for making the next kefir. Filtered kefir milk can be improved by flavoring (incubating) again for 24 hours at room temperature or it would be better if stored in a refrigerator at 8 °C for 24 hours. Kefir milk can be stored at that temperature for at least one week.

Kefir seedlings consist of granules (grains) that are about the size of a wheat seed to walnut seeds. The grains grow from a very small size and will continue to grow during incubation. As much as 50 g of wet kefir granules can grow to double within 7-10 days if transferred to 500 ml of fresh milk within six weeks. The way to grow kefir seeds can be used full milk, skim milk, or whei milk that has been neutralized.

The seeds of kefir seeds consist of microorganisms that are surrounded by a slime-shaped matrix. The matrix consists of a polysaccharide sugar called kefiran (this is produced by certain bacteria). Kefir seeds also consist of a mixture of various bacteria and yeast (yeast), each of which microorganisms play a role in the formation of taste and structure of kefir.

Some species found in kefir seeds include Lactococcus lactis, Lactobacillus acidophilus, L. kefir, L. kefirgranum, and L. parakefir which function in the formation of lactic acid from lactose. L. kefiranofaciens as mucous forming (kefir grain matrix), Leuconostoc sp. forming diethyl from citrate, and Candida kefir forming ethanol and carbon dioxide from lactose. It also found L. brevis and yeast (Torulopsis holmii and Saccharomyces delbrueckii).

Kefir seeds cannot be dried by heating because some of the microorganisms in them will die. Kefir seedlings are still active if preserved by freeze drying. The best way to store kefir seedlings is by transferring old kefir seeds into pasteurized milk on a regular basis, then incubated overnight and stored in a refrigerator at 4-7 °C. 

In this condition, kefir seedlings remain active for about a month. During the fermentation process biochemical changes occur from the substrate due to the activity of heterofermented lactic acid bacteria and alcoholic yeast. Kefir acidity increased from 0.85% to 1.0% (calculated as lactic acid) and the pH decreased to below 3.0. 

In addition, carbon dioxide is formed so that the product has a carbonate taste. The change forms the taste of kefir as desired. During fermentation a polymer is formed consisting of sugar units (galactose and glucose) in the same amount called kefiran. Kefiran amounts to about 25% of the dry weight of kefir grains and is synthesized with new microorganism cells. During fermentation, acetoin and diacetyl compounds are formed.

The nutritional content of kefir is almost the same as the nutrition of kefir milk ingredients. The nutritional advantage of kefir compared to fresh milk is that the acid formed can extend the shelf life, prevent the growth of spoilage microorganisms so as to prevent milk damage, and prevent the growth of pathogenic microorganisms thereby increasing the safety of kefir products. Lactic acid bacteria in kefir have various health benefits. 

Among them are probiotics that can suppress the growth of bacteria that cause digestive tract diseases, because lactic acid bacteria produce antimicrobial compounds, including bacteriocin, hydrogen peroxide, and various antibiotics. Lactic acid bacteria form colonies and create an environment in the digestive tract in such a way that can prevent the growth of pathogenic bacteria that enter the body, thereby being able to prevent diarrhea caused by pathogenic bacteria.

Lactic acid bacteria can also prevent urinary tract infections, reduce the risk of cancer or tumors in the digestive tract and other organs, reduce blood serum cholesterol levels, reduce the risk of coronary heart disease, stimulate the formation of the immune system, help patients with lactose intolerance in consuming milk, and facilitate Release my self. Because it is beneficial for health, kefir is classified in functional drinks.

The scientific basis for the assumption that consuming milk fermented products containing lactic acid bacteria can reduce blood serum cholesterol levels thereby reducing the risk of coronary heart disease, has not been scientifically proven. However, there are several studies that strengthen this suspicion, namely:
  1. Some strains of lactic acid bacteria are able to metabolize cholesterol from food in the small intestine so that it is not absorbed by the body.
  2. Some strains of lactic acid bacteria are able to do salt deconyugation in the small intestine to prevent re-absorption by the body so that it stimulates the liver to synthesize more salt when it is from serum cholesterol. These two things can reduce serum cholesterol levels.
In addition, several studies also prove that consuming fermented milk products containing lactic acid bacteria can reduce the risk of cancer or tumors in the digestive tract. Therefore, lactic acid bacteria that live in fermented milk products suppress the growth of other bacteria in the digestive tract. 

While unwanted bacteria in the digestive tract produce certain enzymes, for example betaglukuronidase and azoreductase which can convert procarcinogenic compounds in food into carcinogens (eg nitrite to nitrosamine), which are cancer-causing compounds. Control of the growth of unwanted bacteria that can reduce the formation of carcinogens thereby reducing the risk of colon cancer. Lactic acid bacteria also stimulate the movement of contents of the digestive tract thereby reducing the concentration of procarcinogens and carcinogens in the digestive tract.

Lactose-intolerance or the inability to digest lactose occurs because a person cannot produce the enzyme beta-galactosidase by small intestinal epithelial cells due to genetic disorders. If the person consumes milk, lactose in the small intestine cannot be digested into galactose and glucose before being transported into the body for further metabolism. Lactose molecules that cannot be absorbed by the body then enter the large intestine and are hydrolyzed by bacteria that produce betagalactosidase. 

The galactose and glucose formed will be metabolized by homofermentative and heterofermentative bacteria that produce acid and a number of gases in the large intestine so that the person will suffer from diarrhea, bloating, and stomach pain.

Fermented milk products are very good for people with lactose-intolerance because most of the lactose has been broken down by lactic acid bacteria so that the lactose content is low. Besides the seed (starter) kefir is also a source of the enzyme beta-galactosidase to break down lactose in milk.

Single Cell Protein

Single cell protein is the use of microorganisms such as bacteria, fungi, and algae to meet the needs of human protein. This single cell protein was developed because it saw the nature of microorganisms that are able to reproduce much faster than animals and plants. Bacteria can multiply in less than 1 hour at optimum conditions. The generation time of yeast is 1-3 hours, algae is 2-6 hours, while the rather long one is mold 4-12 hours. 

These advantages and coupled with the fact that microorganism cells are generally rich in protein that is approximately 80% can cause a single cell protein can be produced. Based on these two ideas, the ability of microorganisms to produce proteins is much faster than any organism. As a comparison: 500 kg of cattle can produce only 1 kg of protein / day, 500 kg of soybean plants can only produce 40 kg of protein per day. Meanwhile, 500 kg of yeast is able to produce 50 tons of protein per day (McKane, 1996). 

Such rapid protein production and the complete essential amino acid content of organisms that are used as single cell proteins (PST) have better comparative values than proteins produced by plants that are prone to lysine amino acid deficiency. Another important reason is that single cell protein can be produced cheaply with very abundant raw materials in Indonesia.

Single cell protein raw materials can come from various wastes, leather mill waste, paper mill waste, petroleum, and so on.

In the process of making single cell proteins, potential microorganisms are cultured in substrates made from various kinds of waste. In Indonesia, PST production has been tried using crude oil, tapioca flour, molasses, sulfite (paper mill waste), and so on.

Petroleum is the first and most efficient raw material in making PST. But petroleum is also very much needed as fuel, so it is not popular. Indonesia as an agricultural country is very rich with other raw materials.

Not all microorganisms can be used in the process of making PST, several requirements that need to be met, including:
  1. During the process does not produce poison.
  2. Does not require complicated living requirements.
  3. Fast growing and multiplying.
  4. Easy to harvest.
Some microbes that have potential in the production of PST include bacteria groups: Bacillus, Hydrogenomonas, Methanomonas, Pseudomonas, yeast groups: Candida, Rhodotularia, Endomycopsis, Saccharomyces, fungal groups: Pleurotus, Agaricus, Lentinus, and microalgae groups: Chlorella, Sclotularia, Endomycopsis, Saccharomyces, fungal groups: Pleurotus, Agaricus, Lentinus, and microalgae groups: Chlorella, Scalledmus, Scenedesmus, Scenedesmus, Scenedesmus, Spirulina. Chorella, apart from being a raw material for PST production, is also an additional food ingredient for humans which is widely marketed today which is sold in tin cans. Likewise with Spirulina. A diagram of the PST production process is presented in the following figure.

Figure: General Diagram of SCP (Single Cell Protein) Production Process / Stages
Figure: General Diagram of SCP (Single Cell Protein) Production Process / Stages


Biosensors are devices that contain biological material (living organisms or cell products) and have the ability to respond to specific chemicals. This response is connected to the sensor system and is monitored through a readable electrical instrument.

Biosensors are widely used in the field of environmental and health monitoring, for example: metabolic poisons in water can be detected by measuring the intensity of light produced by bacterial cells in the luminisens event. Bacteria Photobacterium phosphoreum can produce light when ATP is available.

Therefore, compounds that inhibit metabolism (which also means inhibiting the formation of ATP) will reduce the ability of cells to produce light, with a light detector can be read the intensity of the light produced, which then translates into the presence or absence of metabolic toxins earlier. Another use of biosensors is to measure glucose levels in the blood.

This tool consists of glucose receptors. When this glucose receptor drops with a blood sample to be measured it will bind the glucose contained in the blood. How many glucose molecules that bind to these glucose receptors indicate blood glucose levels and can be read on the scale available on the device.

Biological Control

Biological control offers attractive options or additions to the use of conventional methods to control plant diseases. Biological control agents for microorganisms are preferred because they are less detrimental to the environment but their action performance is more complicated, making it difficult for agents to develop their resilience.

The success and failure of biological control in controlling plant pathogens is very dependent on the mechanisms of biological control agents. Each antagonistic microorganism has its own mechanism, and can have more than one inhibitory mechanism. The mechanism of inhibition of a biological control agent for antagonistic fungi is different from antagonistic bacteria, as well as others.

The main mechanism can be in the form of direct parasitism (eg mycoparasitism, bacteriophage infection) and nutritional competition or antibiosis. Nutrition competition plays a major role in almost all biological control agents. In addition to competition for nutrition, competition for living space. Nutrition can affect antibiotic production, and nutrition itself is affected by water availability. Antagonistic fungi can show different inhibitory mechanisms (Table).

Table: Some Examples of Disease Suppression Mechanisms by Biological Control Agents

 Mechanism Biological controlling agent Disease (pathogen) Host
  1. Pseudomonas putida
  2. Erwinia herbicola
  3. Pseudomonas syringae
  4. Pseudomonas fluorescens
  5. Pseudomonas putida
  6. Pseudomonas aeruginosa
  1.  Seedlings (Pythium ultimum)
  2. Freeze temperature damage (Pseudomonas syringae, Erwinia herbicola)
  3. Frozen temperature damage (Pseudomonas syringae)
  4. Seedlings (Pythium ultimum)
  5. Fusarium wilt (Fusarium oxysporum)
  6. Seedlings (Pythium splendans)
  1.  peas, soybeans
  2. corn
  3. corn, beans
  4. cotton
  5. carnation
  6. tomato
 Parasitism / Predation
  1.  Enterobacter cloacea
  2. Serratia marcescens
  3. Escherichia coli
  4. Pseudomonas spp. (chitinase-producing recombinant)
  1.  Seedlings (Pythium ultimum)
  2. Kapri wilt (Fusarium oxysporum f.sp.pisi)
  3. Rhizoctonia root rot (Rhizoctonia solani)
  4. Sclerotium root rot (Sclerotium rolfsii)
  5. Radish wilt (Fusarium Oxysporum f.sp. redolens)
  1.  cucumber
  2. pease
  3. Bean
  4. bean radish
  1.  Pseudomonas spp.
  2. Pseudomonas fluorescens
  1.  Fusarium wilt (Fusarium oxysporum f.sp. dianthi)
  2. Hawar hello (Pseudomonas syringae)
  1.  Carnation
  2. bean

The mechanism of inhibiting biological control agents usually uses the results of secondary metabolism, whether in the form of antibiotics, toxins, enzymes, hormones, or parasitism. A strong approach to understanding the mechanism is to use gene expression from mutants for biological control functions. 

The biochemical basis for gene expression (eg loss of antibiotic or ciderophore production) can be determined. Finally, functions can be created through gene supplementation techniques, together with the restoration of biological control activities. Proven experimental requirements for involving certain mechanisms in biological control have been formulated.

The postulate on the mechanism of involvement in the biological control of microorganisms (Handelsman & Parke, 1989 in Andrews, 1990) is as follows.
  • Mechanisms (competition, mycoparasitism, or others) that are related to effective strains as biological control agents.
  • Mechanisms that are linked to direct influence (vitality, growth)
  • Loss of mechanism in mutants is related to loss of relative effectiveness in wild species.
  • Recovery mechanism that is related to recovery effectiveness.
  • The tolerance of pathogens (mutants) to the mechanism that is attributed to the removal of diseases that are not hindered in the presence of biological control agents.
  • Recovered pathogenic (mutant) susceptibility to the mechanism associated with loss of ability to cause disease in the presence of biological control agents.
Other microorganisms that are used and have been widely marketed throughout the world in the form of cans under the brand name "DOOM", with the microorganism it contains is Bacillus thuringiensis. The bacteria are able to produce spores in the form of poison crystals called botulinin poison. Each strain of this bacterium is able to produce specific toxins for certain insects.

Purified bacteria or poisons are then dried and sprayed on plants. If eaten by caterpillars or larvae, insect pests will cause damage to the food digestive apparatus. The weakness of this poison is quickly disappear when sprayed, because it has deterioration in the field. The way to overcome this is that the pesticide is packaged in the form of dead cells. 

You are certainly also familiar with several terms such as bioassay, biomining, bioremediation, biodegradation, and so on. These terms are closely related to the role of beneficial microorganisms, and in those processes microorganism services are utilized by humans. In bioassays, microorganisms are used to analyze the content of certain substances contained in an ingredient. 

Technology develops thanks to the ability of people to see changes in the "behavior" of microorganisms due to the presence of a certain substance, for example Aspergillus niger which has black spores, and will turn gray when in substances where the microorganism is grown does not contain copper . On the basis of this knowledge one can use Aspergillus niger to find out whether copper is present in a particular material by looking at changes in the color of the mold spores.