Beneficial Microorganisms and Their Use

Microorganisms are far more often helpful than harmful. Throughout history, humans have used them to make food and medicine, and the use of microbes to make bread, cheese, and wine is as old as civilization itself.

Beyond food, microorganisms form essential links in the food chains that support the plants and animals we eat, aid digestion in the guts of animals and humans, and are sometimes eaten directly (as with algae and mushrooms). This article surveys the many ways microbes are put to use, from the kitchen to industry, agriculture, medicine, and the environment.

Figure: Use of microorganisms to produce different products

Biochemical and fermentation reactions carried out by microbes are used to produce products for promoting health (such as amino acids, hormones, probiotics, antibiotics), etc. or producing beneficial metabolites (such as enzymes,  pickles, fructose used in soft drinks, artificial sweeteners, beer, wine, alcohols).

Today, hundreds of different substances are manufactured with the aid of microorganisms, and this post contains the most common use of such beneficial microorganisms.

Food Supplements

Yeasts are an excellent source of protein and vitamins and are used as supplements in processed foods, mainly in animal feeds. Algal cultures such as Scenedesmus and Chlorellahave been cultivated in various countries and used as ingredients in ice cream.

Figure: Food and Pharmaceutical applications of Spirulina (Image source)

Single-cell protein (SCP) is an important, high-yield, relatively inexpensive source of protein-rich food used in animal feed. Cyanobacterium Spirulina is a good source of protein, and dried Spirulina is about 65% protein. The cyanobacteria are harvested, sun-dried, washed to remove sand and made into cakes for human consumption.

Fermented Dairy Products

Microorganisms produce fermented dairy products, such as cultured buttermilk, yogurt, kefir, cheese, koumiss, etc. Fermented dairy products are a source of probiotics, prebiotics, and bioactive compounds. Dairy products can be used as nutraceutical agents and functional foods.

Figure: Fermented dairy products and their use

The most common lactic acid bacteria (LAB) used to ferment milk are Streptococcus thermophilus, usually paired with Lactobacillus or Bifidobacterium species. For example, yogurt is made by adding Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus to milk; acidophilus milk uses Lactobacillus acidophilus. The full range of fermented foods and the microbes behind them is covered in the article on fermented foods.

Fermented Food Products

Microorganisms produce various fermented foods and products such as vinegar, sauerkraut, pickles, olives, poi, soy sauce, soy products, and fermented meats.

Bread Production

Yeast (a particular Saccharomyces cerevisiae strain) is used as a leavening agent in the bakery industry for making bread. During fermentation, yeast cells produce little alcohol and much carbon dioxide.

As the carbon dioxide bubbles become trapped in the dough, they cause the dough to increase in bulk and acquire a lighter, finer texture. When the dough is baked, the alcohol and carbon dioxide is driven off, and the bread becomes soft and porous because of spaces created by carbon dioxide bubbles.

Beer, Wine, and Spirits Production

Alcoholic beverages such as beer and wine are made by fermenting sugary juices. Spirits, such as whiskey, rum, and gin, are made by fermenting and distilling the fermented products. Specific strains of the yeast Saccharomyces are used as fermenters to produce alcoholic beverages.

Figure: Role of microorganisms in producing alcoholic beverages (image source; Ref-5)

Cereal grains (usually malted barley) are used to make beer. Most wine is made from grape juice, although wine can be made from any fruit juice. Spirits are made from the fermentation of a variety of foods, mainly malted barley (Scotch whiskey), corn (bourbon), potatoes (vodka), wine or fruit juice (brandy), rye (rye whiskey, gin), and molasses (rum).

Biofertilizers and Biopesticides

Many microorganisms, such as fungi or bacteria, are useful in agriculture since they are attractive eco-friendly alternatives to mineral fertilizers and chemical pesticides. We have seen increased applications of biofertilizers and biopesticides in recent years, mostly owing to their eco-friendly benefits. These microbes supply nutrients to crops, control phytopathogens, and stimulate plant growth.

Figure: Influence of biofertilizers on plant growth (Image source: Ref-3)

Rhizobium, Azospirillum, Azotobacter, arbuscular mycorrhiza fungi (AMF),Azolla, and Cyanobacteria are used as biofertilizers. These bacteria or fungi promote plant growth by nitrogen-fixing, phosphate solubilization, or secreting plant growth-promoting substances.

Bacillus is one of the most employed bacteria in agriculture, both as biofertilizers and biopesticides. Bacillus thuringiensis is one of the most used biopesticides worldwide.

Probiotics

Probiotics are live beneficial microorganisms (bacteria and yeasts) taken as food supplements or, in some cases, as disease-control agents, to support a healthy gut community. Because this is a large topic in its own right, it is covered fully in the dedicated article on probiotics and prebiotics.

Figure: Probiotics and antibiotics

Organic Acids and Solvent Production

Genetically engineered microorganisms can be used to manufacture organic acids and solvents. The acids include acetic, lactic, and citric acids. The solvents include ethanol (ethyl alcohol), butanol, acetone, and glycerol.

Ethanol for industrial application is produced the same way as making alcoholic beverages. Newer methods of ethanol production by using thermophilic clostridia, Zymomonas mobilis, and Pachysolen tannophilus are under the trial phase.

Clostridium acetobutylicum is used to produce acetone and butanol, and the oxidation of ethanol by acetic acid bacteria produces vinegar. Aspergillus niger is the main industrial producer of citric acid. Lactic acid is produced by lactic acid bacteria and is covered in detail in the article on lactic acid fermentation.

Antibiotics Production

Various microorganisms are grown in large fermenters to produce antibiotics. For example, strains of Penicillium chrysogenum are used to produce penicillin. The large-scale vessels used for this are described in the article on bioreactors.

To combat drug resistance and to increase the potency of antibiotics. Pharmaceutical industries produce semi-synthetic antibiotics, made partly by microorganisms and partly by chemists.

Enzymes Production

Microorganisms are being used to synthesize enzymes used in industrial processes. Enzymes such as proteases, amylases, lipase, lactase, and invertase are produced using specific organisms.

These enzymes have huge industrial applications and are also used in households; for example, proteolytic enzymes and lipase are essential components of drain cleaners.

Amino Acid Production

Humans and animals cannot synthesize eight essential amino acids, so they must be provided in the diet. Many essential amino acids such as lysine, glutamic acid, phenylalanine, aspartic acid, and tryptophan are manufactured by microbial fermentation.

Mutant strains of Corynebacterium glutamicum are used to produce lysine, which is used as animal feed supplements. Mutant strains of C. glutamicum are also used to produce glutamic acid. Glutamic acid is used to make flavor enhancer monosodium glutamate (MSG).

Vaccine and Hormone Production

Microorganisms are the major tools of genetic engineering. Several products important to humans, such as interferons, vaccines, vitamins, and hormones, are now produced economically by microbes because of genetic engineering.

Hormones such as insulin, human growth hormone, and somatostatin are made using modified strains of Escherichia coli made using **recombinant DNA technology.**Steroid hormones such as cortisone are produced using microorganisms through bioconversion using a mold Rhizopus nigricans.

Bacteriophage Therapy

Bacteriophages are the natural enemies of bacteria but are harmless to animals, plants, and humans. Phage therapy mainly utilizes obligately lytic phages to kill their respective bacterial hosts while leaving human cells intact and reducing the broader impact on commensal bacteria that often results from antibiotic use.

Figure: Phage therapy

Using highly specific phages, humans are selectively targeting MDR pathogens to treat various infections caused by them. Various clinical phage trials are ongoing to evaluable phage as therapeutic options to kill three critical priority pathogens, Acinetobacter baumannii, Pseudomonas aeruginosa, and members of the family Enterobacteriaceae.

Bioremediation

Bioremediation is the use of living organisms to remove or neutralize environmental pollutants through their metabolism. Many microbes, including some Pseudomonas species, can break down petroleum hydrocarbons. The Exxon Valdez oil spill cleanup in 1989 is a well-known example: rather than adding new microbes, workers applied fertilizers to speed up the growth and oil-degrading activity of the microbes already present on the shoreline. Geobacter metallireducens can convert soluble uranium into an insoluble form, and so can be used to remove uranium from contaminated soil and water.

Figure: Bioremediation (Source:nature)

Microorganisms have the potential to be the major tools for waste management. Various organisms (fungi, algae, and bacteria) are being used to degrade oil spills, remove toxic materials from soil, and digest explosives that are too dangerous to handle.

Microbial Mining

Biomining, using microbes to extract metals of economic interest from less concentrated ores, is a new approach in mining industries. As the ore is getting less concentrated, few mining companies are using microorganisms in their mining process.

Figure: Biomining: heap bioleaching process to obtain copper on an industrial scale (source).

Acidithiobacillus ferrooxidans (formerly Thiobacillus ferrooxidans), a chemolithotrophic acidophilic bacterium, oxidizes minerals so that metals such as copper are released into a water-soluble form that can be extracted. Other bacteria used in mining include Acidithiobacillus thiooxidans and Leptospirillum ferrooxidans.

How to Remember

Given this is a broad survey that ranks well, a light How to Remember that organizes the breadth is more useful than mnemonics for each use.

Six arenas where microbes work for us.
Food and drink (bread, cheese, beer), agriculture (biofertilizers, biopesticides), medicine (antibiotics, vaccines, insulin), industry (enzymes, acids, solvents), environment (bioremediation, waste), and mining (bioleaching). Sort any example into one of the six and the survey holds together.

The workhorses show up everywhere.
A few genera do a huge share of the work: Saccharomyces (bread, beer, wine), Lactobacillus (dairy, pickles), Aspergillus (citric acid, enzymes), Bacillus (biopesticides, enzymes), and E. coli (recombinant insulin and hormones). Learn the workhorses and you cover most examples.

Genetic engineering changed the medicine column.
Insulin, human growth hormone, and many vaccines are now made by putting human genes into microbes (mostly E. coli). The microbe becomes a tiny factory. That single idea, recombinant DNA, underlies most modern microbial pharma.

Key exam facts in one table

Where Students Get Confused

Are microbes mostly harmful?
No. The disease-causing microbes get the attention, but the large majority of microbes are harmless or useful. This article surveys just how much of modern food, medicine, agriculture, and industry depends on them.

How is insulin made by bacteria?
The human insulin gene is inserted into E. coli using recombinant DNA technology. The bacterium then produces human insulin as it grows. The microbe is essentially a living factory following a human genetic instruction.

Did adding Pseudomonas clean up the Exxon Valdez spill?
Not quite. The cleanup worked mainly by adding fertilizer to boost the oil-degrading microbes already living on the shoreline, rather than introducing new bacteria. The native microbes did the work once they were fed.

What is the difference between a biofertilizer and a biopesticide?
Both use living microbes in agriculture, but a biofertilizer supplies nutrients or promotes plant growth (for example, nitrogen-fixing Rhizobium), while a biopesticide controls pests or plant pathogens (for example, Bacillus thuringiensis). Some microbes, like Bacillus, are used for both.

How can microbes be used in mining?
In bioleaching, acid-loving bacteria such as Acidithiobacillus ferrooxidans oxidize ore minerals, releasing metals like copper into a soluble form that can then be recovered. This lets companies extract metal from low-grade ores that would otherwise be uneconomical.

References and further readings

1. Madigan MT, Bender KS, Buckley DH, Sattley WM, Stahl DA. Brock Biology of Microorganisms. 16th ed. New York: Pearson; 2021.
2. Furfaro LL, Payne MS, Chang BJ. Bacteriophage therapy: clinical trials and regulatory hurdles. Front Cell Infect Microbiol. 2018;8:376. https://doi.org/10.3389/fcimb.2018.00376
3. Mahmud AA, Upadhyay SK, Srivastava AK, Bhojiya AA. Biofertilizers: a nexus between soil fertility and crop productivity under abiotic stress. Curr Res Environ Sustain. 2021;3:100063. https://doi.org/10.1016/j.crsust.2021.100063
4. Patel S, Goyal A. Current and prospective insights on food and pharmaceutical applications of Spirulina. Curr Trends Biotechnol Pharm. 2013;7:681–695.
5. Macedo NJ, Brigham CJ. From beverages to biofuels: the journeys of ethanol-producing microorganisms. Int J Biotechnol Wellness Ind. 2014;3:79–87.