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Previously, different types of microbes and the ways they reproduce were discussed. Some microbes are free-living organisms and others are parasites. Even though the words 'microbe' and 'bacteria' are associated with disease for most people, not all microorganisms are 'bad guys'. This topic looks at the interactions between microorganisms and the human body. Microorganisms can be harmless, beneficial or pathogenic, which means harmful. This chapter looks at the beneficial types of microorganisms.

What are beneficial microorganisms?

Apparently, harmless and beneficial bacteria far outnumber the harmful varieties. Microbes are vital to the environment because they participate in the Earth's element cycles like the carbon and nitrogen cycles. Microorganisms are involved in the production of oxygen, biomass control and 'cleaning' the Earth of remnants of dead organisms.

Some microbes also lead a symbiotic type of lifestyle in most multicellular organisms. The community of beneficial microoraganims living in human intestines is called microflora.

Because microorganisms are capable of producing so many enzymes necessary for the building up and breaking down of organic compounds, bacteria are widely 'employed' by humans.

Nitrogen cycle

Nitrogen is a very important chemical element of all living matter. It is an essential part of amino acids - the building blocks of proteins. Nitrogen in its gaseous form (N2) makes up 78% of the atmosphere, but it cannot be absorbed and used as a nutrient by plants and animals. It must be converted by nitrifying (nitrosomonas) bacteria, so that it can enter food chains as a part of the nitrogen cycle. The nitrogen cycle is the cyclic movement of nitrogen in different chemical forms from the environment to organisms and then back to the environment. The nitrogen cycle consists of several different processes: nitrogen fixation; ammonification (decay); nitrification; and denitrification. See image 1.

The nitrogen cycle is also used in agricultural practices for soil enrichment.

See animation 1.


Microbes 'clean up' waste products and remnants of dead organisms in a process called decomposition. The decomposition or stabilisation of organic matter by biological action is as old as life itself. The controlled microbial decomposition of organic matter is called composting. The final product of composting is called compost. There are two types of composting:

  1. Aerobic- with oxygen.
  2. Anaerobic - without oxygen.

In these processes, bacteria, fungi, moulds, protozoa and other saprophytic organisms feed upon decaying organic materials initially. In the later stages of decomposition, mites, millipedes, centipedes, springtails, beetles and earthworms further break down and enrich these composting materials.


The industrial application of living organisms is called biotechnology. Humans have been using microorganisms for centuries. Today, biotechnology is a fast-developing industry.


Bioremediation is the use of living organisms for cleaning up oil spills and soil and water pollutants. Sewage treatment techniques are based on biofiltration of some toxic organic material by converting it into something that can be safely discharged into the environment. Bacteria that break down environmental pollutants are sometimes called biofilters.


Some microbes are used for medicinal production. One of the most important groups of medicines, antibiotics, is produced by fungi and bacteria. The name antibiotics means 'against life'. It is appropriate, because they attack bacteria and other unicellular organisms that are pathogenic for humans. Most antibiotics used today were found originally in fungi. Fungi are saprophytes, meaning that they get their nourishment from dead animals or plant matter. See image 2.


Billions of bacteria live in the human digestive system. They form over a kilogram of our body weight. These bacteria are referred to as microflora, or gut flora. These bacteria break down food remains that have not been digested earlier in the digestive system. They stop harmful bacteria and fungus from invading the body. The 'gut flora' also produces vitamin K, which is essential for normal blood clotting.

Human microfolora consists of 400 different species of bacteria. Some of these are beneficial and others are potentially harmful. A balance between the two is vital for human health and wellbeing.

One way of maintaining a balance between the beneficial and harmful bacteria in our intestines is to eat the types of food that contain beneficial bacteria. Beneficial bacteria that can be introduced into the digestive system through food are called probiotics. Most commercially-promoted fermented milk products with probiotic properties contain Lactobacillus bacteria or Bifidobacteria. Natural yogurts and Yakult, a fermented milk product, are examples of foods which contain probiotics.

Food industry

Fermentation is the process that produces alcoholic beverages or acidic dairy products. On a cellular level, fermentation is a way of obtaining energy without using oxygen. Fermentation involves the breaking down of complex organic substances into simpler ones.

Food like cheese, pickles, olives, sausages, chocolate, bread, wine, beer and soy sauce are all made with the help of different types of bacteria and yeast. In most of these food products, bacteria play a major role because they produce lactic acid. See image 3.


As bacteria can multiply and mutate easily, some of them are commonly used for scientific research in genetics and molecular biology. Bacteria and viruses also make good 'vehicles' for engineered genes that are inserted into the recipient's DNA.

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1. The community of beneficial microoraganims living in human intestines is called _______.






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