What are Microbes

Microbes are everywhere, but we can’t see them. They make us sick, but we can’t live without them. Microbes are critical to our existence, yet we know so little about them.

We have been conditioned to think of microbes – as disease-causing germs to be eradicated at all costs yet recent interest in this field of study has brought an appreciation for these microscopic living organisms – that do far more good than harm.

Although existing in a largely unseen world, microbes have a major impact on our existence as well as plants. They can control disease through production of antibiotics or by acting as biological control agents and they are a major source of useful products, including pharmaceuticals, food supplements, and insecticidal compounds, and have a key environmental role in decomposition of organic matter, including wood decay and the processing of human wastes.

As the oldest form of life on earth – some strains have existed for billions of years. They can live as individuals or cluster together in communities and exist in the water you drink, the food you eat, and the air you breathe. There are billions of microbes living in your gut, your mouth and covering on your skin – of which over 95% we depend upon to function and maintain our health and well being. Microbes include bacteria, viruses, fungi, algae, and protozoa and represent all the great kingdoms of life. Most of the diversity of life on Earth is represented by microbes.

Some Common Microbes:

Most of the microbes that we encounter or host within our bodies are beneficial – aiding our digestion, communicating with our immune system to regulate our bodies and combat pathogens (harmful bacteria or viruses) which cause health problems such as strep throat, chickenpox and the common cold.

Some examples of common bacteria that aid our lives are:

  • Bacillus thuringiensis – a common soil bacterium that is a natural pest control in gardens and on crops.
  • Arbuscular mycorrhizas – fungus living in the soil that helps crops take up nutrients from the soil.
  • Saccharomyces cerevisiae – a form of yeast used in baking
  • Escherichia coli – one of many kinds of microbes that live in your digestive system to help you digest your food every day.
  • Streptomyces – bacteria in soil that makes an antibiotic used to treat infections.
  • Pseudomonas putida – one of many microbes that clean wastes from sewage water at water treatment plants.
  • Lactobacillus acidophilus – one of the bacteria that turn milk into yogurt.

The Difference Between a Bacteria and a Virus

An important distinction between bacteria and viruses is that antibiotic drugs attack and kill bacteria, but usually have little or no effect against viruses.


Bacteria are single-celled microorganisms that thrive in many different types of environments. Some varieties live in extremes of cold or heat. Others make their home in people’s intestines, where they help digest food. Most bacteria cause no harm to people, but there are exceptions. Infections caused by bacteria include:

– Strep throat
– Tuberculosis
– Urinary tract infections

Inappropriate use of antibiotics has helped create strains of bacterial disease that are resistant to treatment with different types of antibiotic medications.


A Virus is even smaller than bacteria and requires a living host — such as people, plants or animals  to multiply. Otherwise, they can’t survive. When a virus enters your body, it invades some of your cells and takes over the cell machinery, redirecting it to produce the virus. Diseases caused by viruses include:

– Chickenpox
– Common colds

In some cases, such as pneumonia, meningitis and diarrhea can be caused by either type of microbe.




The Human Immunodeficiency Virus or HIV causes the disease we know as AIDS. AIDS is a pandemic—a disease outbreak that is happening all over the world. In 2000 alone, 3,000,000 people died of AIDS. Since the AIDS pandemic began around 1985, almost 22,000,000 people have died from the disease. Right now, HIV infects more than 36,000,000 people across the world, so that death toll will definitely get a lot bigger over the next several years. HIV doesn’t kill people itself. Instead, the virus shuts down a person’s immune defenses—the tools used to fight off invading microbes—by infecting and destroying important immune cells called T cells. Once a person loses too many T cells, his or her body can no longer deal with other microbes that cause infections. HIV merely opens the floodgates. Eventually HIV-infected people become overrun by harmful microbes and die of lung infections, skin infections or other diseases.

The Flu Virus

Every year during what’s called “the flu season” tens of thousands of people get the flu. Despite feeling all achy and lousy for several days, most people eventually beat the virus and recover just fine. Worldwide, the flu virus has killed at least 21,000,000 people.

The Plague

Back in the 14th century, the bacteria that causes bubonic plague, or the Black Death as it was also known, was the deadliest microbe of all. In just a few years, from 1347 to 1351, the plague killed off about 75,000,000 people worldwide, including one-third of the entire population of Europe at that time. The plague bacteria cause painful swellings as large as an orange to form in the armpits, neck and groin. These swellings, often burst open, oozing blood and pus. Blood vessels leak blood that puddles under the skin, giving the skin a blackened look. That’s why the disease became known as the Black Death. At least half of its victims die within a week. The pneumonic form of plague causes victims to sweat heavily and cough up blood that starts filling their lungs. Almost no one survived it during the plague years.

Yersinia pestis is the deadliest microbe ever known, although HIV might catch up to it. Yersinia pestis is still around in the world. Fortunately, with bacteria-killing antibiotics and measures to control the pests—rats and mice—that spread the bacteria, it is being conquered.

Ebola, the Bloody Virus

Ebola is definitely an ugly killer. It is part of a group of viruses that, among other effects on the body, cause the blood to stop clotting. Victims begin oozing blood from their mouths, noses, internal organs, even their eyes. It kills up to almost 90% of those who get infected. With that kind of death rate, Ebola would be the deadliest microbe of all if it was more common.

The Effects of Bacteria on the Human Host

the microbes in the body frequently interact with their human hosts, a key part of what is know as the interactome. The “massive” occurrence of communication via protein-coding genes ensures mutual survival of the microbes and the human host.

Infact the manipulation of the human host cells and resulting inflammatory responses are recurrent strategies used by pathogens that cause harm and disease. Bacteria influence host-cell our gene expression through a number of increasingly well-documented ways


Metagenomics – is a field which looks beyond the effects of individual strains or genomes of microbes, and how whole communities of microbes develop and interact with each other.
Metagenomics provides a way of studying and understanding the differing behaviours of the large majority of microbes based on their make up – historically difficult to culture and classify.

Metagenomic Communities May Cause Disease

For more than a century, researchers have believed that infectious diseases are caused by a single microbial species, as in the case with a minority of diseases such as leprosy

While mounting evidence suggests many chronic diseases are caused by pathogens, rarely have researchers been able to identify a single infectious agent, rather an ever-evolving, patient-specific communitY of microbes – or microbiota that are to blame.  
A greater understanding of metagenomics is therefore key to treating chronic diseases. What is evident however is that patients suffering from chronic diseases have different communities of microbes (or microbiota) and consistently less diversity in the different species of microbes in these communities.