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What is the Human Microbiome and How Do We Keep it Healthy?

What is the Human Microbiome and How Do We Keep it Healthy?

By Erik Galuppo - August 30, 2019

What is the Human Microbiome?

Humans are amazingly complex organisms. Not only are we made up of human cells, but also trillions of microbes. These microbes live in communities throughout our bodies. In fact, every person has more microbes (such as bacteria, viruses, fungi, archaea) than human cells. This collection of all the microbes living within and on us is called the human microbiome or human microbiota.

It is estimated that there are about 37.2 trillion human cells in an adult and about 100 trillion bacterial cells! And that’s not counting the viruses and other microbes. But since microbes are so small, they only add up to about 2.5 pounds of weight in an adult. Or if you put all the microbes in one place, they would occupy about 3 pints (or 6 cups) of volume.

All these microbes play essential roles in basic life processes, from development to daily functioning of our bodies. This is because microbes co-evolved with humans over millions of years. There are all sorts of interactions going on all the time between the microbes and our human cells. A very important role of our microbes is that they resist invading microbes (pathogenic microbes) and help keep our ecosystem stable. Interactions between the microbes and immune system start at birth, and continue throughout life. For example, the microbes of the gut are involved with digestion and getting nutrients and energy from food, in protecting against pathogens, and in constant communication with the immune system.

In other words, don’t think of microbes just as harmful “germs”, but instead think of the microbes within us as beneficial and needed - as partners with our human cells.

Every person has hundreds of different microbial species in communities throughout the body. There are microbes on the skin, in the lungs, the gut, ears, vagina, eyes, mouth, sinuses – everywhere we look. We refer to the microbial community or ecosystem at each site also as a microbiome. For example, in the mouth is the oral microbiome, and in the sinuses is the sinus microbiome. The gastrointestinal tract (intestines and colon) is referred to as the gut microbiome.

The gut microbiome is incredibly densely packed with microbes (up to 100 billion to one trillion cells per milliliter in the large intestine) and rich in the number of microbial species, including between 500 and more than 1000 species of bacteria.

Each body site has different microbes. Not only do we have microbial communities throughout the body, but at each site the communities contain different microbes. Some microbes are common in many sites throughout the body, but others are found only at certain body sites Thus the microbes in the gut microbiome are different than the ear microbiome in an individual.

Every individual has a microbiome unique to that individual. Microbial communities at the different body sites are similar in different people, but with some variations, such as some different species and more of some microbes, less of others. For example, skin microbiomes are similar among different people, but not identical.

Both harmful and beneficial microbes coexist together. One amazing finding has been that we all have both beneficial and what we usually think of as harmful microbes living throughout the body in harmony. Most microbes are symbiotic (both the human body and the microbes benefit), and a minority are potentially harmful microbes. The microbes that have the potential to be harmful are kept in check by beneficial microbes and the immune system, that is, by a healthy balanced community. For example, many healthy people have Staphylococcus aureus and the fungi Candida and Aspergillus in their microbiome at different sites in the body.

Sometimes the microbiome can become imbalanced. When the microbiome becomes imbalanced or “out of whack”, this is known as dysbiosis. For example, when new viruses or bacteria are introduced into the body (such as when we get the flu) an imbalance can occur. Sometimes some of the “potentially harmful” resident bacteria that quietly coexist with the other microbes in times of health, may for some reason increase and cause problems and illness.

Imbalances can also occur with exposure to environmental toxins, a poor diet or lifestyle (e.g. lack of exercise), allergies, stress, certain medicines such as antibiotics, and some household disinfectants.

The microbiomes are different between healthy and sick people. Research is now finding microbial differences at different body sites in a number of illnesses and conditions. For example, the microbiomes are different in healthy skin as compared to skin with acne, in healthy sinuses compared to those with chronic sinusitis, in a healthy gut as compared to a person with diabetes or intestinal bowel disease (IBD). 

What is a healthy microbiome?

A healthy microbiome is one that is balanced – in equilibrium or homeostasis, and is a sign of health. Researchers have studied the gut and its microbiome more than any other site of the body, thus much of the current knowledge of the human microbiome is really about the gut microbiome. The gut is incredibly important for healthy functioning of the body. Chronic inflammation (which is linked to heart disease and cancer) and some diseases are now being linked to the microbes in the gut.

Researchers still do not know exactly what microbes constitute a healthy gut microbiome, but some patterns are emerging. 

Diversity of microbes, and the mix of microbes is important. The more diverse the gut microbiome (more variety of microbes), the healthier it is, and the more it can adapt to disturbances. Also, the actual mix of types of microbes involved in a healthy gut microbiome is important. This is also true for other microbiomes throughout the body. Healthy communities don't have just one important species of bacteria or other microbes, but a mix of microbes, and some mixes work better than others for preventing infections and for health.

Where do we get all the microbes that are in our body?

The initial “seeding” of the human microbiome occurs during birth. The type of microbes a baby receives vary whether the baby is born vaginally (the baby picks up microbes going down the birth canal) or delivered by C-section. Then a baby receives different microbes whether breastfed (gets 100s of microbes from the mother) or formula fed. As the baby starts eating solid foods there are more microbial changes, with different microbes dominating. Over time the dietary pattern (the types of foods one eats) influence the types of microbes that are in the body. How we live our life and what we are exposed to all have an effect on our microbes. For example, going outside, being exposed to dirt and plants (whether playing or gardening ), exposure to cigarette smoke, medicines taken, pets, infections, our lifestyle, and whether we get exercise or not all has an effect. Even living with others results in the exchange of some microbes.

We are constantly exposed to and ingest millions of microbes (bacteria, fungi, viruses) every day. They are in the water we drink (yes, even chlorinated tap water contains microbes), the foods we eat, and the air we breathe. Our immune system and microbes protect us and keep harmful microbes under control.

There are changes over the life-span in our microbiome. The microbiome changes dramatically between birth and the age of 2 years, when it starts to look like an adult microbiome. There are also changes over the life-span, with some species there at all times, while others will come and go. It is thought that as people age, the community of gut microbes become less diverse than in younger people, and that there is an increase in chronic inflammation, which is linked to diseases such as heart disease and cancer.

However, a recent study from China found that the gut microbial communities were very similar among very healthy people in their mid 30s to over 100 years in age. The researchers thought this was due to an active healthy lifestyle and good diet.

Can we change our microbiome?

Yes, we can change our microbiome to a degree. While some microbes are common to all people, some other microbes are found only in some people, or the proportion of microbial species can vary among people. We now know that certain microbes are linked to chronic inflammation and diseases, while other microbes are linked to health and the absence of inflammation.

A person’s diet has a key role in what microbes live in the gut. What one eats (a person’s general dietary pattern) feeds some types of microbes and not others, and this determines what lives in the gut microbial community. A goal should be to lower chronic inflammation by feeding and nurturing beneficial microbes. With a change in diet, microbial changes can occur rapidly, within a few weeks. But to maintain the microbial changes one must continue with the new dietary pattern, so as to feed and nourish the beneficial bacteria.

High fiber diets lower inflammation in the gut and body, while low fiber diets increase inflammation. A Western style diet with lots of highly processed foods, lots of meat, high-fat foods, little dietary fiber, refined grains, sugary drinks and desserts feeds microbes that are linked to chronic inflammation and disease. On the other hand, a diet rich in real whole plant foods and fiber, such as fruits, vegetables, whole grains, nuts, legumes, and seeds is linked to beneficial microbes and health.

Some medicines and medical practices alter our microbiome. Wide scale use of antibiotics is especially concerning because antibiotics kill both harmful and beneficial microbes. Antibiotics have a disruptive effect on gut microbial species and also microbial species at other sites in the body, such as the sinuses. Antibiotics can absolutely be life-saving, but medical experts now say they are over-used and should be used only when necessary, in both human medical treatments and in farming practices.

How do we know all this about the microbiome? Finding out about the trillions of microbes in and on our bodies only happened with the development of modern technologies using genetic sequencing. In the past decade, this area of research has exploded. Finding out what lives in our gut microbiome is now done by analyzing the microbes in the stool (feces), while other body sites are typically swabbed and the microbes analyzed. The old methods of “taking cultures” only shows some microbes, and not all the vast diversity of microbes.

Several large projects have been studying the human microbiome, such as the Human Microbiome Project (conducted by the National Institute of Health) and the American Gut Project (a crowdsourced global citizen science effort).

There is much we don't know about our microbial communities. We are learning enormous amounts with each passing year.

The future may involve using certain microbes as medical treatments. Probiotics! The beneficial bacteria Lactobacillus sakei, in the product Lanto Sinus, is already being used by many to treat sinusitis.

Fun fact: We each give off a personal microbial cloud with its own microbial signature. The microbes (bacteria, fungi, viruses) are given off with every movement, every exhalation, every burp and fart, and they go in the air around the person and settle around him or her.

In summary: Think of our bodies as a collective “we”. We’re an ecosystem composed of both human cells and trillions of microbes. We should try to live a healthy lifestyle and to eat well to nourish both our bodies and our microbes.


American Society for Microbiology - especially the FAQ page, the report, and supplements.

Blaser, Martin J – Missing Microbes. New York: Henry Holt and Company, 2014.

Gut Microbiota for Health site reports on research. One recent (Aug. 2019) article: Diet and lifestyle outweigh genetic background in shaping gut microbiome across nonhuman and human primates

The Scientist. Numerous articles on the human microbiome. Including a series on the human microbiome and health.

Ward, T, Knights, D & Gale, C.A. Infant fungal communities: current knowledge and research opportunities. BMC Medicine, Volume 15, Article 30, 2017.

Yong, Ed – I Contain Multitudes. New York: Harper Collins Publishers, 2016.


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