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Our personal little Critters: Introduction to the Human Microbiome

Until I became chronically ill and started my healing journey I had never really given much thought to the microbes living in and on my body: my microbiome. I had heard about the gut flora and how probiotics are supposed to support digestion but I was never aware how important it actually was for my health and how many of these little critters actually lived in and on our bodies!

Ever since I learned that one of the root causes of my troubles was a so called dysbiosis, an imbalance in my gut microbiota, I’ve become very passionate about the subject and believe that if everybody knew more about the microbiome we could take better care of our health.

Therefore this post is designed as a short introduction to the human microbiome.

While the study of the human microbiome is still in its early stages and an active area of research, we can already say that it plays a huge role in human health and behavior.

Developments in DNA screening techniques and a decrease in their price has made these recent advancements possible. With DNA screening it is possible to capture all the bacteria, not just the ones that can be grown in a Petri dish (as previously).

The human microbiome consists of over 100 trillion bacteria. For every human cell there’s ten microbial cells and to the 23.000 genes we inherit from our parents there’s about 4 million microbial genes. So really, we’re only 10% human! 99% of our genome is microbial! And together they weigh around three pounds which is about the same as our brain. Crazy, right!?

So looking at these numbers we just cannot ignore our microbiome – it is essential to human health.

The most important roles these little critters play are the maintenance of our immune system, the digestion of foods and defending us against pathogens.

But they also ferment fibers that we cannot digest whilst creating important nutrients in turn. They contribute to our metabolism, hormone function and even affect our behavior, mood and thoughts!

The microbiome is not only composed of bacteria but also of viruses, fungi and protozoa. Each region of the body has a distinct set of microbes living on it.

These microbes change dynamically over a person’s lifetime.

It is believed that a baby’s gut is sterile and that our first set of microbes is acquired during birth in the mother’s birth canal and then through breast milk. The microbiome then matures until the age of three. In that time we accumulate microbes from our surroundings. The immune system matures at the same time and learns which set of microbes are our own (friends) and which ones are foreign invaders (foe).

Prevention of this process (c-section, too much hygiene, antibiotics) can have a huge impact on our health later in life and predisposes us to an array of chronic health problems.

After that period of time the microbiome remains dynamic but the main changes occur in its relative abundance and diversity. Because all strains have their preferred environment in which they thrive, changing that environment can have a huge impact.

The main factors that manipulate our microbiome are: age, diet, genetics, physiology and antibiotics.

As I mentioned before, a child’s microbiome is highly dynamic. It then becomes very complex and a lot more stable in adulthood and as all other body functions decrease with old age so does the diversity and stability of the microbiome.

Both a person’s long term dietary habits but also short term changes in these habits can lead to a shift in the kinds of microbes that live in our gut. The long term diet will determine which types of bacteria we harbor most, according to the types of foods that we (and the certain microbes) eat most. However, changing the diet over a short period of time can also change the abundance of different microbes in gut. But the degree of the change will only be as dramatic as the change in diet.

Antibiotics have the most drastic effect on the microbiome, especially if administered more than once in a shorter period of time. They kill most bacteria, not just the ones they’re supposed to target. Some bacteria can grow resistant to antibiotics and as other bacteria are wiped out, they can dominate the gut.

The effects of antibiotics vary individually and also depend on the kind of antibiotic (broad-spectrum antibiotics generally have the most devastating effect).

The time it takes to recover the original microbiome is highly individual but is usually possible after just one use of antibiotics – though it may take many months. However, studies have shown that it becomes harder to recover with subsequent uses of antibiotics.

Although studies so far suggest that the presence or absence of certain genes can change the relative abundance of certain species, most studies have found that the environment plays a more important role to the composition of the microbiome than genes.

Physiology (metabolism, hormone levels, immune function etc) can have a big impact on, and also be impacted by, the microbiome. This can for example lead to conditions like obesity and depression.

Because the microbiome is so dynamic it offers the possibility to manipulate it through the factors I’ve just mentioned.

A diet high in processed foods will usually lead to a dysbiosis, especially in a person who’s microbiome is already impaired from birth and early childhood. Refined sugars, carbs and additives feed yeasts which are the body’s waste recyclers. In large numbers they often cause problems.

This can be further impaired by the use of antibiotics which also kill all the beneficial bacteria that would counteract pathogens.

The more our microbiome is out of balance, the more problems usually arise. Damage can be done pretty quick, restoring the damage takes a long time and determination.

There is hope that with continuing research and understanding of the microbiome our war against germs will turn into working with them and using them to our advantage. Because the microbiome is so dynamic, it offers the chance to manipulate it and that could be the future of medicine.

There are already treatments available that use bacteria as therapy, such as FMT (Fecal Microbiota Transplant). Hopefully the future will see more possibilities but until then we can nurture and restore our microbiome with whole foods, fermented foods and probiotics and treat those little bugs as the friends & helpers they can be…

One of the leading microbiome researchers, Rob Knight, gave a really good TED Talk which sums this topic up beautifully. Watch it here.

Introduction To The Human Microbiome Sources:


photo credit: Mycobacterium tuberculosis Bacteria via photopin (license)

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