2kg, 90% of our cells, billion of genes… this is The Microbiome!

Let’s talk about a subject that fascinates me: our microbiota.

You’ve probably heard that our intestines, and more specifically our large intestines, are populated by billions of bacteria. This is a fairly recent discovery. Also, researchers not sure how to identify these unicellular beings living in our digestive tract, called it “flora”, in reference to the classification of plants.

 A minority of bacteria can be “cultivated” on a petri dish in the laboratory. It is therefore difficult to know all the micro-organisms that live in our womb However, scientists have distinguished three main families of bacteria:

  • The Firmicutes
  • Bacteroidetes
  • Actinobacteria

There is even a 4th: Proteobacteria

We are starting to know a little more about the microbiota, considered today as an organ in its own right, specific to everyone.


Let me tell you about an experience that marked me.

Mice underwent antibiotic treatment. Their intestinal flora has therefore been partially destroyed. Indeed, antibiotics kill the bacteria that cause the disease, but also the “good” bacteria living in our intestines.

The researchers then fed these mice with bacteria from other mice. The treated mice began to behave like the mice from which they received their bacteria.

Impressive, isn’t it?

Of course, it is not possible to say the same for human beings, but this experience is a good start to show how the study of the microbiota is far from having finished surprising us.


A microbiota modification can trigger intestine disorders and a weakening of the immune system.

In this article I am gonna try to teach you a little more about these billions of microbes living inside our gut.


Let’s start by a simple explication to understand about whom we talk about

A bacteria is an unicellar organisum, meaning it owns only one cell. Thus, it can’t be seen with our eyes. Some bacteria can breathe: they are using oxygen to produce energy. Other use fermentation.


What is our intestine composition?

Many microbes are living in our gut. We can find:

  • Many different bacteria species
  • Virus
  • Yeast
  • Protozoa
  • Fungus

Bacteria?! Isn’t it dangerous?

Sure, some can cause diseases like cholera, leprosy or tuberculosis. However, there are essential for our life.

Not convinced yet?

Don’t worry, human body plans everything! Our gut wall is protected by the epithelium which releases antimicrobial peptide, and its covered  with mucus.


Why do we have so many bacteria?

This is simple: without them, we couldn’t live! Even if we can’t see them, we can sometimes feel and smell their presence.

For example, heaps of bacteria are living in our skin, which can explain our smell after a good workout. Indeed, our sweat is composed with water with minerals, proteins, lactate and urea which is a perfect kind of food for our armpit bacteria! It’s not the sweat which smells bad, but more a chemical component produced by our bacteria. The more we wait for a shower, the longer the bacteria have time to feed on our sweat and produce this bad smell.

We can smell them as well after a little moment in the loo. 1g of poo contains more bacteria than there are Human of Earth!



Ok, bacteria make me smell, so how can they be benefit for me?!

First, remember that we have 10 times more bacteria than we have cell. Around 2kg indicated on the scale doesn’t really own to us, it’s the weight of our 10 billion of microbes!

To help you to understand, try to see bacteria as tenant of our flat (our body) and they pay the rent and quarter with Energy. It’s a symbiosis, scientific word to describe this winning-winning Relationship. Bacteria feed themselves of fibers, food part our intestine are not able to digest, and produce short chain fatty acids (SCFAs) which, in turn, are kind of food for our gut cells.

Bacteria can produce many different kind of substances: gas, fatty acid, fat…

It’s not over!

  • They synthetize vitamins such as K vitamin, B group vitamins as the biotin (B7), cobalamin (B12), folates (B9), acid pantothenic (B5), pyridoxine(B6), riboflavin (B2) et thiamine (B1).

For example the K2 vitamin plays an important role in blood coagulation, and the most of it is produced in our gut! Studies show that people following a poor-vitamin-K diet for 4 weeks do not have any deficiency signs. However, the one who get an antibiotic treatment before this experiment seen their prothrombin decrease.


  • They play a role in our immune defence

80% of our immune cells are in our gut. In the same time we are putting food inside our body, we are ingesting microbes as well. These microbes are going to stimulate our immune cells.

Our microbiota is a barrier against pathogenic microbes. How? Let’s use a metaphor. You proably already wanted to buy a ticket for a concert but it was full? Well inside our gut it’s the same: places are limited. Is the room is already busy, others microbes can’t stay, and this is for our good!


  • They limit toxin impact produced by pathogenic microbes by:
        • deteriorate then
        • act on their synthesis
        • modify their enterocytes (gut cell) sensitivity to this toxins


  • They produce protective substances

The most famous one is the butyrate. This short chain fatty acid coming from fiber fermentation by bacteria. Its play a very important role in our intestine: thanks to it, the pH decrease helping “good” bacteria development, Energy source for our colon cell and is a natural anti-inflammatory. Butyrate may prevent colon cancer thanks to its ability to induce cancerous cells apoptosis (cell death).


  • They recycle, synthesize or deteriorate our hormones. 20% of T4 (thyroid hormone) is converted to T3 (active form) in our gut.


How the microbiote born?

When we are in our mum belly’s, our gut is “clean”. The first microbes coming inside us is during birth. Our microbiome is “adult” at age 3. The way we are born (natural or C-section), our food, environment, antibiotics consumption and other treatment affect its content.


Our microbiote is like our fingerprint : belongs to us and is unique.


What happen if our microbiota is disturbed?

If an imbalance occurs, it’s not symbiosis anymore but a dysbiosis. 3 mains reasons express this unbalance:

  • An unbalance between pathogenic and benefit microbes and anti or pro-inflammatory agents. 
  • Prevalence of some microbes
  • Shortage or absence of some microbes such as Faecalibacterium prausnitzii (Fprau).

Let’s talk a little bit more about this bacteria. In mouses, Fprau have benefits effects: this specie decrease inflammation and produce a molecule which protect the gut. Researchers observed in people sufuring of IBD (inflammatory bowel disease), Fprau is less present and this shortage worsen the disease. Moreover, people suffuring from IBS have very often this shortage. Thus, few leads are in study. Patients could get this bacteria as a probiotic, but some scientist suggest to ingest directly the protein synthesized by Fprau, the MAM (Micronial Anti-inflammatory Molecule) as a medicine


Remember: There is no bad or good bacteria (some exceptions exist). It’s more about the quantity , where they are and the way they interact with other microbes which matter.


When the gut wall is damaged, the bacteria crossing through the enterocytes is easier. This trigger an inflammation which can stay for a while and disturb the gut wall if nothing is done.


Where else can we find bacteria?

We do not have only the intestine microbiote, we also get microbiote of:

  • The skin
  • The noze/ mouth/pharynx
  • The lungs
  • The vagina for women

However, intestine microbiome is the most “populated


Bacteria are not living only inside of us. Billions of bacteria exist in different kinf of products or places. Here some examples:

  • Lactobacillus bulgaricus, in yogurth
  • Escherichia coli, in our digestive system
  • Mycobacterium tuberculosis, responsible of the famous disease: the tuberculosis
  • Clostridium tetani, causing the tetanos.

Other: the spirulina, seaweed used as an iron supplement. It is not really a seaweed but a  cyanobacteria.

A what?!

A cyanobacteri is a bacteria using the sun energy to synthesize its chemical. They can use different pigments to attract light. In the case of the spirulina, its pigment are blue-green.


How bacteria reproduce?

Bacteria are asexual organism: no cuddle for them! To reproduce a cell divide in two identical cells. For some species a single bacteria can give birth to billions other in 48h! 


New treatments

New treatment are appearing for the last few years, such as faecal transplantation. Probiotics are easy to find, and fermented food become more and more popular.


How can we preserve our microbiome?

  • Avoid antibiotics when it’s not necessary
  • Avoid process food
  • Favour natural product, high in fibers




See your microbiote as a garden. You have to make sure the soil (your gut) is high in nutrients allow your plants (microbes) to growth. You have to pay attention to weed (process food), and to toxics which can alter growth and trigger diseases. You have to crop the most diverse plant as possible: diversity is the key!





To go further:

  • Gut: The inside story of our body’s most underrated organ , Gulia Enders
  • Podcast, My amazing body, The gut microbiome
  • Study: Ian Rowland et at, 2018. Gut microbiota functions: metabolism of nutrients and other food components. Eur J Nutr; 57 (1): 1-24
  • Ask the doctor – The gut, disponible sur Netflix Shalin Neik, Sandro Demaio, Renee Lim
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