The Microbiome of the Gut

We are used to thinking of bacteria as bad things, but many (if not most) are beneficial to us and not to be got rid of. In fact, over 95% of the World’s known bacteria are harmless to humans and more than half the bacteria in our digestive tract can live nowhere else. We each have our own unique blend of gut microbes, which plays a large part in individual differences in health (e.g. weight, mood and immunity).


Our gut microbiome weighs about 2kg and contains 100 trillion bacteria of a thousand different species. Their number increases down the gastrointestinal tract, so we have most in the lower parts of the large intestine and rectum.


What do gut bacteria do for us?

  • Breakdown otherwise indigestible foodstuffs
  • Release energy into the gut
  • Manufacture vitamins
  • Breakdown toxins
  • Train our immune system.



In the womb we consist 100% of human cells, but once the sterile bubble of the amniotic sac is burst at birth we eventually become 90% microbial as our entire body is colonised by microbes. We pick up a large quota of our bacterial population from our mothers during and after birth. That is why babies born by Caesarean section or those who are not breast fed are prone to developing allergies.


In this way, useful gut flora are passed on down the generations so that different cultures have the ability to digest foods that others would struggle with (e.g. most of the Japanese population has a gut bacterium that aids the digestion of seaweed, and many Africans are able to break down fibrous plants more easily than Europeans thanks to their gut bacteria).




It takes three years for our gut flora to stabilise. Our diet and lifestyle shape our microbiome, so if we eat a lot of one food item it will encourage bacteria that can utilise it and they will out compete those that can’t. Stress can also affect our gut flora as it alters the conditions in the gastrointestinal tract.


Research has shown that there are three main gut types linked to the predominant family of bacteria in the gut. It is interesting that traditional medical practices from India and China at least have categorized people according to what diet suits them best, which is undoubtedly a reflection of their gut flora type. So although these ancient cultures did not have the technology to identify bacteria, they could identify and categorise their effect as well as being able to modify it in order to promote health.



Bacteria are used in many food products to pre-digest it for us, as in yoghurt, and even add vitamins, as in the case of sauerkraut. Or to add flavor as in cheese or bouquet in wine. About 90% of our nutrition comes from what we eat and 10% is provided by our gut flora.



Prebiotics are foodstuffs that pass undigested into the large intestine and nourish beneficial bacteria there. Harmful bacteria cannot use prebiotics. Sugar is not a prebiotic because although it may be beneficial to some health-giving bacteria it also benefits tooth-rotting bacteria in the mouth. Examples of particularly potent prebiotics are asparagus, endives, artichokes, leeks, onions and garlic, but all whole fruits and vegetables are prebiotic as they contain the fibre that our good bacteria crave. If your diet is low in these, introduce them gradually to avoid bloating and wind!


Probiotics are edible living bacteria that promote health. They do this in three ways:

  • They produce fatty acids that optimize the efficiency of the gut lining to absorb nutrients.
  • They protect against harmful bacteria by taking up all the space and resources available in the gut.
  • They help our immune system and can be used to alleviate diarrhoea, prevent colds and protect against allergies.


You can read more about probiotics here.



Like me, you may be surprised to learn that about 80% of our immune system is located in the gut. Our gut bacteria train our immune system to distinguish between good guys and bad guys, so that it doesn’t destroy useful microbes or our own cells. It is gut bacteria that are responsible for blood types. It is a breakdown in the communication between the immune system and our gut flora that results in auto-immune diseases.



Research into the gut microbiome is still only in its infancy. There is still much to learn. For example, the influence of gut bacteria on our metabolism and so our weight has been under investigation for less than five years, and using probiotics is still a case of trial and error. We remain ignorant of over 60% of our gut flora.


If you would like to learn more about the gut microbiome, I can recommend 10% Human: how your body’s microbes hold the key to health and happiness by Alanna Collen.