The Gut, Germs and your Microbiota (Part 1)

Updated: Aug 29

If you eat on the run so to speak you are setting yourself up for improper digestion. That can create a whole host of problems related to IBS and other intestinal issues.



This colony is so important that it is truly the centre of our personal universe. If it’s not healthy, we are not healthy. Fact!


“This orchestra of information makes sure that the whole event (digestion) is coordinated whilst letting your brain know that has been fed and enough is enough. But it’s open to being tricked and food manufacturers know how to manipulate it at several levels.”

The Gut

You cannot understand the process of being healthy if you do not understand the basics of how your gut works. And the reason why is because it is the place that we meet the outside world. It is also the location of one of our most important “organs”, the microbiota or microbial colony which shares our journey through life


We did not really appreciate the extent or importance of this colony of mainly bacteria until quite recently. Up until a few years ago the gut was the place where we digested food. We knew that there were a few bacteria living there which were thought to be beneficial. As we could not grow most of them in a lab we had no idea of the complexity of our gut ecosystem. But after the technology that mapped the human genome was developed we discovered this amazing other world inside us. A world that literally runs our body. An amazing story of co-evolution that is truly the pinnacle of evolution.


The individual parts are easy to understand. The gut is a 22 foot long tube starting at the mouth and finishing at your anus. If you laid it out on a flat surface it would cover a tennis court. It has more nerves in it than the spinal cord and is home to eighty percent or more of our immune cells. We pour eights litres of fluid into it everyday to digest food, thats the equivalent to a quarter of all the water in our body! We absorb 97% back in the small and large intestine.


Eating and digestion is a parasympathetic activity and should occur when you can rest and digest. The Sympathetic state (fight, fright and flight) occurs when running around being busy, exercising and being stressed etc, inhibits and shuts down digestion. This is important as it dictates when you should be eating. If you eat on the run so to speak you are setting yourself up for improper digestion. That can create a whole host of problems related to IBS and other intestinal issues.


The whole process is exquisitely complex.


The mouth and teeth are the point of entry. Teeth are designed to cut, tear and grind a variety of food. Ours are those of an omnivore, adaptable and flexible. We can manage most food sources and our bite is pretty strong. Teeth grind food into small pieces. This process matters, so like granny said, chew your food before swallowing.


The other important structures in the mouth are the tonsils. The first place our immune cells sample foods and other objects passing by. They are key components to a complex process. More on this later.


The oesophagus, a 40 cm muscular tube connects the mouth to the stomach. It’s not just a tube though, it like the tonsils analyses food as it passes down on its way to the stomach.


The stomach uses extremely strong acid to sterilise food and start the digestive process. It’s a very muscular bag with the ability to churn and mix what we eat. As an expandable storage bag it allows us to eat a large quantity of food in a short period of time and then digest it over three to four hours. That’s why you don’t and should not need to be endlessly snacking.


The stomach empties its contents bit by bit into the first section of the small intestine, the duodenum. In an average person this process takes four hours to complete. The duodenum is perhaps the most complex place in the entire gut. This short section of the tube is lined with a special sensors which are able to analyse the content of your meal. It can recognise whether it has a high or low fat content, the amount of carbs and protein. This information is then sent to several places including the brain, gallbladder, pancreas, stomach and the rest of the small and large intestine.


The gallbladder sitting beneath the liver is a storage vessel full of green detergent called bile. If you consume a high fat meal then the gallbladder sends extra bile down to the intestine to break up fat globules. If you want to see how that works take some olive oil and add it a bowl of warm water. Watch it float. Then add a few drops of washing up liquid, stir and watch the fat globules that had been floating on the surface dissolve into a milky mixture. Thats what bile does to your lunch.


The pancreas is also located here and shares a common entry into the duodenum with the bile drainage tube, the bile duct. The pancreas produces a range of chemicals called enzymes which breaks the food down into small units that can be absorbed into the body in the next long section of the small intestine. It also produces bicarbonate which neutralises stomach acid.


This whole process of mixing your food with the correct amount of bile and different enzymes is exquisitely complex. It is influenced and controlled by your brain, nerves in the gut wall and pancreas, and about 30 hormones and other messaging molecules which work both locally and across the whole body. This orchestra of information makes sure that the whole event is coordinated whilst letting your brain know that has been fed and enough is enough. But it’s open to being tricked and food manufacturers know how to manipulate it at several levels.


The now liquid food travels through the small intestine where most of the nutrients are absorbed. Once the liquid food reaches the end of the small intestine it flows in the caecum, the first part of the large intestine. This is home to the majority of your microbial colony. In the large intestine plant fibres are broken down to feed the colony of bacteria. These in turn supply some specific nutrients to us, including several anti- inflammatory chemicals. The most important being the short chain fatty acids and of these the most important being a substance called Butyrate.


The other role of the large intestine is to reabsorb nearly all of the 8 litres leaving only 200 mls to pass out of the body in faeces.


More in Part Two soon.

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