Bacteria live everywhere around us, on our skin, even inside our body. There are bacteria that cause disease, which we call pathogens, but there are also good bacteria that live inside us and help us by taking up space, so pathogens cannot multiply inside us. Quite a few good, friendly bacteria live in our digestive system and help with the process of digestion. Below is a diagram of the human digestive system:
Friendly bacteria in the digestive system live mainly in the colon (the large intestine) and in the part of the small intestine which is further away from the stomach. The rest of the small intestine, the oesophagus and the stomach are bacteria-free. Digestive enzymes and hydrochloric acid in the stomach make it impossible for bacteria to survive there.
It is estimated that around 100 trillion friendly bacteria live in our gut. If we were to extract them, they would have a mass of 1 kg. There are between 300 and 1000 different species, with 50 of them the most common. About a third of all bacteria in the gut belong to the Bacteroides species. Other species are Lactobacillus, the bacteria commonly used in probiotic foods such as live yoghurt, Escherichia species, such as E. coli, some Clostridium bacteria, the Fusobacteria, the Eubacteria, members of the Bifidobacteria group and the less common Peptostreptococcus, Ruminococcus and Peptococcus.
Friendly gut bacteria have evolved in order to withstand the hard conditions of our digestive system. Bacteroides species coat themselves with a layer of sugar that they remove from the cells of the intestinal wall. They disguise themselves, so our immune system does not fight them.
The main advantage of having friendly bacteria in the gut is protection against harmful bacteria that would otherwise cause infection and invade the cells of the intestinal wall. Additionally, bacteria help with the digestion of materials that we are unable to digest, like hard plant material. A lot of the vitamins from vegetables would be wasted if it wasn't for the friendly bacteria that digest them for us. Some species produce vitamins K and B that is hard for us to obtain from food. They also maintain the acidity balance and break down some drugs, hormones not needed anymore and toxins that would be potentially dangerous to our health.
The population of bacteria in our gut is renewed regularly; about half the dry mass of our faeces consists of bacteria.
It is possible that some friendly species of bacteria may acquire extra genetic material that would make them turn harmful and produce toxins. An example is the E. coli. If such an infection is established, we get food poisoning. It is very important that we cook food very well to ensure no bacteria in it survive before we eat it.