Bacteria and the Gut

Mar 5, 2017 by

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Or you can read it the old-fashioned way below…

There has been a lot of press in recent years regarding the bacteria in the gut – the gut microbiome. It is true that our bodies are home to trillions of tiny organisms, and the majority of these live in our GI tract. There are some in our mouths, in our stomachs, and throughout the different parts of the small and large intestine.

There is still a lot that we don’t know about these organisms that live inside of our GI tracts.  In fact, some of the things that we thought we knew years ago have now been shown to be wrong.  It’s definitely important to not jump too quickly at any news that breaks regarding this topic.

When there are trillions of organisms hanging out, there is a lot that must be learned in order to fully understand what is going on! But it is clear that the GI tract and its bacteria play a vital role in the absorption, digestion, and excretion functions of the GI tract. They also have impact that we never would have expected, including on our immune systems and on the development of allergies.

All of this means that understanding the bacteria in our guts is almost as important as understanding the structure and function of the GI tract.  So let’s get to it!

Bacteria and Our Bodies

Many different types of bacteria are located all over our bodies. Some of you might have had a dental procedure in the past and the dentist may have prescribed an antibiotic. This isn’t because he was worried about infecting you during the surgery. It’s actually because he was worried that the bacteria living in your mouth might get into your blood where it doesn’t belong.

In fact, it is the bacteria that is always present on our skin that causes most of the infections in the little scrapes and cuts that we get in our everyday lives. When our bacteria stay where they are supposed to, they benefit us. But sometimes they go where they are not supposed to, and that other part of our body is not equipped to deal with that type of bacteria.

Long story short, the human body has found that it can be healthier and stronger when it builds relationships with certain types of bacteria.  Although we often look at these organisms as the enemy, our bodies would beg to disagree!

Bacteria in the Gut

When a baby is born, there is no bacteria found in his or her gut. However, within about 48 hours, the gut becomes filled with bacteria. These bacteria have been found to be different depending on whether the baby is breastfed or formula-fed.  It is likely that this ties into some of the other conditions that are now being associated with breastfeeding versus formula-feeding, but that is a topic for another book!

The important thing to note here is how sensitive the gut flora actually is to diet and environment. As humans grow older, our guts become less sensitive to these little changes, but larger and persistent changes can still impact our microbiomes.

Different factors can affect the numbers and types of bacteria that live in our guts. Some of these factors cannot be changed, such as age, gender, and genetic inheritance. But other factors that have a large impact can be changed, such as infections and diets. Alterations to these factors can lead to GI symptoms, including bloating, pain, nausea, vomiting, diarrhea, constipation, and more.

Gut Bacteria: Function

Believe it or not, the bacteria in our gut actually serve a purpose. They are present in a symbiotic relationship with our bodies. In other words, when we feed the bacteria that live in our gut, the bacteria give something helpful back in return.

This may come in the form of digestion – bacteria can sometimes be helpful in digesting substances that are difficult for our bodies to break down.  This allows our bodies to absorb nutrients that we might not have been able to access otherwise.  Different bacterial species are capable of breaking down different items, so having a variety of species may improve our nutritional status.

Some bacteria produce substances that our bodies need. Bifidobacterium produces substances that help to bulk up our immune systems. Other bacteria actually produce some of the vitamins that we need to live, including Vitamin K (crucial for blood clotting) and the B Vitamin family. And still other bacteria even produce small fatty acids that the human body can use as an energy source!

But as you might expect, there are ways that this symbiotic relationship can go a little bit wrong.  We’ll discuss how this can happen at the end of this article.

Gut Bacteria: Location


Various types of bacteria live all over our gums and teeth. They show up pretty quickly after we’re born and never go away. These bacteria are credited with causing such nuisances as cavities and oral infections. Research is still being done to better understand the difference between ‘healthy’ and ‘infectious’ bacteria in the mouth. This is not as relevant to chronic GI conditions as the rest of the GI tract, so we won’t spend any more time here.


The stomach is an incredibly acidic environment.  It was previously thought to be fatal to all bacteria.  That is, until a species called Helicobacter pylori (H. pylori) was discovered.  This species is actually able to survive in highly acidic environments, such as the one found in the stomach.

The stomach should, ideally, be a bacteria-free environment.  But although H. pylori is not a natural inhabitant of the human stomach, humans can become colonized by it.  This infection causes various symptoms including stomach pain, increased nausea, decreased appetite, bloating, and weight loss. Anyone with a GI condition can see how much these symptoms can overlap with what they are already experiencing.

The tests to check for H. pylori are very simple – breath and stool.  As this infection can worsen the symptoms of another condition, it makes sense to have the test completed if you have these symptoms. Some medications that suppress stomach acid may interfere with the tests and must be stopped a couple of weeks before it is completed.  If you are already having your stomach ‘scoped’ by your doctor, he can even collect samples during this test (more info on that here).

Small Intestine

As we move into the small intestine, it becomes normal to see some bacteria, although not many.  Only a few species of bacteria will be found, including names that are familiar to many people – lactobacillus and enterococcus. These bacteria are considered standard and beneficial to GI function.  For some people, there may actually be no bacteria growing in parts of the small intestine, and this is fine.

The very end of the ileum, which marks the end of the small intestine (details here), contains more bacteria than the rest of the small intestine.  This is also where bacteria can begin to creep into a space where they don’t belong, causing something called – Small Intestinal Bacterial Overgrowth (SIBO). These bacteria don’t belong here and are not as well tolerated.  This condition has been found to be commonly associated with IBS, and is discussed more in that section.

Large Intestine

When references are made to the ‘gut flora’ or ‘gut microbiome’, this is usually in relation to the large intestine.  This section of the intestine is home to a huge variety of bacteria.  It is believed there may be as many as 500-1,000 species living in our guts, and a large portion of these have not been identified.

The bacteria that help to digest our foods and produce important vitamins and components that improve our health are found in this part of the GI tract. Believe it or not, there are even some medications that are processed in part by the bacteria that live there.

Gut Bacteria: What Can Go Wrong?

A variety of factors can disrupt the regular function of the GI tract, particularly in relation to bacteria.  Something as simple as taking antibiotics for an infection will actually kill off some of the bacteria in the gut. This change in the makeup of the gut flora causes some people to experience diarrhea when taking certain antibiotics.  Or certain bacteria may produce air when they break down certain food products, which our bodies interpret as gas.

I mentioned before that the stomach is typically free of bacteria because it is so acidic. This acidic environment has the added benefit of killing off any bacteria that might have been swallowed before they reach the intestine. Reducing the acidity of the stomach (ie, by taking medications that suppress stomach acid) can increase the chances of new bacteria making a home in your gut, or moving to places where they don’t belong.

The motion of the GI tract can also have an impact on keeping bacteria where they belong. The constant forward movement that results from peristalsis keeps bacteria moving down the GI tract and into the large intestine. When this is disrupted, it can also increase the chances of bacteria living somewhere unusual. In a similar way, an intestinal obstruction or an unusually shaped intestine can have the same result.

The pancreas is responsible for excreting bile, which also has some antibiotic effects. This helps to keep the number of bacteria present in the small intestine to a minimum. Thus, having reduced pancreatic activity may also lead to bacteria taking up residence in an unusual location.

Now What?

As you can see, there are a number of ways that the bacteria in our guts help us to stay healthy.  But there are also changes that can make us feel not so well.  Understanding the way that the GI tract functions and the importance of bacteria to this function is crucial to taking control of your health.

Next: The Brain and the Gut

Or refer back to the GI Tract Info Hub.

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