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Looking After your Gut

16 February 2020 | 8 mins read | Looking After your Gut

When you hear the word “bacteria” what do you think of?

Germs? Infections? A cold, or the flu? Dirt?

Or do you think about the fact that at this exact moment you have trillions of bacterial cells living within your intestines,

helping your body to digest food,

fight off infection,

and even communicate with your brain?

These bacteria are the largest part of the “gut microbiome”.

Scientists have known for many years that our intestines are full of bacteria. But only in the last decade has it become possible to look at the hundreds of different species of bacteria in our intestines and to understand how they work with each other and with the rest of our bodies.

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What Do These Bacteria Do, And How Do They Do It?

Our bodies are unable to digest a large part of the fiber that we eat. This fiber is found in foods such as fruits, vegetables, and whole grains, such as barley, oats, apples, asparagus, onions, chicory root, bananas, garlic, dandelion root, wheat bran, and berries.

Fortunately, our gut bacteria thrive on indigestible fiber and metabolize it (break it down and re-use the parts separately or together) for us. During the process of metabolizing the fiber, different substances are released. Some of these substances are useful on their own, and others start a cascade of communication with other cells in our body in order to provide an essential function.

For example, one type of these substances helps to:

  • Provide energy for the cells in our intestines which communicate with other parts of our body.
  • Make sure that the inner surface of our intestines is covered in mucus so that food can pass smoothly through the tube. This mucus also prevents harmful bacteria or viruses from passing through the intestines into the blood.
  • Increase the production of IgA. IgA is a protein that helps to fight disease.
  • Decrease neuroinflammation (Neuro = brain/nervous system). Since neuroinflammation is thought to cause many neurodegenerative diseases such as Parkinson’s disease, this is an exciting area of research.

Similarly, other functions of our microbiome include helping to:

  • Produce vitamins B12, thiamine, riboflavin, and vitamin K.
  • Produce hormones that tell the body when to store fat and determine how an individual stores fat.
  • Send signals to alert the body’s immune system when harmful substances are detected.
  • Control communication between the brain and the gut.
  • Prevent insulin resistance – a key factor in type 2 diabetes.

This is only a very short list. The microbiome provides many other known functions, and most likely many additional functions that have not yet been discovered.

Just as a recipe works best when the right ingredients and the right proportions of ingredients are used, the gut microbiome works best with the right mix of different species of bacteria. In general, the greater the diversity of bacteria, the better.

What Determines the Mix And Composition Of Our Gut Microbiome?

Until we are born, we have few or no microbes in our gut. Microbes are transferred from mother to newborn during birth as the baby passes through the vagina. Therefore, a baby’s microbiomes resemble the mother’s microbiome. Babies who are born via Caesarean section have few microbes during the first month of life, but they usually catch up by 6 months of age.

In addition, many other factors are involved, including:

  • Microbes are transferred from mother to baby during breastfeeding. For optimal transfer of bacteria, breastfeeding is recommended for at least 6 months.
  • Physical environment. Groups of people living in the same environment, such as a village in Japan, a city in Switzerland, or a jungle in Peru have microbiomes that are more similar to one another than to microbiomes of people living in other environments.

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  • The food we eat. Our microbiome thrives on
    • high fiber foods.
    • fermented foods such as kimchi, sauerkraut, and kombucha.
    • live bacteria-containing yogurt. Check the label or ingredient list for words such as “live cultures” or “lactobacillus” or “Bifidobacterium”. Yogurt without added sugar is best.

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  • Supplements for our microbiome are called prebiotics’’ or ‘probiotics’, and they are very different.
    • Prebiotics contain the parts of fibrous foods we eat that our bacteria crave. Taking prebiotics is like “feeding” your bacteria.
    • Probiotics are the actual living bacteria. Whereas high fiber foods feed existing bacteria, fermented foods or foods such as yogurt add to the diversity and number of our bacteria. The bacteria can also be put into a capsule and sold in stores, and the package will advertise the number of bacteria and the type or types. Unfortunately, it is not unusual for regulators to find that what is advertised and what is inside the capsule are not the same. Purchase probiotics only from reputable brands.
  • Antibiotic use

Antibiotics do not target just ‘bad’ bacteria. Every time you take an antibiotic, you wipe out part of your microbiome. Current research shows that while the microbiome generally recovers, some changes are permanent. Any change in the balance of types of bacteria will affect the way our gut functions. Antibiotics are not only in the medication we intentionally take, but they are also in meat from animals who have been given antibiotics in their feed.

(Although antibiotic use can cause an imbalance in the microbiome, it is extremely important that you take the full course of prescribed antibiotics. If you only take enough antibiotics to clear up your symptoms, but not to remove all of the targeted bacteria, the remaining bacteria can become resistant to the antibiotic. You will be unable to treat subsequent infections, and you might transmit the resistant bacteria to someone else.)

  • Fecal transplants.

In a very effective procedure called a fecal transplant, ‘good’ bacteria from a donor’s feces (poop) are transferred directly into someone else’s intestines. In most countries, this procedure is currently approved only for treating C. diff (Clostridium difficile) infections. C. diff is a bacterium that grows out of control during antibiotic use and can cause severe chronic diarrhea and inflammation. A lot of research is being done on treating other diseases, both intestinal and non-intestinal, with fecal transplants.

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Is Having A Healthy Gut Directly Related to The Microbiome?

Without a healthy microbiome, you are unlikely to have a healthy gut, although problems related to your microbiome might take years to appear.

Some intestinal diseases are linked to a less diverse microbiome. For example, people with Crohn’s disease or ulcerative colitis have less diversity in their gut bacteria. They also have a predominance of certain types of bacteria.

But remember that the impact of the microbiome extends beyond the gut. Scientists have been studying the brain’s role in those diseases, and they believe there may be a connection between stress and the inflammation seen in Crohn’s and ulcerative colitis. This does not mean that inflammatory bowel diseases are caused by stress. Although stress can trigger acute episodes of inflammatory bowel disease, the disease itself appears to come from the physiological condition of the gut microbiome.

Related reading:

The microbiome is not the only cause of poor gut health. Other causes include:

  • Congenital disorders
  • Structural differences
  • Genetic disorders
  • Diseases such as cancer or diabetes
  • Abdominal surgery
  • Injury
  • Lifestyle and bowel habits

It is very interesting to understand that our gut microbiome affects not only our intestines but the rest of the body as well. In the future, as scientists learn more about the functions of all the species in our microbiome, we may be able to prevent or treat many diseases connected with the health of our gut microbiome. In the meantime, feed your bacteria well and they will take good care of you!

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Sources: – – NCBI, 2, 3, 4

Jill Garner
Jill GarnerRegistered Nurse and Diabetes Educator