gut microbiome everything to know

Gut Microbiome: Everything You Need to Know

The only guide to the gut microbiome you'll ever need

Gut health and the gut microbiome are terms you hear a lot nowadays. This is because scientists now have a growing body of evidence on its impact on many aspects of our health.

The gut microbiome is composed of the microorganisms that inhabit our digestive tract or gut. This is from our mouth to our large intestine.

These bacteria play a significant role in the digestion and absorption of nutrients. They also help boost immunity and our overall health.

Without these microorganisms, we would not be able to survive.

What is the gut microbiome?

The gut microbiome is an ecosystem composed of billions of microorganisms that live in our digestive tract.

The largest populations live in the small and large intestine.


These microorganisms of several thousand species include both good and bad bacteria, fungi, and even parasites and viruses. 

In healthy individuals, there is a balance in the populations of these microorganisms – the bad ones and the good ones, and this creates an “ecosystem” in the digestive tract.

Diversity in the species of bacteria is important. This is because different types of bacteria have different functions that are necessary to our health.

Good bacteria are called probiotics, a term that may be familiar to you. But have you heard of prebiotics?

These are substances in our diet like soluble fiber and resistant starch that feeds and strengthens the probiotics in our gut. 

Each individual has a unique microbiome that changes through time, from infancy to old age.

It is affected by genetics, a mother’s microbiome during childbirth and breastfeeding, as well as diet, environmental exposure, antibiotics, among other things.

What is the importance of the gut microbiome?

In recent years, many studies have focused on the gut microbiome. We are only now finding out the role it plays in all aspects of our health and life.

Especially the impact on the development of chronic diseases like diabetes, as well as our mental health and mood.

The key discoveries so far have been:

1. Supports digestion

Bifidobacteria is one of the first species to take hold in the human gut. It helps babies digest breast milk

Good bacteria in the gut break down indigestible fibers. This in turn, results in the production of short-chain fatty acids

2. Helps immunity

Gut microbes, which come from our environment, are important in the development of immunity, gut health, and overall health.

A study in the European Journal of Microbiology & Immunology looked further into this. Researchers reported that mice raised in a germ-free environment did not develop a microbiome.

Instead, they developed autoimmune conditions and had lower levels of antibodies essential for immunity.

The good bacteria in our gut also fight bad or pathogenic bacteria from taking hold or causing an imbalance. This can result in illness or disease.

3. Supports brain and mental health

Our gut is directly connected to our brain via the brain-gut axis.

As stated in this study from 2016, the gut microbiome influences regular mental processes, serotonin levels, and our overall mental state via the brain-gut axis.

It may also be involved in the development of certain neurological and mental conditions. 

4. Helps with production of Short-Chain Fatty Acids (SCFAs)


When bacteria in our gut digest fiber, particularly soluble fiber and resistant starch, they produce short-chain fatty acids (SCFAs).

This study found that SCFAs may help prevent certain diseases, including certain cancers, ulcerative colitis, and Crohn’s disease.

They have also been found to have a role in metabolism, inflammation, and the environment in the gut.

5. Facilitates nutrient absorption

The gut microbiome helps maintain the integrity of the gut. This includes the intestinal barrier, which keeps the contents of the digestive tract within it.

If “leaked” onto the outside of the digestive tract, it could cause infection and disease.

At the same time, however, the intestinal barrier and the microorganisms in our gut facilitate nutrient absorption, an exchange that allows nutrients from food to be released into our body.

6. Synthesizes Vitamin K

As stated in this study, bacteria in the gut synthesizes vitamin K, which is essential for blood clotting, wound formation, and bone development.

What does the gut microbiome need to function well? 

Eat a healthy diet

A healthy diet plays a large role in maintaining the gut microbiome.

A balanced diet with food rich in probiotics can help replenish the population of good bacteria in our gut. Examples of these foods are yogurt, sauerkraut, kefir, and kimchi

Prebiotics is a type of fiber present in foods like oatmeal, beans, and psyllium husk, These foods promote good bacteria. It helps to strengthen and increase their population.

Polyphenols are another substance that contributes to better gut health.

They are naturally found in berries, coffee, tea, and dark chocolate. Polyphenols are the substances that give these foods their bitter, astringent-like flavors.

In this study, it was found that polyphenols can modify the composition of the gut microbiome. Also, they can modify the immune response in our gut.

With more people cutting sugar out of their diets, the consumption of artificial sweeteners is on the rise. Some of these sweeteners include aspartame, present in many diet versions of beverages

However, as mentioned in this study, evidence now suggests that these substances disrupt the balance of the gut microbiome. 

One important thing to note is if you think there is a certain food that upsets your digestion. For example, milk or wheat. So it is best to avoid it because it can disrupt the balance in the gut environment. 


Get adequate, restful sleep

Growing evidence, such as from this 2019 study, points toward sleep deprivation affecting the diversity in the gut microbiome. And this microbiome is an important aspect of gut health.

A bit like a chicken-and-egg situation, it also works the other way around: gut health and the microbiome also affect sleep quality.

Which one comes first, we don’t know, but it is best to make it a priority to get adequate, restful sleep.

Exercise regularly

How many times have we been told about the benefits of regular exercise? Well, it also has the power to positively alter the gut microbiome.

Aerobic exercise, in particular, popularly known as cardio, has been found in this Gut Microbes study from 2019 to increase the populations of certain good bacteria in the gut.

This could explain why many individuals with gastrointestinal disorders benefit greatly from regular exercise. 

Related: Can You Exercise Too Much?

Use antibiotics only when needed

Antibiotics like amoxicillin, cephalexin, and clindamycin are a lifesaver when we need them. However, not only do they kill harmful bacteria in our gut, they kill the good bacteria as well.

It is best to take antibiotics only when we need them.

And when we do take them, to increase our consumption of probiotic foods like yogurt, kefir, and sauerkraut, and prebiotic-rich food like oats.

Probiotic and prebiotic capsules may also be taken.

What is one type of bacteria found in a healthy gut microbiome?

There are thousands of species of bacteria that are part of the gut microbiome.

All of them are important but of these, certain kinds of bacteria are important for certain functions, such as the digestion of lactose, a type of sugar found in milk.


Digestive issues with lactose, known as lactose intolerance, is a common condition that can cause bloating, flatulence, and diarrhea. 

This article published in The American Journal of Clinical Nutrition found that probiotics like lactobacillus and bifidobacterium naturally present in yogurt are said to improve lactose absorption.

This could be why although yogurt is a dairy product, many lactose-intolerant individuals don’t find difficulty digesting it.


It is said that human beings are actually “superorganisms”. This is because of the number of bacteria that live within us, and with who we have a mutually beneficial relationship.

While this may sound strange, our gut health plays an important role in our overall health – mental health included.

It is wise to find ways to incorporate healthy lifestyle practices.

You can start small, by consuming pro-and prebiotic foods that you like, doing light exercise regularly, and sleeping at the same time every day.

All of these will contribute to better gut health, overall well-being, and definitely to a happier you!