What Is the Gut Microbiome? Gut Bacteria, Diversity and Diet Explained

You may already be familiar with the term “gut flora”.

It is often mentioned alongside yoghurt, fermented foods, dietary fibre and probiotics, and in recent years there has also been growing interest in everyday habits that support gut health.

When reading about gut flora, however, you may come across statements such as:

“Just increase the good bacteria.”
“Reduce the bad bacteria.”
“There is an ideal ratio of bacteria.”

These ideas can be useful as a simple introduction to gut bacteria, but current microbiome research shows that the gut ecosystem is much more complex.

The human gut contains an enormous number of microorganisms, and their composition differs from person to person. Diet, age, living environment and many other factors are also associated with these differences.

For this reason, research today looks not only at specific bacteria but also at the overall composition, diversity and functions of gut microorganisms, as well as their interactions with the human body.

In this article, we explain the basics of gut flora and the gut microbiome, what gut bacteria do, microbial diversity, the relationship with diet, probiotics and prebiotics, and what to know about gut microbiome testing.

What is gut flora?

Our digestive tract contains a vast number of microorganisms.

The large intestine in particular is home to many different types of bacteria, and the community they form is commonly referred to as the gut microbiota or intestinal microbiota.

The expression gut flora became widely used because the way different microbial populations exist together was compared with communities of plants growing in the same environment.

Gut flora and gut microbiota are closely related terms

Several terms are commonly used, including:

• Gut flora
• Gut microbiota
• Intestinal microbiota

In everyday health information, “gut flora” is still widely used, while “gut microbiota” is more common in medical and scientific research.

“Microbiota” and “microbiome”

You may also frequently see the terms gut microbiota and gut microbiome.

In general, “microbiota” refers to the microorganisms living in a particular environment.

“Microbiome” is often used more broadly to include the microbial community together with its genetic material, functions and related biological features.

However, the way these terms are used can vary somewhat between research fields.

In this article, we use the familiar term “gut flora” as well as “gut microbiome” where appropriate.

What microorganisms live in the gut?

When people hear “gut flora”, they often think mainly of bacteria.

Gut bacteria are indeed a major focus of microbiome research, but bacteria are not the only microorganisms found in the human digestive tract.

The gut can contain:

• Bacteria
• Archaea
• Fungi
• Viruses

Together, these microorganisms form a highly complex ecosystem.

It cannot be explained only as “good” and “bad” bacteria

Gut bacteria have traditionally been described using simple categories such as “beneficial bacteria”, “harmful bacteria” and “opportunistic bacteria”.

This can be a useful way to introduce the subject, but current microbiome research shows that it is difficult to classify every microorganism in the gut into only these three groups.

Even the same type of microorganism may behave differently depending on surrounding microbes, diet and the intestinal environment.

For this reason, the gut microbiome is increasingly viewed as a complex ecosystem in which many different microorganisms coexist and interact with one another.

Gut microbiota composition varies from person to person

There are substantial individual differences in the gut microbiome, and factors such as dietary culture, age and living environment are associated with differences in microbial composition.

In other words, no two people necessarily have exactly the same gut microbiome.

What do gut bacteria do?

Gut bacteria do more than simply live inside the digestive tract.

They use some of the components from the foods we eat and produce a variety of substances through their metabolism.

These microbial activities and their interactions with the human body are major areas of current gut microbiome research.

They use components derived from food

Not everything we eat is completely digested and absorbed before reaching the large intestine.

Some forms of dietary fibre and other components that are difficult for human digestive enzymes to break down can reach the large intestine, where they may be used by gut bacteria.

During this process, gut bacteria produce a range of metabolites.

Short-chain fatty acids and other metabolites

When gut bacteria ferment certain food-derived components, they can produce substances known as short-chain fatty acids.

Common examples include:

• Acetate
• Propionate
• Butyrate

Short-chain fatty acids are among the important microbial metabolites studied in research into the relationship between gut bacteria and the human body, including their relationship with various physiological functions.

The relationship with bile acids and vitamins

Gut bacteria are also involved in the metabolism of bile acids.

Some gut bacteria are also known to participate in the metabolism of certain vitamins, and researchers continue to investigate the many substances produced or modified by intestinal microorganisms.

Interactions with the human body

The intestinal tract is one of the body’s major interfaces with food, microorganisms and other substances originating outside the body.

For this reason, many studies investigate interactions between gut microorganisms, intestinal cells and the immune system.

The relationship between gut bacteria and the human body is highly complex, and health status cannot be determined from the presence or amount of one particular bacterium alone. Research into interactions between the gut microbiome and the human body, including the intestinal and immune systems, is continuing.

What is a “healthy” gut microbiome?

When thinking about the gut microbiome, many people naturally wonder:

“Is my gut microbiome in a good state?”

However, current research has not established one single “ideal” gut microbial composition that applies to everyone.

There is no fixed percentage of “good bacteria” that is right for everyone

Some health information refers to supposedly ideal percentages of beneficial, harmful and opportunistic bacteria.

However, the human gut microbiome varies greatly between individuals, and the microorganisms detected can also differ depending on the analytical and classification methods used.

For this reason, it is difficult to judge everyone’s gut microbiome as simply “good” or “bad” based on a fixed bacterial ratio.

Diversity is also being studied

One of the characteristics studied when evaluating the gut microbiome is microbial diversity.

Diversity does not simply mean having a large number of bacteria. It can also refer to the richness and distribution of different types of microorganisms within the gut ecosystem.

Many studies have investigated associations between gut microbial diversity and health, but it is also too simplistic to say that “higher diversity always means better health”.

What microbes are doing may be as important as which microbes are there

Modern gut microbiome research investigates not only which microorganisms are present, but also:

• What genes they carry
• What substances they produce
• How they interact with other microorganisms
• How they respond to changes such as diet

In other words, their functions are also an important area of research.

Rather than looking for one simple answer such as “this bacterium is good”, researchers increasingly study the gut microbial community as an interconnected ecosystem.

What can change the gut microbiome?

The gut microbiome does not remain exactly the same throughout life.

Its composition can change in association with factors such as diet, age and living environment.

Diet

Diet is one of the factors most extensively studied in relation to the gut microbiome.

Because gut microorganisms use some of the components in the foods we eat, many studies have investigated relationships between daily dietary patterns, microbial composition and microbial metabolism.

Plant foods containing dietary fibre, as well as dietary fats, proteins, fermented foods and many other nutritional factors, are all areas of research.

Age

The gut microbiome also changes with age.

Microbial composition changes substantially during infancy and early childhood before developing into a relatively more stable adult-like microbiome.

Even during adulthood, the gut microbiome may continue to change in association with diet, living environment, health status and other factors.

Where and how we live

Food culture and living environments differ considerably between countries and regions.

Differences in location, lifestyle and dietary habits are also associated with differences in the gut microbiome.

Medicines, especially antibiotics

Medicines can also affect the gut microbiome.

Antibiotics act against bacteria and may therefore affect not only the bacteria being treated but also other bacterial populations living in the gut.

However, necessary antibiotics should not be stopped simply because of concerns about the gut microbiome.

Antibiotics and other medicines should be used appropriately according to the instructions of a doctor or pharmacist.

No single factor determines the gut microbiome

The gut microbiome is not determined by diet alone, age alone or any other single factor.

Genetic background, diet, living environment, medicines, age and many other factors can all contribute to the individual microbial community found in each person.

For this reason, rather than thinking that “one particular food will create the ideal gut microbiome”, it is more useful to consider daily diet and lifestyle as a whole.

The relationship between diet and the gut microbiome

Diet is one of the everyday factors most closely studied in relation to the gut microbiome.

Some of the food we eat reaches the large intestine and is used by gut bacteria. For this reason, researchers have widely studied how what we eat relates to microbial composition and metabolism.

However, this does not mean that eating one particular food will automatically create an “ideal” gut microbiome.

Responses can vary between individuals, and the overall diet, existing gut microbiome, living environment and many other factors may all play a role.

Dietary fibre and gut bacteria

Dietary fibre is one of the nutritional components most extensively studied in relation to the gut microbiome.

Some types of dietary fibre are not readily digested by human digestive enzymes and can reach the large intestine.

Some of this fibre can then be used by gut bacteria, which may produce short-chain fatty acids and other metabolites during fermentation.

Dietary fibre can be found in many foods, including:

• Vegetables
• Fruit
• Legumes
• Whole grains
• Root vegetables
• Mushrooms
• Seaweed
• Nuts and seeds

Rather than relying on one particular food, eating a variety of foods can also help provide a broader range of nutrients alongside dietary fibre.

How much dietary fibre should adults consume?

The World Health Organization (WHO) recommends that adults consume at least 25g of naturally occurring dietary fibre per day.

However, suddenly increasing fibre intake by a large amount may cause bloating or digestive discomfort in some people.

If your current diet is relatively low in fibre, one approach is to gradually include more vegetables, legumes, fruit and whole grains.

The variety of plant foods may also matter

Gut microbiome research examines not only the amount of dietary fibre but also dietary diversity.

Combining a variety of foods such as vegetables, fruit, legumes, grains, nuts and seeds also provides gut microorganisms with a wider range of food-derived compounds.

Rather than searching for one special food specifically for the gut microbiome, a good starting point is to build variety into your everyday diet.

Fermented foods and the gut microbiome

When people think about gut health, foods such as yoghurt, natto, kimchi and miso often come to mind.

Fermented foods are produced using microorganisms and/or their enzymes to create changes in the original food.

Humans have used fermentation for centuries to alter flavour, texture, preservation and other characteristics of food.

Fermented foods are not automatically probiotics

One important point is that fermented foods and probiotics are not the same thing.

Microorganisms are used to produce fermented foods, but living microorganisms may not always remain in the final product.

Even when live microorganisms are present, this does not automatically mean that the food meets the scientific definition of a probiotic.

For example, some fermented foods are heat-treated, meaning that microorganisms involved in fermentation may no longer be alive when the food is consumed.

Other fermented foods, including certain yoghurts, may contain live microorganisms.

Fermented foods and gut microorganisms are also being studied

Research into the relationship between fermented foods and the gut microbiome is continuing.

Dietary intervention studies in healthy adults have, for example, investigated associations between diets containing higher amounts of fermented foods and gut microbial diversity.

However, fermented foods vary greatly in the microorganisms used, their production methods and their nutritional composition.

For this reason, it is better not to assume that every fermented food will act in the same way. They can instead be considered one of many food choices within an everyday diet.

What are probiotics, prebiotics and synbiotics?

When reading about the gut microbiome, you may encounter the terms:

• Probiotics
• Prebiotics
• Synbiotics

The names are similar, but their meanings are different.

What are probiotics?

In scientific terminology, probiotics are defined as live microorganisms that, when administered in adequate amounts, confer a health benefit on the host.

Lactic acid bacteria and bifidobacteria are well-known examples, but this does not mean that every lactic acid bacterium automatically qualifies as a probiotic.

When evaluating probiotic research, it is important to consider not only the microbial species but also the specific strain.

Different strains within the same species can have different characteristics, so findings from one particular strain cannot automatically be applied to all lactic acid bacteria or bifidobacteria.

What are prebiotics?

In scientific terminology, a prebiotic is defined as a substrate that is selectively utilised by host microorganisms and confers a health benefit.

Certain dietary fibres and oligosaccharides are among the substances studied as prebiotics.

However, not all dietary fibre is a prebiotic.

Dietary fibre is a broad nutritional category, while a substance must meet specific criteria — including selective utilisation by host microorganisms — to be classified scientifically as a prebiotic.

What are synbiotics?

Synbiotics combine live microorganisms with substrates that are selectively utilised by host microorganisms.

They are commonly understood as combinations involving probiotics and prebiotics, although the scientific definition of synbiotics has become more specifically defined in recent years.

More bacteria does not necessarily mean better

Probiotic products often state the number of microorganisms they contain.

However, it is not possible to judge a product simply by assuming that a higher bacterial count must always be better.

In research, factors such as the specific strain, the amount used and the conditions under which it was studied can all be important.

For this reason, the word “probiotic” itself should not be interpreted as describing one identical function shared by every product.

What can gut microbiome tests tell you?

In recent years, direct-to-consumer gut microbiome tests have become more widely available. These services generally involve collecting a stool sample and sending it for analysis.

Some people use these tests simply because they are curious about which microorganisms may be present in their gut.

Analysing gut microbial composition from stool

Many commercial gut microbiome tests analyse microbial genetic material found in stool and provide reports on the types and relative proportions of microorganisms detected.

Different companies may use different analytical technologies, databases and reporting methods.

Test results cannot diagnose your overall health

At present, direct-to-consumer gut microbiome test results alone cannot diagnose whether someone has a disease or predict their future health.

It is also difficult to classify someone as simply “healthy” or “unhealthy” based on the percentage of one particular microorganism.

Gut microbiome testing is a developing area with considerable research interest, but its routine clinical use is still being investigated and validated.

Different testing services may produce different results

Studies comparing multiple direct-to-consumer microbiome testing services have found examples in which the same reference samples produced differences in the microorganisms detected and the results reported by different services.

Differences in analytical methods, databases and data-processing techniques may contribute to these variations.

For this reason, microbiome test results are best viewed not as an absolute measure of health but as one source of information for learning more about your gut microorganisms.

Everyday eating habits with the gut microbiome in mind

As we have seen, the gut microbiome is highly complex.

It is not as simple as eating one particular food to increase a specific bacterium or relying on one supplement alone.

One of the most practical things to consider in everyday life is the overall pattern of your diet.

Eat a variety of foods

Consider including a variety of vegetables, fruit, legumes, grains, root vegetables, mushrooms, seaweed, nuts and seeds in your diet.

You do not need to aim for a perfect diet every day.

Small changes can add variety — choosing a different vegetable from yesterday, including less-refined grains, or adding a serving of legumes, for example.

Include foods that provide dietary fibre

Dietary fibre has long been studied in relation to gut microorganisms.

Rather than immediately relying on supplements alone, you can first consider whether there are opportunities to include more fibre-containing foods in your everyday meals.

Fermented foods can be one of many food choices

Many people regularly eat fermented foods such as yoghurt, natto, miso and kimchi.

Fermented foods are not automatically the same as probiotics, but they have been part of many food cultures for generations.

They can be enjoyed as one of many food choices according to your preferences and how your body responds to them.

There is no need to become overly strict about “gut health”

As interest in the gut microbiome grows, it can be easy to feel that you “must” eat a particular food every day or that you need to increase a specific bacterium.

However, there is no single definition of a healthy gut microbiome that applies equally to everyone.

Rather than severely restricting your diet or consuming large amounts of one particular food, it is more sensible to focus on a balanced eating pattern that you can maintain comfortably.

Do not automatically assume ongoing digestive symptoms are caused by the gut microbiome

Constipation, diarrhoea, abdominal pain and bloating can have many different causes.

If symptoms are persistent or severe, it is important not to assume that they are simply caused by an “imbalanced gut microbiome” and rely only on foods or supplements. Seek appropriate medical advice when necessary.

Summary | The gut microbiome is a complex ecosystem unique to each person

The gut microbiome is a complex ecosystem formed by the many microorganisms living in the intestinal tract. Gut bacteria are involved in the metabolism of food-derived components and can produce a range of metabolites, including short-chain fatty acids.

At the same time, there is no universally established “ideal” microbial composition. Research continues to investigate microbial diversity, function, diet, living environment and many other factors associated with the gut microbiome.

Rather than focusing on one particular bacterium or food, it is useful to understand that the gut microbiome differs from person to person and to consider everyday diet from a broader perspective.